Daily Papers

The Multiplane Image (MPI), containing a set of fronto-parallel RGBA layers, is an effective and efficient representation for view synthesis from sparse inputs. Yet, its fixed structure limits the performance, especially for surfaces imaged at oblique angles. We introduce the Structural MPI (S-MPI), where the plane structure approximates 3D scenes concisely. Conveying RGBA contexts with geometrically-faithful structures, the S-MPI directly bridges view synthesis and 3D reconstruction. It can not only overcome the critical limitations of MPI, i.e., discretization artifacts from sloped surfaces and abuse of redundant layers, and can also acquire planar 3D reconstruction. Despite the intuition and demand of applying S-MPI, great challenges are introduced, e.g., high-fidelity approximation for both RGBA layers and plane poses, multi-view consistency, non-planar regions modeling, and efficient rendering with intersected planes. Accordingly, we propose a transformer-based network based on a segmentation model. It predicts compact and expressive S-MPI layers with their corresponding masks, poses, and RGBA contexts. Non-planar regions are inclusively handled as a special case in our unified framework. Multi-view consistency is ensured by sharing global proxy embeddings, which encode plane-level features covering the complete 3D scenes with aligned coordinates. Intensive experiments show that our method outperforms both previous state-of-the-art MPI-based view synthesis methods and planar reconstruction methods.

The imperative need to scale computation across numerous nodes highlights the significance of efficient parallel computing, particularly in the realm of Message Passing Interface (MPI) integration. The challenging parallel programming task of generating MPI-based parallel programs has remained unexplored. This study first investigates the performance of state-of-the-art language models in generating MPI-based parallel programs. Findings reveal that widely used models such as GPT-3.5 and PolyCoder (specialized multi-lingual code models) exhibit notable performance degradation, when generating MPI-based programs compared to general-purpose programs. In contrast, domain-specific models such as MonoCoder, which are pretrained on MPI-related programming languages of C and C++, outperform larger models. Subsequently, we introduce a dedicated downstream task of MPI-based program generation by fine-tuning MonoCoder on HPCorpusMPI. We call the resulting model as MPIrigen. We propose an innovative preprocessing for completion only after observing the whole code, thus enabling better completion with a wider context. Comparative analysis against GPT-3.5 zero-shot performance, using a novel HPC-oriented evaluation method, demonstrates that MPIrigen excels in generating accurate MPI functions up to 0.8 accuracy in location and function predictions, and with more than 0.9 accuracy for argument predictions. The success of this tailored solution underscores the importance of domain-specific fine-tuning in optimizing language models for parallel computing code generation, paving the way for a new generation of automatic parallelization tools. The sources of this work are available at our GitHub MPIrigen repository: https://github.com/Scientific-Computing-Lab-NRCN/MPI-rigen

MPI derived datatypes are an abstraction that simplifies handling of non-contiguous data in MPI applications. These datatypes are recursively constructed at runtime from primitive Named Types defined in the MPI standard. More recently, the development and deployment of CUDA-aware MPI implementations has encouraged the transition of distributed high-performance MPI codes to use GPUs. Such implementations allow MPI functions to directly operate on GPU buffers, easing integration of GPU compute into MPI codes. This work first presents a novel datatype handling strategy for nested strided datatypes, which finds a middle ground between the specialized or generic handling in prior work. This work also shows that the performance characteristics of non-contiguous data handling can be modeled with empirical system measurements, and used to transparently improve MPI_Send/Recv latency. Finally, despite substantial attention to non-contiguous GPU data and CUDA-aware MPI implementations, good performance cannot be taken for granted. This work demonstrates its contributions through an MPI interposer library, TEMPI. TEMPI can be used with existing MPI deployments without system or application changes. Ultimately, the interposed-library model of this work demonstrates MPI_Pack speedup of up to 242000x and MPI_Send speedup of up to 59000x compared to the MPI implementation deployed on a leadership-class supercomputer. This yields speedup of more than 917x in a 3D halo exchange with 3072 processes.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

Models using structured state space sequence (S4) layers have achieved state-of-the-art performance on long-range sequence modeling tasks. An S4 layer combines linear state space models (SSMs), the HiPPO framework, and deep learning to achieve high performance. We build on the design of the S4 layer and introduce a new state space layer, the S5 layer. Whereas an S4 layer uses many independent single-input, single-output SSMs, the S5 layer uses one multi-input, multi-output SSM. We establish a connection between S5 and S4, and use this to develop the initialization and parameterization used by the S5 model. The result is a state space layer that can leverage efficient and widely implemented parallel scans, allowing S5 to match the computational efficiency of S4, while also achieving state-of-the-art performance on several long-range sequence modeling tasks. S5 averages 87.4% on the long range arena benchmark, and 98.5% on the most difficult Path-X task.

A key challenge in neural architecture search (NAS) is quickly inferring the predictive performance of a broad spectrum of networks to discover statistically accurate and computationally efficient ones. We refer to this task as model performance inference (MPI). The current practice for efficient MPI is gradient-based methods that leverage the gradients of a network at initialization to infer its performance. However, existing gradient-based methods rely only on heuristic metrics and lack the necessary theoretical foundations to consolidate their designs. We propose GradSign, an accurate, simple, and flexible metric for model performance inference with theoretical insights. The key idea behind GradSign is a quantity {\Psi} to analyze the optimization landscape of different networks at the granularity of individual training samples. Theoretically, we show that both the network's training and true population losses are proportionally upper-bounded by {\Psi} under reasonable assumptions. In addition, we design GradSign, an accurate and simple approximation of {\Psi} using the gradients of a network evaluated at a random initialization state. Evaluation on seven NAS benchmarks across three training datasets shows that GradSign generalizes well to real-world networks and consistently outperforms state-of-the-art gradient-based methods for MPI evaluated by Spearman's {\rho} and Kendall's Tau. Additionally, we integrate GradSign into four existing NAS algorithms and show that the GradSign-assisted NAS algorithms outperform their vanilla counterparts by improving the accuracies of best-discovered networks by up to 0.3%, 1.1%, and 1.0% on three real-world tasks.

Large language models (LLMs) have demonstrated remarkable success as foundational models, benefiting various downstream applications through fine-tuning. Recent studies on loss scaling have demonstrated the superior performance of larger LLMs compared to their smaller counterparts. Nevertheless, training LLMs with billions of parameters poses significant challenges and requires considerable computational resources. For example, training a one trillion parameter GPT-style model on 20 trillion tokens requires a staggering 120 million exaflops of computation. This research explores efficient distributed training strategies to extract this computation from Frontier, the world's first exascale supercomputer dedicated to open science. We enable and investigate various model and data parallel training techniques, such as tensor parallelism, pipeline parallelism, and sharded data parallelism, to facilitate training a trillion-parameter model on Frontier. We empirically assess these techniques and their associated parameters to determine their impact on memory footprint, communication latency, and GPU's computational efficiency. We analyze the complex interplay among these techniques and find a strategy to combine them to achieve high throughput through hyperparameter tuning. We have identified efficient strategies for training large LLMs of varying sizes through empirical analysis and hyperparameter tuning. For 22 Billion, 175 Billion, and 1 Trillion parameters, we achieved GPU throughputs of 38.38%, 36.14%, and 31.96%, respectively. For the training of the 175 Billion parameter model and the 1 Trillion parameter model, we achieved 100% weak scaling efficiency on 1024 and 3072 MI250X GPUs, respectively. We also achieved strong scaling efficiencies of 89% and 87% for these two models.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

We present the design of a new large scale orchestration layer for accelerators. Our system, Pathways, is explicitly designed to enable exploration of new systems and ML research ideas, while retaining state of the art performance for current models. Pathways uses a sharded dataflow graph of asynchronous operators that consume and produce futures, and efficiently gang-schedules heterogeneous parallel computations on thousands of accelerators while coordinating data transfers over their dedicated interconnects. Pathways makes use of a novel asynchronous distributed dataflow design that lets the control plane execute in parallel despite dependencies in the data plane. This design, with careful engineering, allows Pathways to adopt a single-controller model that makes it easier to express complex new parallelism patterns. We demonstrate that Pathways can achieve performance parity (~100% accelerator utilization) with state-of-the-art systems when running SPMD computations over 2048 TPUs, while also delivering throughput comparable to the SPMD case for Transformer models that are pipelined across 16 stages, or sharded across two islands of accelerators connected over a data center network.

State-space models (SSMs) have recently emerged as a framework for learning long-range sequence tasks. An example is the structured state-space sequence (S4) layer, which uses the diagonal-plus-low-rank structure of the HiPPO initialization framework. However, the complicated structure of the S4 layer poses challenges; and, in an effort to address these challenges, models such as S4D and S5 have considered a purely diagonal structure. This choice simplifies the implementation, improves computational efficiency, and allows channel communication. However, diagonalizing the HiPPO framework is itself an ill-posed problem. In this paper, we propose a general solution for this and related ill-posed diagonalization problems in machine learning. We introduce a generic, backward-stable "perturb-then-diagonalize" (PTD) methodology, which is based on the pseudospectral theory of non-normal operators, and which may be interpreted as the approximate diagonalization of the non-normal matrices defining SSMs. Based on this, we introduce the S4-PTD and S5-PTD models. Through theoretical analysis of the transfer functions of different initialization schemes, we demonstrate that the S4-PTD/S5-PTD initialization strongly converges to the HiPPO framework, while the S4D/S5 initialization only achieves weak convergences. As a result, our new models show resilience to Fourier-mode noise-perturbed inputs, a crucial property not achieved by the S4D/S5 models. In addition to improved robustness, our S5-PTD model averages 87.6% accuracy on the Long-Range Arena benchmark, demonstrating that the PTD methodology helps to improve the accuracy of deep learning models.

LLMs have seen rapid adoption in all domains. They need to be trained on high-end high-performance computing (HPC) infrastructures and ingest massive amounts of input data. Unsurprisingly, at such a large scale, unexpected events (e.g., failures of components, instability of the software, undesirable learning patterns, etc.), are frequent and typically impact the training in a negative fashion. Thus, LLMs need to be checkpointed frequently so that they can be rolled back to a stable state and subsequently fine-tuned. However, given the large sizes of LLMs, a straightforward checkpointing solution that directly writes the model parameters and optimizer state to persistent storage (e.g., a parallel file system), incurs significant I/O overheads. To address this challenge, in this paper we study how to reduce the I/O overheads for enabling fast and scalable checkpointing for LLMs that can be applied at high frequency (up to the granularity of individual iterations) without significant impact on the training process. Specifically, we introduce a lazy asynchronous multi-level approach that takes advantage of the fact that the tensors making up the model and optimizer state shards remain immutable for extended periods of time, which makes it possible to copy their content in the background with minimal interference during the training process. We evaluate our approach at scales of up to 180 GPUs using different model sizes, parallelism settings, and checkpointing frequencies. The results show up to 48times faster checkpointing and 2.2times faster end-to-end training runtime compared with the state-of-art checkpointing approaches.

Message-passing graph neural networks (MPNNs) emerged as powerful tools for processing graph-structured input. However, they operate on a fixed input graph structure, ignoring potential noise and missing information. Furthermore, their local aggregation mechanism can lead to problems such as over-squashing and limited expressive power in capturing relevant graph structures. Existing solutions to these challenges have primarily relied on heuristic methods, often disregarding the underlying data distribution. Hence, devising principled approaches for learning to infer graph structures relevant to the given prediction task remains an open challenge. In this work, leveraging recent progress in exact and differentiable k-subset sampling, we devise probabilistically rewired MPNNs (PR-MPNNs), which learn to add relevant edges while omitting less beneficial ones. For the first time, our theoretical analysis explores how PR-MPNNs enhance expressive power, and we identify precise conditions under which they outperform purely randomized approaches. Empirically, we demonstrate that our approach effectively mitigates issues like over-squashing and under-reaching. In addition, on established real-world datasets, our method exhibits competitive or superior predictive performance compared to traditional MPNN models and recent graph transformer architectures.

State space models (SSM) have recently been shown to be very effective as a deep learning layer as a promising alternative to sequence models such as RNNs, CNNs, or Transformers. The first version to show this potential was the S4 model, which is particularly effective on tasks involving long-range dependencies by using a prescribed state matrix called the HiPPO matrix. While this has an interpretable mathematical mechanism for modeling long dependencies, it introduces a custom representation and algorithm that can be difficult to implement. On the other hand, a recent variant of S4 called DSS showed that restricting the state matrix to be fully diagonal can still preserve the performance of the original model when using a specific initialization based on approximating S4's matrix. This work seeks to systematically understand how to parameterize and initialize such diagonal state space models. While it follows from classical results that almost all SSMs have an equivalent diagonal form, we show that the initialization is critical for performance. We explain why DSS works mathematically, by showing that the diagonal restriction of S4's matrix surprisingly recovers the same kernel in the limit of infinite state dimension. We also systematically describe various design choices in parameterizing and computing diagonal SSMs, and perform a controlled empirical study ablating the effects of these choices. Our final model S4D is a simple diagonal version of S4 whose kernel computation requires just 2 lines of code and performs comparably to S4 in almost all settings, with state-of-the-art results for image, audio, and medical time-series domains, and averaging 85\% on the Long Range Arena benchmark.

In this study, we propose a simple method for fault-tolerant Strassen-like matrix multiplications. The proposed method is based on using two distinct Strassen-like algorithms instead of replicating a given one. We have realized that using two different algorithms, new check relations arise resulting in more local computations. These local computations are found using computer aided search. To improve performance, special parity (extra) sub-matrix multiplications (PSMMs) are generated (two of them) at the expense of increasing communication/computation cost of the system. Our preliminary results demonstrate that the proposed method outperforms a Strassen-like algorithm with two copies and secures a very close performance to three copy version using only 2 PSMMs, reducing the total number of compute nodes by around 24\% i.e., from 21 to 16.

Existing checkpointing approaches seem ill-suited for distributed training even though hardware limitations make model parallelism, i.e., sharding model state across multiple accelerators, a requirement for model scaling. Consolidating distributed model state into a single checkpoint unacceptably slows down training, and is impractical at extreme scales. Distributed checkpoints, in contrast, are tightly coupled to the model parallelism and hardware configurations of the training run, and thus unusable on different configurations. To address this problem, we propose Universal Checkpointing, a technique that enables efficient checkpoint creation while providing the flexibility of resuming on arbitrary parallelism strategy and hardware configurations. Universal Checkpointing unlocks unprecedented capabilities for large-scale training such as improved resilience to hardware failures through continued training on remaining healthy hardware, and reduced training time through opportunistic exploitation of elastic capacity. The key insight of Universal Checkpointing is the selection of the optimal representation in each phase of the checkpointing life cycle: distributed representation for saving, and consolidated representation for loading. This is achieved using two key mechanisms. First, the universal checkpoint format, which consists of a consolidated representation of each model parameter and metadata for mapping parameter fragments into training ranks of arbitrary model-parallelism configuration. Second, the universal checkpoint language, a simple but powerful specification language for converting distributed checkpoints into the universal checkpoint format. Our evaluation demonstrates the effectiveness and generality of Universal Checkpointing on state-of-the-art model architectures and a wide range of parallelism techniques.

High-performance sparse matrix-matrix (SpMM) multiplication is paramount for science and industry, as the ever-increasing sizes of data prohibit using dense data structures. Yet, existing hardware, such as Tensor Cores (TC), is ill-suited for SpMM, as it imposes strict constraints on data structures that cannot be met by unstructured sparsity found in many applications. To address this, we introduce (S)parse (Ma)trix Matrix (T)ensor Core-accelerated (SMaT): a novel SpMM library that utilizes TCs for unstructured sparse matrices. Our block-sparse library leverages the low-level CUDA MMA (matrix-matrix-accumulate) API, maximizing the performance offered by modern GPUs. Algorithmic optimizations such as sparse matrix permutation further improve performance by minimizing the number of non-zero blocks. The evaluation on NVIDIA A100 shows that SMaT outperforms SotA libraries (DASP, cuSPARSE, and Magicube) by up to 125x (on average 2.6x). SMaT can be used to accelerate many workloads in scientific computing, large-model training, inference, and others.

Sparse matrices, more specifically SpGEMM kernels, are commonly found in a wide range of applications, spanning graph-based path-finding to machine learning algorithms (e.g., neural networks). A particular challenge in implementing SpGEMM kernels has been the pressure placed on DRAM memory. One approach to tackle this problem is to use an inner product method for the SpGEMM kernel implementation. While the inner product produces fewer intermediate results, it can end up saturating the memory bandwidth, given the high number of redundant fetches of the input matrix elements. Using an outer product-based SpGEMM kernel can reduce redundant fetches, but at the cost of increased overhead due to extra computation and memory accesses for producing/managing partial products. In this thesis, we introduce a novel SpGEMM kernel implementation based on the row-wise product approach. We leverage atomic instructions to merge intermediate partial products as they are generated. The use of atomic instructions eliminates the need to create partial product matrices. To evaluate our row-wise product approach, we map an optimized SpGEMM kernel to a custom accelerator designed to accelerate graph-based applications. The targeted accelerator is an experimental system named PIUMA, being developed by Intel. PIUMA provides several attractive features, including fast context switching, user-configurable caches, globally addressable memory, non-coherent caches, and asynchronous pipelines. We tailor our SpGEMM kernel to exploit many of the features of the PIUMA fabric. This thesis compares our SpGEMM implementation against prior solutions, all mapped to the PIUMA framework. We briefly describe some of the PIUMA architecture features and then delve into the details of our optimized SpGEMM kernel. Our SpGEMM kernel can achieve 9.4x speedup as compared to competing approaches.

Increasing test-time compute for LLMs shows promise across domains but remains underexplored in code generation, despite extensive study in math. In this paper, we propose S*, the first hybrid test-time scaling framework that substantially improves the coverage and selection accuracy of generated code. S* extends the existing parallel scaling paradigm with sequential scaling to push performance boundaries. It further leverages a novel selection mechanism that adaptively generates distinguishing inputs for pairwise comparison, combined with execution-grounded information to robustly identify correct solutions. We evaluate across 12 Large Language Models and Large Reasoning Model and show: (1) S* consistently improves performance across model families and sizes, enabling a 3B model to outperform GPT-4o-mini; (2) S* enables non-reasoning models to surpass reasoning models - GPT-4o-mini with S* outperforms o1-preview by 3.7% on LiveCodeBench; (3) S* further boosts state-of-the-art reasoning models - DeepSeek-R1-Distill-Qwen-32B with S* achieves 85.7% on LiveCodeBench, approaching o1 (high) at 88.5%. Code will be available under https://github.com/NovaSky-AI/SkyThought.

Large language models (LLMs) such as GPT-3, OPT, and LLaMA have demonstrated remarkable accuracy in a wide range of tasks. However, training these models can incur significant expenses, often requiring tens of thousands of GPUs for months of continuous operation. Typically, this training is carried out in specialized GPU clusters equipped with homogeneous high-speed Remote Direct Memory Access (RDMA) network interface cards (NICs). The acquisition and maintenance of such dedicated clusters is challenging. Current LLM training frameworks, like Megatron-LM and Megatron-DeepSpeed, focus primarily on optimizing training within homogeneous cluster settings. In this paper, we introduce Holmes, a training framework for LLMs that employs thoughtfully crafted data and model parallelism strategies over the heterogeneous NIC environment. Our primary technical contribution lies in a novel scheduling method that intelligently allocates distinct computational tasklets in LLM training to specific groups of GPU devices based on the characteristics of their connected NICs. Furthermore, our proposed framework, utilizing pipeline parallel techniques, demonstrates scalability to multiple GPU clusters, even in scenarios without high-speed interconnects between nodes in distinct clusters. We conducted comprehensive experiments that involved various scenarios in the heterogeneous NIC environment. In most cases, our framework achieves performance levels close to those achievable with homogeneous RDMA-capable networks (InfiniBand or RoCE), significantly exceeding training efficiency within the pure Ethernet environment. Additionally, we verified that our framework outperforms other mainstream LLM frameworks under heterogeneous NIC environment in terms of training efficiency and can be seamlessly integrated with them.

Federated Learning (FL) typically involves a large-scale, distributed system with individual user devices/servers training models locally and then aggregating their model updates on a trusted central server. Existing systems for FL often use an always-on server for model aggregation, which can be inefficient in terms of resource utilization. They may also be inelastic in their resource management. This is particularly exacerbated when aggregating model updates at scale in a highly dynamic environment with varying numbers of heterogeneous user devices/servers. We present LIFL, a lightweight and elastic serverless cloud platform with fine-grained resource management for efficient FL aggregation at scale. LIFL is enhanced by a streamlined, event-driven serverless design that eliminates the individual heavy-weight message broker and replaces inefficient container-based sidecars with lightweight eBPF-based proxies. We leverage shared memory processing to achieve high-performance communication for hierarchical aggregation, which is commonly adopted to speed up FL aggregation at scale. We further introduce locality-aware placement in LIFL to maximize the benefits of shared memory processing. LIFL precisely scales and carefully reuses the resources for hierarchical aggregation to achieve the highest degree of parallelism while minimizing the aggregation time and resource consumption. Our experimental results show that LIFL achieves significant improvement in resource efficiency and aggregation speed for supporting FL at scale, compared to existing serverful and serverless FL systems.

We present a new approach for the approximate K-nearest neighbor search based on navigable small world graphs with controllable hierarchy (Hierarchical NSW, HNSW). The proposed solution is fully graph-based, without any need for additional search structures, which are typically used at the coarse search stage of the most proximity graph techniques. Hierarchical NSW incrementally builds a multi-layer structure consisting from hierarchical set of proximity graphs (layers) for nested subsets of the stored elements. The maximum layer in which an element is present is selected randomly with an exponentially decaying probability distribution. This allows producing graphs similar to the previously studied Navigable Small World (NSW) structures while additionally having the links separated by their characteristic distance scales. Starting search from the upper layer together with utilizing the scale separation boosts the performance compared to NSW and allows a logarithmic complexity scaling. Additional employment of a heuristic for selecting proximity graph neighbors significantly increases performance at high recall and in case of highly clustered data. Performance evaluation has demonstrated that the proposed general metric space search index is able to strongly outperform previous opensource state-of-the-art vector-only approaches. Similarity of the algorithm to the skip list structure allows straightforward balanced distributed implementation.

Structural pruning enables model acceleration by removing structurally-grouped parameters from neural networks. However, the parameter-grouping patterns vary widely across different models, making architecture-specific pruners, which rely on manually-designed grouping schemes, non-generalizable to new architectures. In this work, we study a highly-challenging yet barely-explored task, any structural pruning, to tackle general structural pruning of arbitrary architecture like CNNs, RNNs, GNNs and Transformers. The most prominent obstacle towards this goal lies in the structural coupling, which not only forces different layers to be pruned simultaneously, but also expects all removed parameters to be consistently unimportant, thereby avoiding structural issues and significant performance degradation after pruning. To address this problem, we propose a general and {fully automatic} method, Dependency Graph (DepGraph), to explicitly model the dependency between layers and comprehensively group coupled parameters for pruning. In this work, we extensively evaluate our method on several architectures and tasks, including ResNe(X)t, DenseNet, MobileNet and Vision transformer for images, GAT for graph, DGCNN for 3D point cloud, alongside LSTM for language, and demonstrate that, even with a simple norm-based criterion, the proposed method consistently yields gratifying performances.

State space models (SSM) have been widely applied for the analysis and visualization of large sequential datasets. Sequential Monte Carlo (SMC) is a very popular particle-based method to sample latent states from intractable posteriors. However, SSM is significantly influenced by the choice of the proposal. Recently Hamiltonian Monte Carlo (HMC) sampling has shown success in many practical problems. In this paper, we propose an SMC augmented by HMC (HSMC) for inference and model learning of nonlinear SSM, which can exempt us from learning proposals and reduce the model complexity significantly. Based on the measure preserving property of HMC, the particles directly generated by transition function can approximate the posterior of latent states arbitrarily well. In order to better adapt to the local geometry of latent space, the HMC is conducted on Riemannian manifold defined by a positive definite metric. In addition, we show that the proposed HSMC method can improve SSMs realized by both Gaussian Processes (GP) and Neural Network (NN).

Despite the promising performance of state space models (SSMs) in long sequence modeling, limitations still exist. Advanced SSMs like S5 and S6 (Mamba) in addressing non-uniform sampling, their recursive structures impede efficient SSM computation via convolution. To overcome compatibility limitations in parallel convolutional computation, this paper proposes a novel non-recursive non-uniform sample processing strategy. Theoretical analysis of SSMs through the lens of Event-Triggered Control (ETC) theory reveals the Non-Stable State (NSS) problem, where deviations from sampling point requirements lead to error transmission and accumulation, causing the divergence of the SSM's hidden state. Our analysis further reveals that adjustments of input sequences with early memories can mitigate the NSS problem, achieving Sampling Step Adaptation (SSA). Building on this insight, we introduce a simple yet effective plug-and-play mechanism, State Memory Replay (SMR), which utilizes learnable memories to adjust the current state with multi-step information for generalization at sampling points different from those in the training data. This enables SSMs to stably model varying sampling points. Experiments on long-range modeling tasks in autoregressive language modeling and Long Range Arena demonstrate the general effectiveness of the SMR mechanism for a series of SSM models.

We propose using Normalizing Flows as a trainable kernel within the molecular dynamics update of Hamiltonian Monte Carlo (HMC). By learning (invertible) transformations that simplify our dynamics, we can outperform traditional methods at generating independent configurations. We show that, using a carefully constructed network architecture, our approach can be easily scaled to large lattice volumes with minimal retraining effort. The source code for our implementation is publicly available online at https://github.com/nftqcd/fthmc.

Efficient parallelization of Large Language Models (LLMs) with long sequences is essential but challenging due to their significant computational and memory demands, particularly stemming from communication bottlenecks in attention mechanisms. While sequence parallelism (SP) has been introduced as a potential solution, existing methods often suffer from limited scalability or inefficiency, rendering their effectiveness. Ring-Attention demonstrates the potential for scaling sequence processing but faces significant limitations due to its reliance on peer-to-peer (P2P) communication and inefficient utilization of network resources. As the degree of SP increases, the quadratic decrease in computation time per step contrasts sharply with the linear reduction in communication volume, exacerbating communication bottlenecks. To address these challenges, we propose TokenRing, a fine-grained parallel framework that leverages bidirectional P2P communication to effectively overlap computation and data transmission. By partitioning the attention block and concurrently transmitting Query and block outputs (i.e., block_out and block_lse) within a fully connected mesh topology, TokenRing achieves significant reductions in communication overhead and better load balancing. These innovations improve the scalability and efficiency of distributed Transformer models, particularly for long-context sequences. Experimental results demonstrate that TokenRing enhances throughput and reduces communication latency. Moreover, its design adapts seamlessly to various multi-GPU interconnect solutions, such as Huawei Ascend, ensuring broad compatibility and cost-effectiveness for distributed LLM inference and training. The code is available at: https://github.com/ACA-Lab-SJTU/token-ring.

We present GSPMD, an automatic, compiler-based parallelization system for common machine learning computations. It allows users to write programs in the same way as for a single device, then give hints through a few annotations on how to distribute tensors, based on which GSPMD will parallelize the computation. Its representation of partitioning is simple yet general, allowing it to express different or mixed paradigms of parallelism on a wide variety of models. GSPMD infers the partitioning for every operator based on limited user annotations, making it convenient to scale existing single-device programs. It solves several technical challenges for production usage, allowing GSPMD to achieve 50% to 62% compute utilization on up to 2048 Cloud TPUv3 cores for models with up to one trillion parameters.

Sequence parallelism (SP), which divides the sequence dimension of input tensors across multiple computational devices, is becoming key to unlocking the long-context capabilities of generative AI models. This paper investigates the state-of-the-art SP approaches, i.e. DeepSpeed-Ulysses and Ring-Attention, and proposes a unified SP approach, which is more robust to transformer model architectures and network hardware topology. This paper compares the communication and memory cost of SP and existing parallelism, including data/tensor/zero/expert/pipeline parallelism, and discusses the best practices for designing hybrid 4D parallelism involving SP. We achieved 86% MFU on two 8xA800 nodes using SP for sequence length 208K for the LLAMA3-8B model. Our code is publicly available on https://github.com/feifeibear/long-context-attention.

In this work we develop a new method, named Sub-graph Permutation Equivariant Networks (SPEN), which provides a framework for building graph neural networks that operate on sub-graphs, while using a base update function that is permutation equivariant, that are equivariant to a novel choice of automorphism group. Message passing neural networks have been shown to be limited in their expressive power and recent approaches to over come this either lack scalability or require structural information to be encoded into the feature space. The general framework presented here overcomes the scalability issues associated with global permutation equivariance by operating more locally on sub-graphs. In addition, through operating on sub-graphs the expressive power of higher-dimensional global permutation equivariant networks is improved; this is due to fact that two non-distinguishable graphs often contain distinguishable sub-graphs. Furthermore, the proposed framework only requires a choice of k-hops for creating ego-network sub-graphs and a choice of representation space to be used for each layer, which makes the method easily applicable across a range of graph based domains. We experimentally validate the method on a range of graph benchmark classification tasks, demonstrating statistically indistinguishable results from the state-of-the-art on six out of seven benchmarks. Further, we demonstrate that the use of local update functions offers a significant improvement in GPU memory over global methods.

Current PEFT methods for LLMs can achieve either high quality, efficient training, or scalable serving, but not all three simultaneously. To address this limitation, we investigate sparse fine-tuning and observe a remarkable improvement in generalization ability. Utilizing this key insight, we propose a family of Structured Sparse Fine-Tuning (S^{2}FT) methods for LLMs, which concurrently achieve state-of-the-art fine-tuning performance, training efficiency, and inference scalability. S^{2}FT accomplishes this by "selecting sparsely and computing densely". It selects a few heads and channels in the MHA and FFN modules for each Transformer block, respectively. Next, it co-permutes weight matrices on both sides of the coupled structures in LLMs to connect the selected components in each layer into a dense submatrix. Finally, S^{2}FT performs in-place gradient updates on all submatrices. Through theoretical analysis and empirical results, our method prevents forgetting while simplifying optimization, delivers SOTA performance on both commonsense and arithmetic reasoning with 4.6% and 1.3% average improvements compared to LoRA, and surpasses full FT by 11.5% when generalizing to various domains after instruction tuning. Using our partial backpropagation algorithm, S^{2}FT saves training memory up to 3times and improves latency by 1.5-2.7times compared to full FT, while delivering an average 10% improvement over LoRA on both metrics. We further demonstrate that the weight updates in S^{2}FT can be decoupled into adapters, enabling effective fusion, fast switch, and efficient parallelism for serving multiple fine-tuned models.

Structured state space sequence (S4) models have recently achieved state-of-the-art performance on long-range sequence modeling tasks. These models also have fast inference speeds and parallelisable training, making them potentially useful in many reinforcement learning settings. We propose a modification to a variant of S4 that enables us to initialise and reset the hidden state in parallel, allowing us to tackle reinforcement learning tasks. We show that our modified architecture runs asymptotically faster than Transformers in sequence length and performs better than RNN's on a simple memory-based task. We evaluate our modified architecture on a set of partially-observable environments and find that, in practice, our model outperforms RNN's while also running over five times faster. Then, by leveraging the model's ability to handle long-range sequences, we achieve strong performance on a challenging meta-learning task in which the agent is given a randomly-sampled continuous control environment, combined with a randomly-sampled linear projection of the environment's observations and actions. Furthermore, we show the resulting model can adapt to out-of-distribution held-out tasks. Overall, the results presented in this paper show that structured state space models are fast and performant for in-context reinforcement learning tasks. We provide code at https://github.com/luchris429/popjaxrl.

Clustering non-Euclidean data is difficult, and one of the most used algorithms besides hierarchical clustering is the popular algorithm Partitioning Around Medoids (PAM), also simply referred to as k-medoids clustering. In Euclidean geometry the mean-as used in k-means-is a good estimator for the cluster center, but this does not exist for arbitrary dissimilarities. PAM uses the medoid instead, the object with the smallest dissimilarity to all others in the cluster. This notion of centrality can be used with any (dis-)similarity, and thus is of high relevance to many domains and applications. A key issue with PAM is its high run time cost. We propose modifications to the PAM algorithm that achieve an O(k)-fold speedup in the second ("SWAP") phase of the algorithm, but will still find the same results as the original PAM algorithm. If we relax the choice of swaps performed (while retaining comparable quality), we can further accelerate the algorithm by eagerly performing additional swaps in each iteration. With the substantially faster SWAP, we can now explore faster initialization strategies, because (i) the classic ("BUILD") initialization now becomes the bottleneck, and (ii) our swap is fast enough to compensate for worse starting conditions. We also show how the CLARA and CLARANS algorithms benefit from the proposed modifications. While we do not study the parallelization of our approach in this work, it can easily be combined with earlier approaches to use PAM and CLARA on big data (some of which use PAM as a subroutine, hence can immediately benefit from these improvements), where the performance with high k becomes increasingly important. In experiments on real data with k=100,200, we observed a 458x respectively 1191x speedup compared to the original PAM SWAP algorithm, making PAM applicable to larger data sets, and in particular to higher k.

Large Language Models (LLMs) have demonstrated impressive performance across various downstream tasks. When training these models, there is a growing inclination to process more tokens on larger training scales but with relatively smaller model sizes. Zero Redundancy Optimizer (ZeRO), although effective in conventional training environments, grapples with scaling challenges when confronted with this emerging paradigm. To this end, we propose a novel LLM training framework AMSP, which undertakes a granular partitioning of model states, encompassing parameters (P), gradient (G), and optimizer states (OS). Specifically, AMSP(1) builds a unified partitioning space, enabling independent partitioning strategies for P, G, and OS; (2) incorporates a scale-aware partitioner to autonomously search for optimal partitioning strategies: (3) designs a dedicated communication optimizer to ensure proficient management of data placement discrepancies arising from diverse partitioning strategies. Our evaluations show that AMSP achieves up to 90.3% scaling efficiency across 1024 GPUs.

We study the problem of visualizing large-scale and high-dimensional data in a low-dimensional (typically 2D or 3D) space. Much success has been reported recently by techniques that first compute a similarity structure of the data points and then project them into a low-dimensional space with the structure preserved. These two steps suffer from considerable computational costs, preventing the state-of-the-art methods such as the t-SNE from scaling to large-scale and high-dimensional data (e.g., millions of data points and hundreds of dimensions). We propose the LargeVis, a technique that first constructs an accurately approximated K-nearest neighbor graph from the data and then layouts the graph in the low-dimensional space. Comparing to t-SNE, LargeVis significantly reduces the computational cost of the graph construction step and employs a principled probabilistic model for the visualization step, the objective of which can be effectively optimized through asynchronous stochastic gradient descent with a linear time complexity. The whole procedure thus easily scales to millions of high-dimensional data points. Experimental results on real-world data sets demonstrate that the LargeVis outperforms the state-of-the-art methods in both efficiency and effectiveness. The hyper-parameters of LargeVis are also much more stable over different data sets.

Scaling up Large Language Model(LLM) training involves fitting a tremendous amount of training parameters across a limited number of workers. However, methods like ZeRO-3 that drastically reduce GPU memory pressure often incur heavy communication to ensure global synchronization and consistency. Established efforts such as ZeRO++ use secondary partitions to avoid inter-node communications, given that intra-node GPU-GPU transfer generally has more bandwidth and lower latency than inter-node connections. However, as more capable infrastructure like Frontier, equipped with AMD GPUs, emerged with impressive computing capability, there is a need for investigations on the hardware topology and to develop targeted strategies to improve training efficiency. In this work, we propose a collection of communication and optimization strategies for ZeRO++ to reduce communication costs and improve memory utilization. In this paper, we propose a 3-level hierarchical partitioning specifically for the current Top-1 supercomputing cluster, Frontier, which aims at leveraging various bandwidths across layers of communications (GCD-GCD, GPU-GPU, and inter-node) to reduce communication overhead. For a 20B GPT model, we observe a 1.71x increase in TFLOPS per GPU when compared with ZeRO++ up to 384 GCDs and a scaling efficiency of 0.94 for up to 384 GCDs. To the best of our knowledge, our work is also the first effort to efficiently optimize LLM workloads on Frontier AMD GPUs.

When considering a model architecture, there are several ways to reduce its memory footprint. Historically, popular approaches included selecting smaller architectures and creating sparse networks through pruning. More recently, randomized parameter-sharing (RPS) methods have gained traction for model compression at start of training. In this paper, we comprehensively assess the trade-off between memory and accuracy across RPS, pruning techniques, and building smaller models. Our findings demonstrate that RPS, which is both data and model-agnostic, consistently outperforms/matches smaller models and all moderately informed pruning strategies, such as MAG, SNIP, SYNFLOW, and GRASP, across the entire compression range. This advantage becomes particularly pronounced in higher compression scenarios. Notably, even when compared to highly informed pruning techniques like Lottery Ticket Rewinding (LTR), RPS exhibits superior performance in high compression settings. This points out inherent capacity advantage that RPS enjoys over sparse models. Theoretically, we establish RPS as a superior technique in terms of memory-efficient representation when compared to pruning for linear models. This paper argues in favor of paradigm shift towards RPS based models. During our rigorous evaluation of RPS, we identified issues in the state-of-the-art RPS technique ROAST, specifically regarding stability (ROAST's sensitivity to initialization hyperparameters, often leading to divergence) and Pareto-continuity (ROAST's inability to recover the accuracy of the original model at zero compression). We provably address both of these issues. We refer to the modified RPS, which incorporates our improvements, as STABLE-RPS.

Dense linear layers are the dominant computational bottleneck in foundation models. Identifying more efficient alternatives to dense matrices has enormous potential for building more compute-efficient models, as exemplified by the success of convolutional networks in the image domain. In this work, we systematically explore structured matrices as replacements for dense matrices. We show that different structures often require drastically different initialization scales and learning rates, which are crucial to performance, especially as models scale. Using insights from the Maximal Update Parameterization, we determine the optimal scaling for initialization and learning rates of these unconventional layers. Finally, we measure the scaling laws of different structures to compare how quickly their performance improves with compute. We propose a novel matrix family containing Monarch matrices, the Block Tensor-Train (BTT), which we show performs better than dense matrices for the same compute on multiple tasks. On CIFAR-10/100 with augmentation, BTT achieves exponentially lower training loss than dense when training MLPs and ViTs. BTT matches dense ViT-S/32 performance on ImageNet-1k with 3.8 times less compute and is more efficient than dense for training small GPT-2 language models.

Data sharding, a technique for partitioning and distributing data among multiple servers or nodes, offers enhancements in the scalability, performance, and fault tolerance of extensive distributed systems. Nonetheless, this strategy introduces novel challenges, including load balancing among shards, management of node failures and data loss, and adaptation to evolving data and workload patterns. This paper proposes an innovative approach to tackle these challenges by empowering self-healing nodes with adaptive data sharding. Leveraging concepts such as self-replication, fractal regeneration, sentient data sharding, and symbiotic node clusters, our approach establishes a dynamic and resilient data sharding scheme capable of addressing diverse scenarios and meeting varied requirements. Implementation and evaluation of our approach involve a prototype system simulating a large-scale distributed database across various data sharding scenarios. Comparative analyses against existing data sharding techniques highlight the superior scalability, performance, fault tolerance, and adaptability of our approach. Additionally, the paper delves into potential applications and limitations, providing insights into the future research directions that can further advance this innovative approach.

The Stable Diffusion Model (SDM) is a prevalent and effective model for text-to-image (T2I) and image-to-image (I2I) generation. Despite various attempts at sampler optimization, model distillation, and network quantification, these approaches typically maintain the original network architecture. The extensive parameter scale and substantial computational demands have limited research into adjusting the model architecture. This study focuses on reducing redundant computation in SDM and optimizes the model through both tuning and tuning-free methods. 1) For the tuning method, we design a model assembly strategy to reconstruct a lightweight model while preserving performance through distillation. Second, to mitigate performance loss due to pruning, we incorporate multi-expert conditional convolution (ME-CondConv) into compressed UNets to enhance network performance by increasing capacity without sacrificing speed. Third, we validate the effectiveness of the multi-UNet switching method for improving network speed. 2) For the tuning-free method, we propose a feature inheritance strategy to accelerate inference by skipping local computations at the block, layer, or unit level within the network structure. We also examine multiple sampling modes for feature inheritance at the time-step level. Experiments demonstrate that both the proposed tuning and the tuning-free methods can improve the speed and performance of the SDM. The lightweight model reconstructed by the model assembly strategy increases generation speed by 22.4%, while the feature inheritance strategy enhances the SDM generation speed by 40.0%.

Extending the context length (i.e., the maximum supported sequence length) of LLMs is of paramount significance. To facilitate long context training of LLMs, sequence parallelism has emerged as an essential technique, which scatters each input sequence across multiple devices and necessitates communication to process the sequence. In essence, existing sequence parallelism methods assume homogeneous sequence lengths (i.e., all input sequences are equal in length) and therefore leverages a single, static scattering strategy for all input sequences. However, in reality, the sequence lengths in LLM training corpora exhibit substantial variability, often following a long-tail distribution, which leads to workload heterogeneity. In this paper, we show that employing a single, static strategy results in inefficiency and resource under-utilization, highlighting the need for adaptive approaches to handle the heterogeneous workloads across sequences. To address this, we propose a heterogeneity-adaptive sequence parallelism method. For each training step, our approach captures the variability in sequence lengths and assigns the optimal combination of scattering strategies based on workload characteristics. We model this problem as a linear programming optimization and design an efficient and effective solver to find the optimal solution. Furthermore, we implement our method in a high-performance system that supports adaptive parallelization in distributed LLM training. Experimental results demonstrate that our system outperforms state-of-the-art training frameworks by up to 1.98x.

We describe MGARD, a software providing MultiGrid Adaptive Reduction for floating-point scientific data on structured and unstructured grids. With exceptional data compression capability and precise error control, MGARD addresses a wide range of requirements, including storage reduction, high-performance I/O, and in-situ data analysis. It features a unified application programming interface (API) that seamlessly operates across diverse computing architectures. MGARD has been optimized with highly-tuned GPU kernels and efficient memory and device management mechanisms, ensuring scalable and rapid operations.

Large language models (LLMs) have garnered significant attention in both the AI community and beyond. Among these, the Generative Pre-trained Transformer (GPT) has emerged as the dominant architecture, spawning numerous variants. However, these variants have undergone pre-training under diverse conditions, including variations in input data, data preprocessing, and training methodologies, resulting in a lack of controlled comparative studies. Here we meticulously examine two prominent open-sourced GPT architectures, GPT-NeoX and LLaMA, leveraging the computational power of Frontier, the world's first Exascale supercomputer. Employing the same materials science text corpus and a comprehensive end-to-end pipeline, we conduct a comparative analysis of their training and downstream performance. Our efforts culminate in achieving state-of-the-art performance on a challenging materials science benchmark. Furthermore, we investigate the computation and energy efficiency, and propose a computationally efficient method for architecture design. To our knowledge, these pre-trained models represent the largest available for materials science. Our findings provide practical guidance for building LLMs on HPC platforms.

Language model training in distributed settings is limited by the communication cost of gradient exchanges. In this short note, we extend recent work from Malladi et al. (2023), using shared randomness to perform distributed fine-tuning with low bandwidth. The method is a natural decentralized extension of memory-efficient Simultaneous Perturbation Stochastic Approximation (SPSA). Each iteration, each machine seeds a Random Number Generator (RNG) to perform local reproducible perturbations on model weights and calculate and exchange scalar projected gradients, which are then used to update each model. By using a (machine, sample) identifier as the random seed, each model can regenerate one another's perturbations. As machines only exchange single-byte projected gradients, this is highly communication efficient. There are also potential privacy benefits, as projected gradients may be calculated on different training data, and models never access the other's data. Our approach not only drastically reduces communication bandwidth requirements but also accommodates dynamic addition or removal of machines during the training process and retains the memory-efficient and inference-only advantages of recent work. We perform proof-of-concept experiments to demonstrate the potential usefulness of this method, building off of rich literature on distributed optimization and memory-efficient training.

Message passing neural networks (MPNNs) have been shown to suffer from the phenomenon of over-squashing that causes poor performance for tasks relying on long-range interactions. This can be largely attributed to message passing only occurring locally, over a node's immediate neighbours. Rewiring approaches attempting to make graphs 'more connected', and supposedly better suited to long-range tasks, often lose the inductive bias provided by distance on the graph since they make distant nodes communicate instantly at every layer. In this paper we propose a framework, applicable to any MPNN architecture, that performs a layer-dependent rewiring to ensure gradual densification of the graph. We also propose a delay mechanism that permits skip connections between nodes depending on the layer and their mutual distance. We validate our approach on several long-range tasks and show that it outperforms graph Transformers and multi-hop MPNNs.

Designing effective positional encodings for graphs is key to building powerful graph transformers and enhancing message-passing graph neural networks. Although widespread, using Laplacian eigenvectors as positional encodings faces two fundamental challenges: (1) Non-uniqueness: there are many different eigendecompositions of the same Laplacian, and (2) Instability: small perturbations to the Laplacian could result in completely different eigenspaces, leading to unpredictable changes in positional encoding. Despite many attempts to address non-uniqueness, most methods overlook stability, leading to poor generalization on unseen graph structures. We identify the cause of instability to be a "hard partition" of eigenspaces. Hence, we introduce Stable and Expressive Positional Encodings (SPE), an architecture for processing eigenvectors that uses eigenvalues to "softly partition" eigenspaces. SPE is the first architecture that is (1) provably stable, and (2) universally expressive for basis invariant functions whilst respecting all symmetries of eigenvectors. Besides guaranteed stability, we prove that SPE is at least as expressive as existing methods, and highly capable of counting graph structures. Finally, we evaluate the effectiveness of our method on molecular property prediction, and out-of-distribution generalization tasks, finding improved generalization compared to existing positional encoding methods.

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive to information contained at distant nodes. Despite recent methods introduced to mitigate this issue, an understanding of the causes for over-squashing and of possible solutions are lacking. In this theoretical work, we prove that: (i) Neural network width can mitigate over-squashing, but at the cost of making the whole network more sensitive; (ii) Conversely, depth cannot help mitigate over-squashing: increasing the number of layers leads to over-squashing being dominated by vanishing gradients; (iii) The graph topology plays the greatest role, since over-squashing occurs between nodes at high commute (access) time. Our analysis provides a unified framework to study different recent methods introduced to cope with over-squashing and serves as a justification for a class of methods that fall under graph rewiring.

Graph neural networks (GNNs) emerged recently as a standard toolkit for learning from data on graphs. Current GNN designing works depend on immense human expertise to explore different message-passing mechanisms, and require manual enumeration to determine the proper message-passing depth. Inspired by the strong searching capability of neural architecture search (NAS) in CNN, this paper proposes Graph Neural Architecture Search (GNAS) with novel-designed search space. The GNAS can automatically learn better architecture with the optimal depth of message passing on the graph. Specifically, we design Graph Neural Architecture Paradigm (GAP) with tree-topology computation procedure and two types of fine-grained atomic operations (feature filtering and neighbor aggregation) from message-passing mechanism to construct powerful graph network search space. Feature filtering performs adaptive feature selection, and neighbor aggregation captures structural information and calculates neighbors' statistics. Experiments show that our GNAS can search for better GNNs with multiple message-passing mechanisms and optimal message-passing depth. The searched network achieves remarkable improvement over state-of-the-art manual designed and search-based GNNs on five large-scale datasets at three classical graph tasks. Codes can be found at https://github.com/phython96/GNAS-MP.

Recent advancements in State Space Models (SSMs) have attracted significant interest, particularly in models optimized for parallel training and handling long-range dependencies. Architectures like Mamba have scaled to billions of parameters with selective SSM. To facilitate broader applications using Mamba, exploring its efficiency is crucial. While token reduction techniques offer a straightforward post-training strategy, we find that applying existing methods directly to SSMs leads to substantial performance drops. Through insightful analysis, we identify the reasons for this failure and the limitations of current techniques. In response, we propose a tailored, unified post-training token reduction method for SSMs. Our approach integrates token importance and similarity, thus taking advantage of both pruning and merging, to devise a fine-grained intra-layer token reduction strategy. Extensive experiments show that our method improves the average accuracy by 5.7% to 13.1% on six benchmarks with Mamba-2 compared to existing methods, while significantly reducing computational demands and memory requirements.

Expert parallelism has been introduced as a strategy to distribute the computational workload of sparsely-gated mixture-of-experts (MoE) models across multiple computing devices, facilitating the execution of these increasingly large-scale models. However, the All-to-All communication intrinsic to expert parallelism constitutes a significant overhead, diminishing the MoE models' efficiency. Current optimization approaches offer some relief, yet they are constrained by the sequential interdependence of communication and computation operations. To address this limitation, we present a novel shortcut-connected MoE architecture with overlapping parallel strategy, designated as ScMoE, which effectively decouples communication from its conventional sequence, allowing for a substantial overlap of 70% to 100% with computation. When compared with the prevalent top-2 MoE architecture, ScMoE demonstrates training speed improvements of 30% and 11%, and inference improvements of 40% and 15%, in our PCIe and NVLink hardware environments, respectively, where communication constitutes 60% and 15% of the total MoE time consumption. On the other hand, extensive experiments and theoretical analyses indicate that ScMoE not only achieves comparable but in some instances surpasses the model quality of existing approaches in vision and language tasks.

Despite the recent advances in the field of computational Schr\"odinger Bridges (SB), most existing SB solvers are still heavy-weighted and require complex optimization of several neural networks. It turns out that there is no principal solver which plays the role of simple-yet-effective baseline for SB just like, e.g., k-means method in clustering, logistic regression in classification or Sinkhorn algorithm in discrete optimal transport. We address this issue and propose a novel fast and simple SB solver. Our development is a smart combination of two ideas which recently appeared in the field: (a) parameterization of the Schr\"odinger potentials with sum-exp quadratic functions and (b) viewing the log-Schr\"odinger potentials as the energy functions. We show that combined together these ideas yield a lightweight, simulation-free and theoretically justified SB solver with a simple straightforward optimization objective. As a result, it allows solving SB in moderate dimensions in a matter of minutes on CPU without a painful hyperparameter selection. Our light solver resembles the Gaussian mixture model which is widely used for density estimation. Inspired by this similarity, we also prove an important theoretical result showing that our light solver is a universal approximator of SBs. Furthemore, we conduct the analysis of the generalization error of our light solver. The code for our solver can be found at https://github.com/ngushchin/LightSB

Scaling long-context ability is essential for Large Language Models (LLMs). To amortize the memory consumption across multiple devices in long-context training, inter-data partitioning (a.k.a. Data Parallelism) and intra-data partitioning (a.k.a. Context Parallelism) are commonly used. Current training frameworks predominantly treat the two techniques as orthogonal, and establish static communication groups to organize the devices as a static mesh (e.g., a 2D mesh). However, the sequences for LLM training typically vary in lengths, no matter for texts, multi-modalities or reinforcement learning. The mismatch between data heterogeneity and static mesh causes redundant communication and imbalanced computation, degrading the training efficiency. In this work, we introduce ByteScale, an efficient, flexible, and scalable LLM training framework for large-scale mixed training of long and short sequences. The core of ByteScale is a novel parallelism strategy, namely Hybrid Data Parallelism (HDP), which unifies the inter- and intra-data partitioning with a dynamic mesh design. In particular, we build a communication optimizer, which eliminates the redundant communication for short sequences by data-aware sharding and dynamic communication, and further compresses the communication cost for long sequences by selective offloading. Besides, we also develop a balance scheduler to mitigate the imbalanced computation by parallelism-aware data assignment. We evaluate ByteScale with the model sizes ranging from 7B to 141B, context lengths from 256K to 2048K, on a production cluster with more than 12,000 GPUs. Experiment results show that ByteScale outperforms the state-of-the-art training system by up to 7.89x.

We present the design, implementation and engineering experience in building and deploying MegaScale, a production system for training large language models (LLMs) at the scale of more than 10,000 GPUs. Training LLMs at this scale brings unprecedented challenges to training efficiency and stability. We take a full-stack approach that co-designs the algorithmic and system components across model block and optimizer design, computation and communication overlapping, operator optimization, data pipeline, and network performance tuning. Maintaining high efficiency throughout the training process (i.e., stability) is an important consideration in production given the long extent of LLM training jobs. Many hard stability issues only emerge at large scale, and in-depth observability is the key to address them. We develop a set of diagnosis tools to monitor system components and events deep in the stack, identify root causes, and derive effective techniques to achieve fault tolerance and mitigate stragglers. MegaScale achieves 55.2% Model FLOPs Utilization (MFU) when training a 175B LLM model on 12,288 GPUs, improving the MFU by 1.34x compared to Megatron-LM. We share our operational experience in identifying and fixing failures and stragglers. We hope by articulating the problems and sharing our experience from a systems perspective, this work can inspire future LLM systems research.

The performance of a language model has been shown to be effectively modeled as a power-law in its parameter count. Here we study the scaling behaviors of Routing Networks: architectures that conditionally use only a subset of their parameters while processing an input. For these models, parameter count and computational requirement form two independent axes along which an increase leads to better performance. In this work we derive and justify scaling laws defined on these two variables which generalize those known for standard language models and describe the performance of a wide range of routing architectures trained via three different techniques. Afterwards we provide two applications of these laws: first deriving an Effective Parameter Count along which all models scale at the same rate, and then using the scaling coefficients to give a quantitative comparison of the three routing techniques considered. Our analysis derives from an extensive evaluation of Routing Networks across five orders of magnitude of size, including models with hundreds of experts and hundreds of billions of parameters.

This paper introduces a novel theoretical simplification of the Diffusion Schr\"odinger Bridge (DSB) that facilitates its unification with Score-based Generative Models (SGMs), addressing the limitations of DSB in complex data generation and enabling faster convergence and enhanced performance. By employing SGMs as an initial solution for DSB, our approach capitalizes on the strengths of both frameworks, ensuring a more efficient training process and improving the performance of SGM. We also propose a reparameterization technique that, despite theoretical approximations, practically improves the network's fitting capabilities. Our extensive experimental evaluations confirm the effectiveness of the simplified DSB, demonstrating its significant improvements. We believe the contributions of this work pave the way for advanced generative modeling. The code is available at https://github.com/checkcrab/SDSB.

Physics-informed neural networks (PINNs) leverage neural-networks to find the solutions of partial differential equation (PDE)-constrained optimization problems with initial conditions and boundary conditions as soft constraints. These soft constraints are often considered to be the sources of the complexity in the training phase of PINNs. Here, we demonstrate that the challenge of training (i) persists even when the boundary conditions are strictly enforced, and (ii) is closely related to the Kolmogorov n-width associated with problems demonstrating transport, convection, traveling waves, or moving fronts. Given this realization, we describe the mechanism underlying the training schemes such as those used in eXtended PINNs (XPINN), curriculum regularization, and sequence-to-sequence learning. For an important category of PDEs, i.e., governed by non-linear convection-diffusion equation, we propose reformulating PINNs on a Lagrangian frame of reference, i.e., LPINNs, as a PDE-informed solution. A parallel architecture with two branches is proposed. One branch solves for the state variables on the characteristics, and the second branch solves for the low-dimensional characteristics curves. The proposed architecture conforms to the causality innate to the convection, and leverages the direction of travel of the information in the domain. Finally, we demonstrate that the loss landscapes of LPINNs are less sensitive to the so-called "complexity" of the problems, compared to those in the traditional PINNs in the Eulerian framework.

Voronoi diagrams are essential geometrical structures with numerous applications, particularly astrophysics-driven finite volume methods. While serial algorithms for constructing these entities are well-established, parallel construction remains challenging. This is especially true in distributed memory systems, where each host manages only a subset of the input points. This process requires redistributing points across hosts and accurately computing the corresponding Voronoi cells. In this paper, we introduce a new distributed construction algorithm, which is implemented in our open-source C++ 3-dimensional Voronoi construction framework. Our approach leverages Delaunay triangulation as an intermediate step, which is then transformed into a Voronoi diagram. We introduce the algorithms we implemented for the precise construction and our load-balancing approach and compare the running time with other state-of-the-art frameworks. MadVoro is a versatile tool that can be applied in various scientific domains, such as mesh decomposition, computational physics, chemistry, and machine learning.

A spanning tree T of graph G is a rho-approximate universal Steiner tree (UST) for root vertex r if, for any subset of vertices S containing r, the cost of the minimal subgraph of T connecting S is within a rho factor of the minimum cost tree connecting S in G. Busch et al. (FOCS 2012) showed that every graph admits 2^{O(log n)}-approximate USTs by showing that USTs are equivalent to strong sparse partition hierarchies (up to poly-logs). Further, they posed poly-logarithmic USTs and strong sparse partition hierarchies as open questions. We settle these open questions by giving polynomial-time algorithms for computing both O(log ^ 7 n)-approximate USTs and poly-logarithmic strong sparse partition hierarchies. For graphs with constant doubling dimension or constant pathwidth we improve this to O(log n)-approximate USTs and O(1) strong sparse partition hierarchies. Our doubling dimension result is tight up to second order terms. We reduce the existence of these objects to the previously studied cluster aggregation problem and what we call dangling nets.

Pipeline parallelism has been widely explored, but most existing schedules lack a systematic methodology. In this paper, we propose a framework to decompose pipeline schedules as repeating a building block and we show that the lifespan of the building block decides the peak activation memory of the pipeline schedule. Guided by the observations, we find that almost all existing pipeline schedules, to the best of our knowledge, are memory inefficient. To address this, we introduce a family of memory efficient building blocks with controllable activation memory, which can reduce the peak activation memory to 1/2 of 1F1B without sacrificing efficiency, and even to 1/3 with comparable throughput. We can also achieve almost zero pipeline bubbles while maintaining the same activation memory as 1F1B. Our evaluations demonstrate that in pure pipeline parallelism settings, our methods outperform 1F1B by from 7% to 55% in terms of throughput. When employing a grid search over hybrid parallelism hyperparameters in practical scenarios, our proposed methods demonstrate a 16% throughput improvement over the 1F1B baseline for large language models.

Mixture-of-Experts (MoE) has emerged as a promising sparse paradigm for scaling up pre-trained models (PTMs) with remarkable cost-effectiveness. However, the dynamic nature of MoE leads to rapid fluctuations and imbalances in expert loads during training, resulting in significant straggler effects that hinder training performance when using expert parallelism (EP). Existing MoE training systems attempt to mitigate these effects through expert rearrangement strategies, but they face challenges in terms of memory efficiency and timeliness of rearrangement. This paper proposes Fully Sharded Sparse Data Parallelism (FSSDP), an innovative approach that tackles the parallelization of MoE layers and potential straggler effects caused by imbalanced expert loads from a new perspective. FSSDP fully shards the parameters and optimizer states of MoE layers across devices and sparsely materializes MoE parameters from scratch in each iteration with two sparse collectives SparseAllGather and SparseReduceScatter. We build Hecate, a high-performance MoE training system that incorporates FSSDP to fully unlock its potential. Hecate introduces heterogeneous sharding, sparse materialization, and re-materialization techniques to construct flexible and efficient expert placements with low memory and communication overhead. Our evaluation reveals that Hecate achieves up to 3.54x speedup compared over state-of-the-art MoE training systems and consistently demonstrates improvements across model architectures and hardware environments.

This paper studies the scale and redshift variation of density and velocity distributions in self-gravitating collisionless dark matter flow by a halo-based non-projection approach. All particles are divided into halo and out-of-halo particles for redshift variation of distributions. Without projecting particle fields onto a structured grid, the scale variation is analyzed by identifying all particle pairs on different scales r. We demonstrate that: i) Delaunay tessellation can be used to reconstruct the density field. The density correlation, spectrum, and dispersion functions were obtained, modeled, and compared with the N-body simulation; ii) the velocity distributions are symmetric on both small and large scales and are non-symmetric with a negative skewness on intermediate scales due to the inverse energy cascade at a constant rate varepsilon_u; iii) On small scales, the even order moments of pairwise velocity Delta u_L follow a two-thirds law (-varepsilon_ur)^{2/3}, while the odd order moments follow a linear scaling langle(Delta u_L)^{2n+1}rangle=(2n+1)langle(Delta u_L)^{2n}ranglelangleDelta u_Lrangler; iv) The scale variation of the velocity distributions was studied for longitudinal velocities u_L or u_L^{'}, pairwise velocity (velocity difference) Delta u_L=u_L^{'}-u_L and velocity sum Sigma u_L=u^{'}_L+u_L. Fully developed velocity fields are never Gaussian on any scale, despite that they can initially be Gaussian; v) On small scales, u_L and Sigma u_L can be modeled by a X distribution to maximize the system entropy; vi) On large scales, Delta u_L and Sigma u_L can be modeled by a logistic or a X distribution; vii) the redshift variation of the velocity distributions follows the evolution of the X distribution involving a shape parameter alpha(z) decreasing with time.

In this work, we present a computing platform named digital twin brain (DTB) that can simulate spiking neuronal networks of the whole human brain scale and more importantly, a personalized biological brain structure. In comparison to most brain simulations with a homogeneous global structure, we highlight that the sparseness, couplingness and heterogeneity in the sMRI, DTI and PET data of the brain has an essential impact on the efficiency of brain simulation, which is proved from the scaling experiments that the DTB of human brain simulation is communication-intensive and memory-access intensive computing systems rather than computation-intensive. We utilize a number of optimization techniques to balance and integrate the computation loads and communication traffics from the heterogeneous biological structure to the general GPU-based HPC and achieve leading simulation performance for the whole human brain-scaled spiking neuronal networks. On the other hand, the biological structure, equipped with a mesoscopic data assimilation, enables the DTB to investigate brain cognitive function by a reverse-engineering method, which is demonstrated by a digital experiment of visual evaluation on the DTB. Furthermore, we believe that the developing DTB will be a promising powerful platform for a large of research orients including brain-inspiredintelligence, rain disease medicine and brain-machine interface.

On the way to Exascale, programmers face the increasing challenge of having to support multiple hardware architectures from the same code base. At the same time, portability of code and performance are increasingly difficult to achieve as hardware architectures are becoming more and more diverse. Today's heterogeneous systems often include two or more completely distinct and incompatible hardware execution models, such as GPGPU's, SIMD vector units, and general purpose cores which conventionally have to be programmed using separate tool chains representing non-overlapping programming models. The recent revival of interest in the industry and the wider community for the C++ language has spurred a remarkable amount of standardization proposals and technical specifications in the arena of concurrency and parallelism. This recently includes an increasing amount of discussion around the need for a uniform, higher-level abstraction and programming model for parallelism in the C++ standard targeting heterogeneous and distributed computing. Such an abstraction should perfectly blend with existing, already standardized language and library features, but should also be generic enough to support future hardware developments. In this paper, we present the results from developing such a higher-level programming abstraction for parallelism in C++ which aims at enabling code and performance portability over a wide range of architectures and for various types of parallelism. We present and compare performance data obtained from running the well-known STREAM benchmark ported to our higher level C++ abstraction with the corresponding results from running it natively. We show that our abstractions enable performance at least as good as the comparable base-line benchmarks while providing a uniform programming API on all compared target architectures.

Scaling deep learning models has been at the heart of recent revolutions in language modelling and image generation. Practitioners have observed a strong relationship between model size, dataset size, and performance. However, structure-based architectures such as Graph Neural Networks (GNNs) are yet to show the benefits of scale mainly due to the lower efficiency of sparse operations, large data requirements, and lack of clarity about the effectiveness of various architectures. We address this drawback of GNNs by studying their scaling behavior. Specifically, we analyze message-passing networks, graph Transformers, and hybrid architectures on the largest public collection of 2D molecular graphs. For the first time, we observe that GNNs benefit tremendously from the increasing scale of depth, width, number of molecules, number of labels, and the diversity in the pretraining datasets, resulting in a 30.25% improvement when scaling to 1 billion parameters and 28.98% improvement when increasing size of dataset to eightfold. We further demonstrate strong finetuning scaling behavior on 38 tasks, outclassing previous large models. We hope that our work paves the way for an era where foundational GNNs drive pharmaceutical drug discovery.

We report a flexible multi-modal mechanics language model, MeLM, applied to solve various nonlinear forward and inverse problems, that can deal with a set of instructions, numbers and microstructure data. The framework is applied to various examples including bio-inspired hierarchical honeycomb design, carbon nanotube mechanics, and protein unfolding. In spite of the flexible nature of the model-which allows us to easily incorporate diverse materials, scales, and mechanical features-it performs well across disparate forward and inverse tasks. Based on an autoregressive attention-model, MeLM effectively represents a large multi-particle system consisting of hundreds of millions of neurons, where the interaction potentials are discovered through graph-forming self-attention mechanisms that are then used to identify relationships from emergent structures, while taking advantage of synergies discovered in the training data. We show that the model can solve complex degenerate mechanics design problems and determine novel material architectures across a range of hierarchical levels, providing an avenue for materials discovery and analysis. Looking beyond the demonstrations reported in this paper, we discuss other opportunities in applied mechanics and general considerations about the use of large language models in modeling, design, and analysis that can span a broad spectrum of material properties from mechanical, thermal, optical, to electronic.

The recent progress of AI can be largely attributed to large language models (LLMs). However, their escalating memory requirements introduce challenges for machine learning (ML) researchers and engineers. Addressing this requires developers to partition a large model to distribute it across multiple GPUs or TPUs. This necessitates considerable coding and intricate configuration efforts with existing model parallel tools, such as Megatron-LM, DeepSpeed, and Alpa. These tools require users' expertise in machine learning systems (MLSys), creating a bottleneck in LLM development, particularly for developers without MLSys background. In this work, we present Redco, a lightweight and user-friendly tool crafted to automate distributed training and inference for LLMs, as well as to simplify ML pipeline development. The design of Redco emphasizes two key aspects. Firstly, to automate model parallism, our study identifies two straightforward rules to generate tensor parallel strategies for any given LLM. Integrating these rules into Redco facilitates effortless distributed LLM training and inference, eliminating the need of additional coding or complex configurations. We demonstrate the effectiveness by applying Redco on a set of LLM architectures, such as GPT-J, LLaMA, T5, and OPT, up to the size of 66B. Secondly, we propose a mechanism that allows for the customization of diverse ML pipelines through the definition of merely three functions, eliminating redundant and formulaic code like multi-host related processing. This mechanism proves adaptable across a spectrum of ML algorithms, from foundational language modeling to complex algorithms like meta-learning and reinforcement learning. Consequently, Redco implementations exhibit much fewer code lines compared to their official counterparts.

Discovering the underlying relationships among variables from temporal observations has been a longstanding challenge in numerous scientific disciplines, including biology, finance, and climate science. The dynamics of such systems are often best described using continuous-time stochastic processes. Unfortunately, most existing structure learning approaches assume that the underlying process evolves in discrete-time and/or observations occur at regular time intervals. These mismatched assumptions can often lead to incorrect learned structures and models. In this work, we introduce a novel structure learning method, SCOTCH, which combines neural stochastic differential equations (SDE) with variational inference to infer a posterior distribution over possible structures. This continuous-time approach can naturally handle both learning from and predicting observations at arbitrary time points. Theoretically, we establish sufficient conditions for an SDE and SCOTCH to be structurally identifiable, and prove its consistency under infinite data limits. Empirically, we demonstrate that our approach leads to improved structure learning performance on both synthetic and real-world datasets compared to relevant baselines under regular and irregular sampling intervals.

Early diagnosis of mild cognitive impairment (MCI) and subjective cognitive decline (SCD) utilizing multi-modal magnetic resonance imaging (MRI) is a pivotal area of research. While various regional and connectivity features from functional MRI (fMRI) and diffusion tensor imaging (DTI) have been employed to develop diagnosis models, most studies integrate these features without adequately addressing their alignment and interactions. This limits the potential to fully exploit the synergistic contributions of combined features and modalities. To solve this gap, our study introduces a novel Hierarchical Alignments and Hierarchical Interactions (HA-HI) method for MCI and SCD classification, leveraging the combined strengths of fMRI and DTI. HA-HI efficiently learns significant MCI- or SCD- related regional and connectivity features by aligning various feature types and hierarchically maximizing their interactions. Furthermore, to enhance the interpretability of our approach, we have developed the Synergistic Activation Map (SAM) technique, revealing the critical brain regions and connections that are indicative of MCI/SCD. Comprehensive evaluations on the ADNI dataset and our self-collected data demonstrate that HA-HI outperforms other existing methods in diagnosing MCI and SCD, making it a potentially vital and interpretable tool for early detection. The implementation of this method is publicly accessible at https://github.com/ICI-BCI/Dual-MRI-HA-HI.git.

We study the realizability of simplicial complexes with a given pair of integer sequences, representing the node degree distribution and the facet size distribution, respectively. While the s-uniform variant of the problem is NP-complete when s geq 3, we identify two populations of input sequences, most of which can be solved in polynomial time using a recursive algorithm that we contribute. Combining with a sampler for the simplicial configuration model [J.-G. Young et al., Phys. Rev. E 96, 032312 (2017)], we facilitate the efficient sampling of simplicial ensembles from arbitrary degree and size distributions. We find that, contrary to expectations based on dyadic networks, increasing the nodes' degrees reduces the number of loops in simplicial complexes. Our work unveils a fundamental constraint on the degree-size sequences and sheds light on further analysis of higher-order phenomena based on local structures.

Temporal networks have been widely used to model real-world complex systems such as financial systems and e-commerce systems. In a temporal network, the joint neighborhood of a set of nodes often provides crucial structural information useful for predicting whether they may interact at a certain time. However, recent representation learning methods for temporal networks often fail to extract such information or depend on online construction of structural features, which is time-consuming. To address the issue, this work proposes Neighborhood-Aware Temporal network model (NAT). For each node in the network, NAT abandons the commonly-used one-single-vector-based representation while adopting a novel dictionary-type neighborhood representation. Such a dictionary representation records a downsampled set of the neighboring nodes as keys, and allows fast construction of structural features for a joint neighborhood of multiple nodes. We also design a dedicated data structure termed N-cache to support parallel access and update of those dictionary representations on GPUs. NAT gets evaluated over seven real-world large-scale temporal networks. NAT not only outperforms all cutting-edge baselines by averaged 1.2% and 4.2% in transductive and inductive link prediction accuracy, respectively, but also keeps scalable by achieving a speed-up of 4.1-76.7x against the baselines that adopt joint structural features and achieves a speed-up of 1.6-4.0x against the baselines that cannot adopt those features. The link to the code: https: //github.com/Graph-COM/Neighborhood-Aware-Temporal-Network.

Accurate prediction of climate in the subseasonal-to-seasonal scale is crucial for disaster readiness, reduced economic risk, and improved policy-making amidst climate change. Yet, S2S prediction remains challenging due to the chaotic nature of the system. At present, existing benchmarks for weather and climate applications, tend to (1) have shorter forecasting range of up-to 14 days, (2) do not include a wide range of operational baseline forecasts, and (3) lack physics-based constraints for explainability. Thus, we propose ChaosBench, a large-scale, multi-channel, physics-based benchmark for S2S prediction. ChaosBench has over 460K frames of real-world observations and simulations, each with 60 variable-channels and spanning for up-to 45 years. We also propose several physics-based, in addition to vision-based metrics, that enables for a more physically-consistent model. Furthermore, we include a diverse set of physics-based forecasts from 4 national weather agencies as baselines to our data-driven counterpart. We establish two tasks that vary in complexity: full and sparse dynamics prediction. Our benchmark is one of the first to perform large-scale evaluation on existing models including PanguWeather, FourCastNetV2, GraphCast, and ClimaX, and finds methods originally developed for weather-scale applications fails on S2S task. We release our benchmark code and datasets at https://leap-stc.github.io/ChaosBench.

Linear sequence modeling approaches, such as linear attention, provide advantages like linear-time training and constant-memory inference over sequence lengths. However, existing sequence parallelism (SP) methods are either not optimized for the right-product-first feature of linear attention or use a ring-style communication strategy, which results in lower computation parallelism, limits their scalability for longer sequences in distributed systems. In this paper, we introduce LASP-2, a new SP method to enhance both communication and computation parallelism when training linear attention transformer models with very-long input sequences. Compared to previous work LASP, LASP-2 rethinks the minimal communication requirement for SP on linear attention layers, reorganizes the whole communication-computation workflow of LASP. In this way, only one single AllGather collective communication is needed on intermediate memory states, whose sizes are independent of the sequence length, leading to significant improvements of both communication and computation parallelism, as well as their overlap. Additionally, we extend LASP-2 to LASP-2H by applying similar communication redesign to standard attention modules, offering an efficient SP solution for hybrid models that blend linear and standard attention layers. Our evaluation on a Linear-Llama3 model, a variant of Llama3 with linear attention replacing standard attention, demonstrates the effectiveness of LASP-2 and LASP-2H. Specifically, LASP-2 achieves training speed improvements of 15.2% over LASP and 36.6% over Ring Attention, with a sequence length of 2048K across 64 GPUs. The Code is released as a part of: https://github.com/OpenSparseLLMs/Linear-MoE.

Designing architectures for deep neural networks requires expert knowledge and substantial computation time. We propose a technique to accelerate architecture selection by learning an auxiliary HyperNet that generates the weights of a main model conditioned on that model's architecture. By comparing the relative validation performance of networks with HyperNet-generated weights, we can effectively search over a wide range of architectures at the cost of a single training run. To facilitate this search, we develop a flexible mechanism based on memory read-writes that allows us to define a wide range of network connectivity patterns, with ResNet, DenseNet, and FractalNet blocks as special cases. We validate our method (SMASH) on CIFAR-10 and CIFAR-100, STL-10, ModelNet10, and Imagenet32x32, achieving competitive performance with similarly-sized hand-designed networks. Our code is available at https://github.com/ajbrock/SMASH

Creating fast and accurate force fields is a long-standing challenge in computational chemistry and materials science. Recently, several equivariant message passing neural networks (MPNNs) have been shown to outperform models built using other approaches in terms of accuracy. However, most MPNNs suffer from high computational cost and poor scalability. We propose that these limitations arise because MPNNs only pass two-body messages leading to a direct relationship between the number of layers and the expressivity of the network. In this work, we introduce MACE, a new equivariant MPNN model that uses higher body order messages. In particular, we show that using four-body messages reduces the required number of message passing iterations to just two, resulting in a fast and highly parallelizable model, reaching or exceeding state-of-the-art accuracy on the rMD17, 3BPA, and AcAc benchmark tasks. We also demonstrate that using higher order messages leads to an improved steepness of the learning curves.

Acceleration of graph applications on GPUs has found large interest due to the ubiquitous use of graph processing in various domains. The inherent irregularity in graph applications leads to several challenges for parallelization. A key challenge, which we address in this paper, is that of load-imbalance. If the work-assignment to threads uses node-based graph partitioning, it can result in skewed task-distribution, leading to poor load-balance. In contrast, if the work-assignment uses edge-based graph partitioning, the load-balancing is better, but the memory requirement is relatively higher. This makes it unsuitable for large graphs. In this work, we propose three techniques for improved load-balancing of graph applications on GPUs. Each technique brings in unique advantages, and a user may have to employ a specific technique based on the requirement. Using Breadth First Search and Single Source Shortest Paths as our processing kernels, we illustrate the effectiveness of each of the proposed techniques in comparison to the existing node-based and edge-based mechanisms.

Exploiting sparsity underlying neural networks has become one of the most potential methodologies to reduce the memory footprint, I/O cost, and computation workloads during inference. And the degree of sparsity one can exploit has become higher as larger model sizes have been considered along with the trend of pre-training giant models. On the other hand, compared with quantization that has been a widely supported option, acceleration through high-degree sparsity is not supported in most computing platforms. In this work, we introduce the first commercial hardware platform supporting high-degree sparsity acceleration up to 32 times -- S4. Combined with state-of-the-art sparse pruning techniques, we demonstrate several-times practical inference speedup on S4 over mainstream inference platforms such as Nvidia T4. We also show that in practice a sparse model of larger size can achieve both higher accuracy and higher throughput on S4 than a dense model of smaller size.

Pipeline parallelism (PP) is widely used for training large language models (LLMs), yet its scalability is often constrained by high activation memory consumption as the number of in-flight microbatches grows with the degree of PP. In this paper, we focus on addressing this challenge by leveraging the under-explored memory offload strategy in PP. With empirical study, we discover that in the majority of standard configurations, at least half, and potentially all, of the activations can be offloaded with negligible overhead. In the cases where full overload is not possible, we introduce a novel selective offload strategy that decreases peak activation memory in a better-than-linear manner. Furthermore, we integrate memory offload with other techniques to jointly consider overall throughput and memory limitation. Our experiments proves that the per-device activation memory effectively reduces with the total number of stages, making PP a stronger alternative than TP, offering up to a 19\% acceleration with even lower memory consumption. The implementation is open-sourced at https://github.com/sail-sg/zero-bubble-pipeline-parallelism{this url}.

Computing the optimal transport distance between statistical distributions is a fundamental task in machine learning. One remarkable recent advancement is entropic regularization and the Sinkhorn algorithm, which utilizes only matrix scaling and guarantees an approximated solution with near-linear runtime. Despite the success of the Sinkhorn algorithm, its runtime may still be slow due to the potentially large number of iterations needed for convergence. To achieve possibly super-exponential convergence, we present Sinkhorn-Newton-Sparse (SNS), an extension to the Sinkhorn algorithm, by introducing early stopping for the matrix scaling steps and a second stage featuring a Newton-type subroutine. Adopting the variational viewpoint that the Sinkhorn algorithm maximizes a concave Lyapunov potential, we offer the insight that the Hessian matrix of the potential function is approximately sparse. Sparsification of the Hessian results in a fast O(n^2) per-iteration complexity, the same as the Sinkhorn algorithm. In terms of total iteration count, we observe that the SNS algorithm converges orders of magnitude faster across a wide range of practical cases, including optimal transportation between empirical distributions and calculating the Wasserstein W_1, W_2 distance of discretized densities. The empirical performance is corroborated by a rigorous bound on the approximate sparsity of the Hessian matrix.

The colossal parameters and computational overhead of Large Language Models (LLMs) challenge their real-world applications. Network pruning, which targets unstructured or structured sparsity by removing redundant parameters, has recently been explored for LLM acceleration. Existing LLM pruning works focus on unstructured pruning, which typically requires special hardware support for a practical speed-up. In contrast, structured pruning can reduce latency on general devices. However, it remains a challenge to perform structured pruning efficiently and maintain performance, especially at high sparsity ratios. To this end, we introduce an efficient structured pruning framework named CFSP, which leverages both Coarse (interblock) and Fine-grained (intrablock) activation information as an importance criterion to guide pruning. The pruning is highly efficient, as it only requires one forward pass to compute feature activations. Specifically, we first allocate the sparsity budget across blocks based on their importance and then retain important weights within each block. In addition, we introduce a recovery fine-tuning strategy that adaptively allocates training overhead based on coarse-grained importance to further improve performance. Experimental results demonstrate that CFSP outperforms existing methods on diverse models across various sparsity budgets. Our code will be available at https://github.com/wyxscir/CFSP.

The fundamental success of large language models hinges upon the efficacious implementation of large-scale distributed training techniques. Nevertheless, building a vast, high-performance cluster featuring high-speed communication interconnectivity is prohibitively costly, and accessible only to prominent entities. In this work, we aim to lower this barrier and democratize large-scale training with limited bandwidth clusters. We propose a new approach called CO2 that introduces local-updating and asynchronous communication to the distributed data-parallel training, thereby facilitating the full overlap of COmunication with COmputation. CO2 is able to attain a high scalability even on extensive multi-node clusters constrained by very limited communication bandwidth. We further propose the staleness gap penalty and outer momentum clipping techniques together with CO2 to bolster its convergence and training stability. Besides, CO2 exhibits seamless integration with well-established ZeRO-series optimizers which mitigate memory consumption of model states with large model training. We also provide a mathematical proof of convergence, accompanied by the establishment of a stringent upper bound. Furthermore, we validate our findings through an extensive set of practical experiments encompassing a wide range of tasks in the fields of computer vision and natural language processing. These experiments serve to demonstrate the capabilities of CO2 in terms of convergence, generalization, and scalability when deployed across configurations comprising up to 128 A100 GPUs. The outcomes emphasize the outstanding capacity of CO2 to hugely improve scalability, no matter on clusters with 800Gbps RDMA or 80Gbps TCP/IP inter-node connections.

Over the last three decades, innovations in the memory subsystem were primarily targeted at overcoming the data movement bottleneck. In this paper, we focus on a specific market trend in memory technology: 3D-stacked memory and caches. We investigate the impact of extending the on-chip memory capabilities in future HPC-focused processors, particularly by 3D-stacked SRAM. First, we propose a method oblivious to the memory subsystem to gauge the upper-bound in performance improvements when data movement costs are eliminated. Then, using the gem5 simulator, we model two variants of LARC, a processor fabricated in 1.5 nm and enriched with high-capacity 3D-stacked cache. With a volume of experiments involving a board set of proxy-applications and benchmarks, we aim to reveal where HPC CPU performance could be circa 2028, and conclude an average boost of 9.77x for cache-sensitive HPC applications, on a per-chip basis. Additionally, we exhaustively document our methodological exploration to motivate HPC centers to drive their own technological agenda through enhanced co-design.

Scaling multi-dimensional transformers to long sequences is indispensable across various domains. However, the challenges of large memory requirements and slow speeds of such sequences necessitate sequence parallelism. All existing approaches fall under the category of embedded sequence parallelism, which are limited to shard along a single sequence dimension, thereby introducing significant communication overhead. However, the nature of multi-dimensional transformers involves independent calculations across multiple sequence dimensions. To this end, we propose Dynamic Sequence Parallelism (DSP) as a novel abstraction of sequence parallelism. DSP dynamically switches the parallel dimension among all sequences according to the computation stage with efficient resharding strategy. DSP offers significant reductions in communication costs, adaptability across modules, and ease of implementation with minimal constraints. Experimental evaluations demonstrate DSP's superiority over state-of-the-art embedded sequence parallelism methods by remarkable throughput improvements ranging from 32.2% to 10x, with less than 25% communication volume.

The formidable model size and demanding computational requirements of Segment Anything Model (SAM) have rendered it cumbersome for deployment on resource-constrained devices. Existing approaches for SAM compression typically involve training a new network from scratch, posing a challenging trade-off between compression costs and model performance. To address this issue, this paper introduces SlimSAM, a novel SAM compression method that achieves superior performance with remarkably low training costs. This is achieved by the efficient reuse of pre-trained SAMs through a unified pruning-distillation framework. To enhance knowledge inheritance from the original SAM, we employ an innovative alternate slimming strategy that partitions the compression process into a progressive procedure. Diverging from prior pruning techniques, we meticulously prune and distill decoupled model structures in an alternating fashion. Furthermore, a novel label-free pruning criterion is also proposed to align the pruning objective with the optimization target, thereby boosting the post-distillation after pruning. SlimSAM yields significant performance improvements while demanding over 10 times less training costs than any other existing methods. Even when compared to the original SAM-H, SlimSAM achieves approaching performance while reducing parameter counts to merely 0.9% (5.7M), MACs to 0.8% (21G), and requiring only 0.1% (10k) of the SAM training data. Code is available at url{http://github.com/czg1225/SlimSAM}.

This paper challenges the well-established paradigm for building any-to-any networks for training Large Language Models (LLMs). We show that LLMs exhibit a unique communication pattern where only small groups of GPUs require high-bandwidth any-to-any communication within them, to achieve near-optimal training performance. Across these groups of GPUs, the communication is insignificant, sparse, and homogeneous. We propose a new network architecture that closely resembles the communication requirement of LLMs. Our architecture partitions the cluster into sets of GPUs interconnected with non-blocking any-to-any high-bandwidth interconnects that we call HB domains. Across the HB domains, the network only connects GPUs with communication demands. We call this network a "rail-only" connection, and show that our proposed architecture reduces the network cost by up to 75% compared to the state-of-the-art any-to-any Clos networks without compromising the performance of LLM training.

The K-core of a graph is the unique maximum subgraph within which each vertex connects to at least K other vertices. The K-core optimal attack problem asks to construct a minimum-sized set of vertices whose removal results in the complete collapse of the K-core. In this paper, we construct a hierarchical cycle-tree packing model which converts a long-range correlated K-core pruning process into static patterns and analyze this model through the replica-symmetric (RS) cavity method of statistical physics. The cycle-tree guided attack (CTGA) message-passing algorithm exhibits superior performance on random regular and Erdos-Renyi graphs. It provides new upper bounds on the minimal cardinality of the K-core attack set. The model of this work may be extended to construct optimal initial conditions for other irreversible dynamical processes.

We present a distributed data structure, which we call the rainbow skip graph. To our knowledge, this is the first peer-to-peer data structure that simultaneously achieves high fault tolerance, constant-sized nodes, and fast update and query times for ordered data. It is a non-trivial adaptation of the SkipNet/skip-graph structures of Harvey et al. and Aspnes and Shah, so as to provide fault-tolerance as these structures do, but to do so using constant-sized nodes, as in the family tree structure of Zatloukal and Harvey. It supports successor queries on a set of n items using O(log n) messages with high probability, an improvement over the expected O(log n) messages of the family tree.

Rendering and inverse-rendering algorithms that drive conventional computer graphics have recently been superseded by neural representations (NR). NRs have recently been used to learn the geometric and the material properties of the scenes and use the information to synthesize photorealistic imagery, thereby promising a replacement for traditional rendering algorithms with scalable quality and predictable performance. In this work we ask the question: Does neural graphics (NG) need hardware support? We studied representative NG applications showing that, if we want to render 4k res. at 60FPS there is a gap of 1.5X-55X in the desired performance on current GPUs. For AR/VR applications, there is an even larger gap of 2-4 OOM between the desired performance and the required system power. We identify that the input encoding and the MLP kernels are the performance bottlenecks, consuming 72%,60% and 59% of application time for multi res. hashgrid, multi res. densegrid and low res. densegrid encodings, respectively. We propose a NG processing cluster, a scalable and flexible hardware architecture that directly accelerates the input encoding and MLP kernels through dedicated engines and supports a wide range of NG applications. We also accelerate the rest of the kernels by fusing them together in Vulkan, which leads to 9.94X kernel-level performance improvement compared to un-fused implementation of the pre-processing and the post-processing kernels. Our results show that, NGPC gives up to 58X end-to-end application-level performance improvement, for multi res. hashgrid encoding on average across the four NG applications, the performance benefits are 12X,20X,33X and 39X for the scaling factor of 8,16,32 and 64, respectively. Our results show that with multi res. hashgrid encoding, NGPC enables the rendering of 4k res. at 30FPS for NeRF and 8k res. at 120FPS for all our other NG applications.

Recently, the Muon optimizer based on matrix orthogonalization has demonstrated strong results in training small-scale language models, but the scalability to larger models has not been proven. We identify two crucial techniques for scaling up Muon: (1) adding weight decay and (2) carefully adjusting the per-parameter update scale. These techniques allow Muon to work out-of-the-box on large-scale training without the need of hyper-parameter tuning. Scaling law experiments indicate that Muon achieves sim!2times computational efficiency compared to AdamW with compute optimal training. Based on these improvements, we introduce Moonlight, a 3B/16B-parameter Mixture-of-Expert (MoE) model trained with 5.7T tokens using Muon. Our model improves the current Pareto frontier, achieving better performance with much fewer training FLOPs compared to prior models. We open-source our distributed Muon implementation that is memory optimal and communication efficient. We also release the pretrained, instruction-tuned, and intermediate checkpoints to support future research.

Structural and Positional Encodings can significantly improve the performance of Graph Neural Networks in downstream tasks. Recent literature has begun to systematically investigate differences in the structural properties that these approaches encode, as well as performance trade-offs between them. However, the question of which structural properties yield the most effective encoding remains open. In this paper, we investigate this question from a geometric perspective. We propose a novel structural encoding based on discrete Ricci curvature (Local Curvature Profiles, short LCP) and show that it significantly outperforms existing encoding approaches. We further show that combining local structural encodings, such as LCP, with global positional encodings improves downstream performance, suggesting that they capture complementary geometric information. Finally, we compare different encoding types with (curvature-based) rewiring techniques. Rewiring has recently received a surge of interest due to its ability to improve the performance of Graph Neural Networks by mitigating over-smoothing and over-squashing effects. Our results suggest that utilizing curvature information for structural encodings delivers significantly larger performance increases than rewiring.

Extensive system scales (i.e. thousands of GPU/TPUs) and prolonged training periods (i.e. months of pretraining) significantly escalate the probability of failures when training large language models (LLMs). Thus, efficient and reliable fault-tolerance methods are in urgent need. Checkpointing is the primary fault-tolerance method to periodically save parameter snapshots from GPU memory to disks via CPU memory. In this paper, we identify the frequency of existing checkpoint-based fault-tolerance being significantly limited by the storage I/O overheads, which results in hefty re-training costs on restarting from the nearest checkpoint. In response to this gap, we introduce an in-memory fault-tolerance framework for large-scale LLM pretraining. The framework boosts the efficiency and reliability of fault tolerance from three aspects: (1) Reduced Data Transfer and I/O: By asynchronously caching parameters, i.e., sharded model parameters, optimizer states, and RNG states, to CPU volatile memory, Our framework significantly reduces communication costs and bypasses checkpoint I/O. (2) Enhanced System Reliability: Our framework enhances parameter protection with a two-layer hierarchy: snapshot management processes (SMPs) safeguard against software failures, together with Erasure Coding (EC) protecting against node failures. This double-layered protection greatly improves the survival probability of the parameters compared to existing checkpointing methods. (3) Improved Snapshotting Frequency: Our framework achieves more frequent snapshotting compared with asynchronous checkpointing optimizations under the same saving time budget, which improves the fault tolerance efficiency. Empirical results demonstrate that Our framework minimizes the overhead of fault tolerance of LLM pretraining by effectively leveraging redundant CPU resources.

Neural architectures that learn potential energy surfaces from molecular data have undergone fast improvement in recent years. A key driver of this success is the Message Passing Neural Network (MPNN) paradigm. Its favorable scaling with system size partly relies upon a spatial distance limit on messages. While this focus on locality is a useful inductive bias, it also impedes the learning of long-range interactions such as electrostatics and van der Waals forces. To address this drawback, we propose Ewald message passing: a nonlocal Fourier space scheme which limits interactions via a cutoff on frequency instead of distance, and is theoretically well-founded in the Ewald summation method. It can serve as an augmentation on top of existing MPNN architectures as it is computationally inexpensive and agnostic to architectural details. We test the approach with four baseline models and two datasets containing diverse periodic (OC20) and aperiodic structures (OE62). We observe robust improvements in energy mean absolute errors across all models and datasets, averaging 10% on OC20 and 16% on OE62. Our analysis shows an outsize impact of these improvements on structures with high long-range contributions to the ground truth energy.

In many real-world applications, graph-structured data used for training and testing have differences in distribution, such as in high energy physics (HEP) where simulation data used for training may not match real experiments. Graph domain adaptation (GDA) is a method used to address these differences. However, current GDA primarily works by aligning the distributions of node representations output by a single graph neural network encoder shared across the training and testing domains, which may often yield sub-optimal solutions. This work examines different impacts of distribution shifts caused by either graph structure or node attributes and identifies a new type of shift, named conditional structure shift (CSS), which current GDA approaches are provably sub-optimal to deal with. A novel approach, called structural reweighting (StruRW), is proposed to address this issue and is tested on synthetic graphs, four benchmark datasets, and a new application in HEP. StruRW has shown significant performance improvement over the baselines in the settings with large graph structure shifts, and reasonable performance improvement when node attribute shift dominates.

Diffusion Magnetic Resonance Imaging (dMRI) plays a crucial role in the noninvasive investigation of tissue microstructural properties and structural connectivity in the in vivo human brain. However, to effectively capture the intricate characteristics of water diffusion at various directions and scales, it is important to employ comprehensive q-space sampling. Unfortunately, this requirement leads to long scan times, limiting the clinical applicability of dMRI. To address this challenge, we propose SSOR, a Simultaneous q-Space sampling Optimization and Reconstruction framework. We jointly optimize a subset of q-space samples using a continuous representation of spherical harmonic functions and a reconstruction network. Additionally, we integrate the unique properties of diffusion magnetic resonance imaging (dMRI) in both the q-space and image domains by applying l1-norm and total-variation regularization. The experiments conducted on HCP data demonstrate that SSOR has promising strengths both quantitatively and qualitatively and exhibits robustness to noise.

This paper introduces a structured memory which can be easily integrated into a neural network. The memory is very large by design and significantly increases the capacity of the architecture, by up to a billion parameters with a negligible computational overhead. Its design and access pattern is based on product keys, which enable fast and exact nearest neighbor search. The ability to increase the number of parameters while keeping the same computational budget lets the overall system strike a better trade-off between prediction accuracy and computation efficiency both at training and test time. This memory layer allows us to tackle very large scale language modeling tasks. In our experiments we consider a dataset with up to 30 billion words, and we plug our memory layer in a state-of-the-art transformer-based architecture. In particular, we found that a memory augmented model with only 12 layers outperforms a baseline transformer model with 24 layers, while being twice faster at inference time. We release our code for reproducibility purposes.

The most popular framework for distributed training of machine learning models is the (synchronous) parameter server (PS). This paradigm consists of n workers, which iteratively compute updates of the model parameters, and a stateful PS, which waits and aggregates all updates to generate a new estimate of model parameters and sends it back to the workers for a new iteration. Transient computation slowdowns or transmission delays can intolerably lengthen the time of each iteration. An efficient way to mitigate this problem is to let the PS wait only for the fastest n-b updates, before generating the new parameters. The slowest b workers are called backup workers. The optimal number b of backup workers depends on the cluster configuration and workload, but also (as we show in this paper) on the hyper-parameters of the learning algorithm and the current stage of the training. We propose DBW, an algorithm that dynamically decides the number of backup workers during the training process to maximize the convergence speed at each iteration. Our experiments show that DBW 1) removes the necessity to tune b by preliminary time-consuming experiments, and 2) makes the training up to a factor 3 faster than the optimal static configuration.

Iterative methods are ubiquitous in large-scale scientific computing applications, and a number of approaches based on meta-learning have been recently proposed to accelerate them. However, a systematic study of these approaches and how they differ from meta-learning is lacking. In this paper, we propose a framework to analyze such learning-based acceleration approaches, where one can immediately identify a departure from classical meta-learning. We show that this departure may lead to arbitrary deterioration of model performance. Based on our analysis, we introduce a novel training method for learning-based acceleration of iterative methods. Furthermore, we theoretically prove that the proposed method improves upon the existing methods, and demonstrate its significant advantage and versatility through various numerical applications.

Preconditioned gradient methods are among the most general and powerful tools in optimization. However, preconditioning requires storing and manipulating prohibitively large matrices. We describe and analyze a new structure-aware preconditioning algorithm, called Shampoo, for stochastic optimization over tensor spaces. Shampoo maintains a set of preconditioning matrices, each of which operates on a single dimension, contracting over the remaining dimensions. We establish convergence guarantees in the stochastic convex setting, the proof of which builds upon matrix trace inequalities. Our experiments with state-of-the-art deep learning models show that Shampoo is capable of converging considerably faster than commonly used optimizers. Although it involves a more complex update rule, Shampoo's runtime per step is comparable to that of simple gradient methods such as SGD, AdaGrad, and Adam.

Learning complex dynamics driven by partial differential equations directly from data holds great promise for fast and accurate simulations of complex physical systems. In most cases, this problem can be formulated as an operator learning task, where one aims to learn the operator representing the physics of interest, which entails discretization of the continuous system. However, preserving key continuous properties at the discrete level, such as boundary conditions, and addressing physical systems with complex geometries is challenging for most existing approaches. We introduce a family of operator learning architectures, structure-preserving operator networks (SPONs), that allows to preserve key mathematical and physical properties of the continuous system by leveraging finite element (FE) discretizations of the input-output spaces. SPONs are encode-process-decode architectures that are end-to-end differentiable, where the encoder and decoder follows from the discretizations of the input-output spaces. SPONs can operate on complex geometries, enforce certain boundary conditions exactly, and offer theoretical guarantees. Our framework provides a flexible way of devising structure-preserving architectures tailored to specific applications, and offers an explicit trade-off between performance and efficiency, all thanks to the FE discretization of the input-output spaces. Additionally, we introduce a multigrid-inspired SPON architecture that yields improved performance at higher efficiency. Finally, we release a software to automate the design and training of SPON architectures.

In biological research, fluorescence staining is a key technique to reveal the locations and morphology of subcellular structures. However, it is slow, expensive, and harmful to cells. In this paper, we model it as a deep learning task termed subcellular structure prediction (SSP), aiming to predict the 3D fluorescent images of multiple subcellular structures from a 3D transmitted-light image. Unfortunately, due to the limitations of current biotechnology, each image is partially labeled in SSP. Besides, naturally, subcellular structures vary considerably in size, which causes the multi-scale issue of SSP. To overcome these challenges, we propose Re-parameterizing Mixture-of-Diverse-Experts (RepMode), a network that dynamically organizes its parameters with task-aware priors to handle specified single-label prediction tasks. In RepMode, the Mixture-of-Diverse-Experts (MoDE) block is designed to learn the generalized parameters for all tasks, and gating re-parameterization (GatRep) is performed to generate the specialized parameters for each task, by which RepMode can maintain a compact practical topology exactly like a plain network, and meanwhile achieves a powerful theoretical topology. Comprehensive experiments show that RepMode can achieve state-of-the-art overall performance in SSP.

Training large neural networks typically requires sharing gradients between accelerators through specialized high-speed interconnects. Drawing from the signal processing principles of frequency decomposition and energy compaction, we demonstrate that synchronizing full optimizer states and model parameters during training is unnecessary. By decoupling momentum updates and allowing controlled divergence in optimizer states across accelerators, we achieve improved convergence compared to state-of-the-art optimizers. We introduce {De}coupled {Mo}mentum (DeMo), a fused optimizer and data parallel algorithm that reduces inter-accelerator communication requirements by several orders of magnitude. This enables training of large neural networks even with limited network bandwidth and heterogeneous hardware. Our method is topology-agnostic and architecture-independent and supports scalable clock-synchronous distributed training with negligible compute and memory overhead. Empirical results show that models trained with DeMo match or exceed the performance of equivalent models trained with AdamW, while eliminating the need for high-speed interconnects when pre-training large scale foundation models. An open source reference PyTorch implementation is published on GitHub at https://github.com/bloc97/DeMo

Large language models (LLMs) with long sequences begin to power more and more fundamentally new applications we use every day. Existing methods for long-sequence LLM training are neither efficient nor compatible with commonly-used training algorithms such as FlashAttention. We design Buff to address these issues. Buff decouples all of the sharding dimensions into a new hierarchical space, and systematically analyzes the memory and communication cost of LLM training. Then, it generates an effective hybrid parallelism strategy. We design a new selective overlap mechanism to mitigate the communication overhead introduced by the hybrid parallelism. We also implement memory management techniques to reduce GPU memory fragmentation. Evaluation results show that Buff generates parallelization strategies that match or outperform existing methods in model FLOPs utilization.

Vector search has emerged as the foundation for large-scale information retrieval and machine learning systems, with search engines like Google and Bing processing tens of thousands of queries per second on petabyte-scale document datasets by evaluating vector similarities between encoded query texts and web documents. As performance demands for vector search systems surge, accelerated hardware offers a promising solution in the post-Moore's Law era. We introduce FANNS, an end-to-end and scalable vector search framework on FPGAs. Given a user-provided recall requirement on a dataset and a hardware resource budget, FANNS automatically co-designs hardware and algorithm, subsequently generating the corresponding accelerator. The framework also supports scale-out by incorporating a hardware TCP/IP stack in the accelerator. FANNS attains up to 23.0times and 37.2times speedup compared to FPGA and CPU baselines, respectively, and demonstrates superior scalability to GPUs, achieving 5.5times and 7.6times speedup in median and 95th percentile (P95) latency within an eight-accelerator configuration. The remarkable performance of FANNS lays a robust groundwork for future FPGA integration in data centers and AI supercomputers.

Recently, language models (LMs), especially large language models (LLMs), have revolutionized the field of deep learning. Both encoder-decoder models and prompt-based techniques have shown immense potential for natural language processing and code-based tasks. Over the past several years, many research labs and institutions have invested heavily in high-performance computing, approaching or breaching exascale performance levels. In this paper, we posit that adapting and utilizing such language model-based techniques for tasks in high-performance computing (HPC) would be very beneficial. This study presents our reasoning behind the aforementioned position and highlights how existing ideas can be improved and adapted for HPC tasks.

The challenge of mapping AI architectures to GPU hardware is creating a critical bottleneck in AI progress. Despite substantial efforts, hand-written custom kernels fail to meet their theoretical performance thresholds, even on well-established operations like linear attention. The diverse hardware capabilities of GPUs might suggest that we need a wide variety of techniques to achieve high performance. However, our work explores whether a small number of key abstractions can drastically simplify the process. We present ThunderKittens (TK), a framework for writing performant AI kernels while remaining easy to use and maintain. Our abstractions map to the three levels of the GPU hierarchy: (1) at the warp-level, we provide 16x16 matrix tiles as basic data structures and PyTorch-like parallel compute operations over tiles, (2) at the thread-block level, we provide a template for overlapping asynchronous operations across parallel warps, and (3) at the grid-level, we provide support to help hide the block launch and tear-down, and memory costs. We show the value of TK by providing kernels that match or outperform prior kernels for a range of AI operations. We match CuBLAS and FlashAttention-3 on GEMM and attention inference performance and outperform the strongest baselines by 10-40% on attention backwards, 8times on state space models, and 14times on linear attention.

Graph neural networks are popular architectures for graph machine learning, based on iterative computation of node representations of an input graph through a series of invariant transformations. A large class of graph neural networks follow a standard message-passing paradigm: at every layer, each node state is updated based on an aggregate of messages from its neighborhood. In this work, we propose a novel framework for training graph neural networks, where every node is viewed as a player that can choose to either 'listen', 'broadcast', 'listen and broadcast', or to 'isolate'. The standard message propagation scheme can then be viewed as a special case of this framework where every node 'listens and broadcasts' to all neighbors. Our approach offers a more flexible and dynamic message-passing paradigm, where each node can determine its own strategy based on their state, effectively exploring the graph topology while learning. We provide a theoretical analysis of the new message-passing scheme which is further supported by an extensive empirical analysis on a synthetic dataset and on real-world datasets.

Large models represent a groundbreaking advancement in multiple application fields, enabling remarkable achievements across various tasks. However, their unprecedented scale comes with significant computational costs. These models, often consisting of billions of parameters, require vast amounts of computational resources for execution. Especially, the expansive scale and computational demands pose considerable challenges when customizing them for particular downstream tasks, particularly over the hardware platforms constrained by computational capabilities. Parameter Efficient Fine-Tuning (PEFT) provides a practical solution by efficiently adapt the large models over the various downstream tasks. In particular, PEFT refers to the process of adjusting the parameters of a pre-trained large models to adapt it to a specific task while minimizing the number of additional parameters introduced or computational resources required. This approach is particularly important when dealing with large language models with high parameter counts, as fine-tuning these models from scratch can be computationally expensive and resource-intensive, posing considerable challenges in the supporting system platform design. In this survey, we present comprehensive studies of various PEFT algorithms, examining their performance and computational overhead. Moreover, we provide an overview of applications developed using different PEFT algorithms and discuss common techniques employed to mitigate computation costs for PEFT. In addition to the algorithmic perspective, we overview various real-world system designs to investigate the implementation costs associated with different PEFT algorithms. This survey serves as an indispensable resource for researchers aiming to understand both the PEFT algorithm and its system implementation, offering detailed insights into recent advancements and practical applications.

Message passing graph neural networks (GNNs) would appear to be powerful tools to learn distributed algorithms via gradient descent, but generate catastrophically incorrect predictions when nodes update asynchronously during inference. This failure under asynchrony effectively excludes these architectures from many potential applications, such as learning local communication policies between resource-constrained agents in, e.g., robotic swarms or sensor networks. In this work we explore why this failure occurs in common GNN architectures, and identify "implicitly-defined" GNNs as a class of architectures which is provably robust to partially asynchronous "hogwild" inference, adapting convergence guarantees from work in asynchronous and distributed optimization, e.g., Bertsekas (1982); Niu et al. (2011). We then propose a novel implicitly-defined GNN architecture, which we call an energy GNN. We show that this architecture outperforms other GNNs from this class on a variety of synthetic tasks inspired by multi-agent systems, and achieves competitive performance on real-world datasets.

The rapid scaling of large language models necessitates more lightweight finetuning methods to reduce the explosive GPU memory overhead when numerous customized models are served simultaneously. Targeting more parameter-efficient low-rank adaptation (LoRA), parameter sharing presents a promising solution. Empirically, our research into high-level sharing principles highlights the indispensable role of differentiation in reversing the detrimental effects of pure sharing. Guided by this finding, we propose Mixture of Shards (MoS), incorporating both inter-layer and intra-layer sharing schemes, and integrating four nearly cost-free differentiation strategies, namely subset selection, pair dissociation, vector sharding, and shard privatization. Briefly, it selects a designated number of shards from global pools with a Mixture-of-Experts (MoE)-like routing mechanism before sequentially concatenating them to low-rank matrices. Hence, it retains all the advantages of LoRA while offering enhanced parameter efficiency, and effectively circumvents the drawbacks of peer parameter-sharing methods. Our empirical experiments demonstrate approximately 8x parameter savings in a standard LoRA setting. The ablation study confirms the significance of each component. Our insights into parameter sharing and MoS method may illuminate future developments of more parameter-efficient finetuning methods.

In bipartite networks, community structures are restricted to being disassortative, in that nodes of one type are grouped according to common patterns of connection with nodes of the other type. This makes the stochastic block model (SBM), a highly flexible generative model for networks with block structure, an intuitive choice for bipartite community detection. However, typical formulations of the SBM do not make use of the special structure of bipartite networks. Here we introduce a Bayesian nonparametric formulation of the SBM and a corresponding algorithm to efficiently find communities in bipartite networks which parsimoniously chooses the number of communities. The biSBM improves community detection results over general SBMs when data are noisy, improves the model resolution limit by a factor of 2, and expands our understanding of the complicated optimization landscape associated with community detection tasks. A direct comparison of certain terms of the prior distributions in the biSBM and a related high-resolution hierarchical SBM also reveals a counterintuitive regime of community detection problems, populated by smaller and sparser networks, where nonhierarchical models outperform their more flexible counterpart.

There are few known exponential speedups for quantum algorithms and these tend to fall into even fewer families. One speedup that has mostly resisted generalization is the use of quantum walks to traverse the welded-tree graph, due to Childs, Cleve, Deotto, Farhi, Gutmann, and Spielman. We show how to generalize this to a large class of hierarchical graphs in which the vertices are grouped into "supervertices" which are arranged according to a d-dimensional lattice. Supervertices can have different sizes, and edges between supervertices correspond to random connections between their constituent vertices. The hitting times of quantum walks on these graphs are related to the localization properties of zero modes in certain disordered tight binding Hamiltonians. The speedups range from superpolynomial to exponential, depending on the underlying dimension and the random graph model. We also provide concrete realizations of these hierarchical graphs, and introduce a general method for constructing graphs with efficient quantum traversal times using graph sparsification.

Sequential models, such as Recurrent Neural Networks and Neural Ordinary Differential Equations, have long suffered from slow training due to their inherent sequential nature. For many years this bottleneck has persisted, as many thought sequential models could not be parallelized. We challenge this long-held belief with our parallel algorithm that accelerates GPU evaluation of sequential models by up to 3 orders of magnitude faster without compromising output accuracy. The algorithm does not need any special structure in the sequential models' architecture, making it applicable to a wide range of architectures. Using our method, training sequential models can be more than 10 times faster than the common sequential method without any meaningful difference in the training results. Leveraging this accelerated training, we discovered the efficacy of the Gated Recurrent Unit in a long time series classification problem with 17k time samples. By overcoming the training bottleneck, our work serves as the first step to unlock the potential of non-linear sequential models for long sequence problems.

Score-based Generative Models (SGMs) have achieved state-of-the-art synthesis results on diverse tasks. However, the current design space of the forward diffusion process is largely unexplored and often relies on physical intuition or simplifying assumptions. Leveraging results from the design of scalable Bayesian posterior samplers, we present a complete recipe for constructing forward processes in SGMs, all of which are guaranteed to converge to the target distribution of interest. We show that several existing SGMs can be cast as specific instantiations of this parameterization. Furthermore, building on this recipe, we construct a novel SGM: Phase Space Langevin Diffusion (PSLD), which performs score-based modeling in a space augmented with auxiliary variables akin to a physical phase space. We show that PSLD outperforms competing baselines in terms of sample quality and the speed-vs-quality tradeoff across different samplers on various standard image synthesis benchmarks. Moreover, we show that PSLD achieves sample quality comparable to state-of-the-art SGMs (FID: 2.10 on unconditional CIFAR-10 generation), providing an attractive alternative as an SGM backbone for further development. We will publish our code and model checkpoints for reproducibility at https://github.com/mandt-lab/PSLD.

The in-memory algorithms for approximate nearest neighbor search (ANNS) have achieved great success for fast high-recall search, but are extremely expensive when handling very large scale database. Thus, there is an increasing request for the hybrid ANNS solutions with small memory and inexpensive solid-state drive (SSD). In this paper, we present a simple but efficient memory-disk hybrid indexing and search system, named SPANN, that follows the inverted index methodology. It stores the centroid points of the posting lists in the memory and the large posting lists in the disk. We guarantee both disk-access efficiency (low latency) and high recall by effectively reducing the disk-access number and retrieving high-quality posting lists. In the index-building stage, we adopt a hierarchical balanced clustering algorithm to balance the length of posting lists and augment the posting list by adding the points in the closure of the corresponding clusters. In the search stage, we use a query-aware scheme to dynamically prune the access of unnecessary posting lists. Experiment results demonstrate that SPANN is 2times faster than the state-of-the-art ANNS solution DiskANN to reach the same recall quality 90% with same memory cost in three billion-scale datasets. It can reach 90% recall@1 and recall@10 in just around one millisecond with only 32GB memory cost. Code is available at: {\footnotesizeblue{https://github.com/microsoft/SPTAG}}.

Recently, various distributed strategies for large language model training have been proposed. However, these methods provided limited solutions for the trade-off between memory consumption and communication cost. In this paper, we rethink the impact of memory consumption and communication costs on the training speed of large language models, and propose a memory-communication balanced strategy set Partial Redundancy Optimizer (PaRO). PaRO provides comprehensive options which reduces the amount and frequency of inter-group communication with minor memory redundancy by fine-grained sharding strategy, thereby improving the training efficiency in various training scenarios. Additionally, we propose a Hierarchical Overlapping Ring (HO-Ring) communication topology to enhance communication efficiency between nodes or across switches in large language model training. Our experiments demonstrate that PaRO significantly improves training throughput by 1.19x-2.50x compared to the SOTA method and achieves a near-linear scalability. The HO-Ring algorithm improves communication efficiency by 36.5% compared to the traditional Ring algorithm.

Lattices are architected metamaterials whose properties strongly depend on their geometrical design. The analogy between lattices and graphs enables the use of graph neural networks (GNNs) as a faster surrogate model compared to traditional methods such as finite element modelling. In this work, we generate a big dataset of structure-property relationships for strut-based lattices. The dataset is made available to the community which can fuel the development of methods anchored in physical principles for the fitting of fourth-order tensors. In addition, we present a higher-order GNN model trained on this dataset. The key features of the model are (i) SE(3) equivariance, and (ii) consistency with the thermodynamic law of conservation of energy. We compare the model to non-equivariant models based on a number of error metrics and demonstrate its benefits in terms of predictive performance and reduced training requirements. Finally, we demonstrate an example application of the model to an architected material design task. The methods which we developed are applicable to fourth-order tensors beyond elasticity such as piezo-optical tensor etc.

The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such abilities. However, another central facet of cognition, single-trial formation of permanent memories of experiences, i.e., episodic memory (EM), has had relatively little focus. Only recently has EM-like functionality been added to Deep Learning (DL) models, e.g., Neural Turing Machine, Memory Networks. However, in these cases: a) EM is implemented as a separate module, which entails substantial data movement (and so, time and power) between the DL net itself and EM; and b) individual items are stored localistically within the EM, precluding realizing the exponential representational efficiency of distributed over localist coding. We describe Sparsey, an unsupervised, hierarchical, spatial/spatiotemporal associative memory model differing fundamentally from mainstream ML models, most crucially, in its use of sparse distributed representations (SDRs), or, cell assemblies, which admits an extremely efficient, single-trial learning algorithm that maps input similarity into code space similarity (measured as intersection). SDRs of individual inputs are stored in superposition and because similarity is preserved, the patterns of intersections over the assigned codes reflect the similarity, i.e., statistical, structure, of all orders, not simply pairwise, over the inputs. Thus, SM, i.e., a generative model, is built as a computationally free side effect of the act of storing episodic memory traces of individual inputs, either spatial patterns or sequences. We report initial results on MNIST and on the Weizmann video event recognition benchmarks. While we have not yet attained SOTA class accuracy, learning takes only minutes on a single CPU.

The ability to computationally generate novel yet physically foldable protein structures could lead to new biological discoveries and new treatments targeting yet incurable diseases. Despite recent advances in protein structure prediction, directly generating diverse, novel protein structures from neural networks remains difficult. In this work, we present a new diffusion-based generative model that designs protein backbone structures via a procedure that mirrors the native folding process. We describe protein backbone structure as a series of consecutive angles capturing the relative orientation of the constituent amino acid residues, and generate new structures by denoising from a random, unfolded state towards a stable folded structure. Not only does this mirror how proteins biologically twist into energetically favorable conformations, the inherent shift and rotational invariance of this representation crucially alleviates the need for complex equivariant networks. We train a denoising diffusion probabilistic model with a simple transformer backbone and demonstrate that our resulting model unconditionally generates highly realistic protein structures with complexity and structural patterns akin to those of naturally-occurring proteins. As a useful resource, we release the first open-source codebase and trained models for protein structure diffusion.

The "pretrain-then-finetune" paradigm is commonly adopted in the deployment of large language models. Low-Rank Adaptation (LoRA), a parameter-efficient fine-tuning method, is often employed to adapt a base model to a multitude of tasks, resulting in a substantial collection of LoRA adapters derived from one base model. We observe that this paradigm presents significant opportunities for batched inference during serving. To capitalize on these opportunities, we present S-LoRA, a system designed for the scalable serving of many LoRA adapters. S-LoRA stores all adapters in the main memory and fetches the adapters used by the currently running queries to the GPU memory. To efficiently use the GPU memory and reduce fragmentation, S-LoRA proposes Unified Paging. Unified Paging uses a unified memory pool to manage dynamic adapter weights with different ranks and KV cache tensors with varying sequence lengths. Additionally, S-LoRA employs a novel tensor parallelism strategy and highly optimized custom CUDA kernels for heterogeneous batching of LoRA computation. Collectively, these features enable S-LoRA to serve thousands of LoRA adapters on a single GPU or across multiple GPUs with a small overhead. Compared to state-of-the-art libraries such as HuggingFace PEFT and vLLM (with naive support of LoRA serving), S-LoRA can improve the throughput by up to 4 times and increase the number of served adapters by several orders of magnitude. As a result, S-LoRA enables scalable serving of many task-specific fine-tuned models and offers the potential for large-scale customized fine-tuning services.

While protein language models (pLMs) have transformed biological research, the scaling laws governing their improvement remain underexplored. By adapting methodologies from NLP scaling laws, we investigated the optimal ratio between model parameters and training tokens within a fixed compute budget. Our study reveals that pLM sizes scale sublinearly with compute budget, showing diminishing returns in performance as model size increases, and we identify a performance plateau in training loss comparable to the one found in relevant works in the field. Our findings suggest that widely-used pLMs might not be compute-optimal, indicating that larger models could achieve convergence more efficiently. Training a 35M model on a reduced token set, we attained perplexity results comparable to larger models like ESM-2 (15B) and xTrimoPGLM (100B) with a single dataset pass. This work paves the way towards more compute-efficient pLMs, democratizing their training and practical application in computational biology.

The sampling of probability distributions specified up to a normalization constant is an important problem in both machine learning and statistical mechanics. While classical stochastic sampling methods such as Markov Chain Monte Carlo (MCMC) or Langevin Dynamics (LD) can suffer from slow mixing times there is a growing interest in using normalizing flows in order to learn the transformation of a simple prior distribution to the given target distribution. Here we propose a generalized and combined approach to sample target densities: Stochastic Normalizing Flows (SNF) -- an arbitrary sequence of deterministic invertible functions and stochastic sampling blocks. We show that stochasticity overcomes expressivity limitations of normalizing flows resulting from the invertibility constraint, whereas trainable transformations between sampling steps improve efficiency of pure MCMC/LD along the flow. By invoking ideas from non-equilibrium statistical mechanics we derive an efficient training procedure by which both the sampler's and the flow's parameters can be optimized end-to-end, and by which we can compute exact importance weights without having to marginalize out the randomness of the stochastic blocks. We illustrate the representational power, sampling efficiency and asymptotic correctness of SNFs on several benchmarks including applications to sampling molecular systems in equilibrium.

Efficiently approximating local curvature information of the loss function is a key tool for optimization and compression of deep neural networks. Yet, most existing methods to approximate second-order information have high computational or storage costs, which can limit their practicality. In this work, we investigate matrix-free, linear-time approaches for estimating Inverse-Hessian Vector Products (IHVPs) for the case when the Hessian can be approximated as a sum of rank-one matrices, as in the classic approximation of the Hessian by the empirical Fisher matrix. We propose two new algorithms as part of a framework called M-FAC: the first algorithm is tailored towards network compression and can compute the IHVP for dimension d, if the Hessian is given as a sum of m rank-one matrices, using O(dm^2) precomputation, O(dm) cost for computing the IHVP, and query cost O(m) for any single element of the inverse Hessian. The second algorithm targets an optimization setting, where we wish to compute the product between the inverse Hessian, estimated over a sliding window of optimization steps, and a given gradient direction, as required for preconditioned SGD. We give an algorithm with cost O(dm + m^2) for computing the IHVP and O(dm + m^3) for adding or removing any gradient from the sliding window. These two algorithms yield state-of-the-art results for network pruning and optimization with lower computational overhead relative to existing second-order methods. Implementations are available at [9] and [17].

Deep learning thrives with large neural networks and large datasets. However, larger networks and larger datasets result in longer training times that impede research and development progress. Distributed synchronous SGD offers a potential solution to this problem by dividing SGD minibatches over a pool of parallel workers. Yet to make this scheme efficient, the per-worker workload must be large, which implies nontrivial growth in the SGD minibatch size. In this paper, we empirically show that on the ImageNet dataset large minibatches cause optimization difficulties, but when these are addressed the trained networks exhibit good generalization. Specifically, we show no loss of accuracy when training with large minibatch sizes up to 8192 images. To achieve this result, we adopt a hyper-parameter-free linear scaling rule for adjusting learning rates as a function of minibatch size and develop a new warmup scheme that overcomes optimization challenges early in training. With these simple techniques, our Caffe2-based system trains ResNet-50 with a minibatch size of 8192 on 256 GPUs in one hour, while matching small minibatch accuracy. Using commodity hardware, our implementation achieves ~90% scaling efficiency when moving from 8 to 256 GPUs. Our findings enable training visual recognition models on internet-scale data with high efficiency.

Large Language Models increasingly rely on distributed techniques for their training and inference. These techniques require communication across devices which can reduce scaling efficiency as the number of devices increases. While some distributed techniques can overlap, and thus, hide this communication with independent computations, techniques such as Tensor Parallelism (TP) inherently serialize communication with model execution. One approach to hide this serialized communication is to interleave it with the producer operation (of the communicated data) in a fine-grained manner. However, this fine-grained interleaving of communication and computation in software can be difficult. Furthermore, as with any concurrent execution, it requires compute and memory resources to be shared between computation and communication, causing resource contention that reduces overlapping efficacy. To overcome these challenges, we propose T3 which applies hardware-software co-design to transparently overlap serialized communication while minimizing resource contention with compute. T3 transparently fuses producer operations with the subsequent communication via a simple configuration of the producer's output address space and requires minor software changes. At the hardware level, T3 adds a lightweight track and trigger mechanism to orchestrate the producer's compute, and communication. It further uses compute-enhanced memories for communication's attendant compute. As a result, T3 reduces resource contention, and efficiently overlaps serialized communication with computation. For important Transformer models like T-NLG, T3 speeds up communication-heavy sublayers by 30% geomean (max 47%) and reduces data movement by 22% geomean (max 36%). Furthermore, T3's benefits persist as models scale: geomean 29% for sublayers in sim500-billion parameter models, PALM and MT-NLG.

Despite recent advancements, most computational methods for molecule optimization are constrained to single- or double-property optimization tasks and suffer from poor scalability and generalizability to novel optimization tasks. Meanwhile, Large Language Models (LLMs) demonstrate remarkable out-of-domain generalizability to novel tasks. To demonstrate LLMs' potential for molecule optimization, we introduce MoMUInstruct, the first high-quality instruction-tuning dataset specifically focused on complex multi-property molecule optimization tasks. Leveraging MoMUInstruct, we develop GeLLM^3Os, a series of instruction-tuned LLMs for molecule optimization. Extensive evaluations across 5 in-domain and 5 out-of-domain tasks demonstrate that GeLLM^3Os consistently outperform state-of-the-art baselines. GeLLM^3Os also exhibit outstanding zero-shot generalization to unseen tasks, significantly outperforming powerful closed-source LLMs. Such strong generalizability demonstrates the tremendous potential of GeLLM^3Os as foundational models for molecule optimization, thereby tackling novel optimization tasks without resource-intensive retraining. MoMUInstruct, models, and code are accessible through https://github.com/ninglab/GeLLMO.

Reinforcement Learning from Human Feedback (RLHF) stands as a pivotal technique in empowering large language model (LLM) applications. Since RLHF involves diverse computational workloads and intricate dependencies among multiple LLMs, directly adopting parallelization techniques from supervised training can result in sub-optimal performance. To overcome this limitation, we propose a novel approach named parameter ReaLlocation, which dynamically redistributes LLM parameters in the cluster and adapts parallelization strategies during training. Building upon this idea, we introduce ReaLHF, a pioneering system capable of automatically discovering and running efficient execution plans for RLHF training given the desired algorithmic and hardware configurations. ReaLHF formulates the execution plan for RLHF as an augmented dataflow graph. Based on this formulation, ReaLHF employs a tailored search algorithm with a lightweight cost estimator to discover an efficient execution plan. Subsequently, the runtime engine deploys the selected plan by effectively parallelizing computations and redistributing parameters. We evaluate ReaLHF on the LLaMA-2 models with up to 4times70 billion parameters and 128 GPUs. The experiment results showcase ReaLHF's substantial speedups of 2.0-10.6times compared to baselines. Furthermore, the execution plans generated by ReaLHF exhibit an average of 26% performance improvement over heuristic approaches based on Megatron-LM. The source code of ReaLHF is publicly available at https://github.com/openpsi-project/ReaLHF .

Foundation models, now powering most of the exciting applications in deep learning, are almost universally based on the Transformer architecture and its core attention module. Many subquadratic-time architectures such as linear attention, gated convolution and recurrent models, and structured state space models (SSMs) have been developed to address Transformers' computational inefficiency on long sequences, but they have not performed as well as attention on important modalities such as language. We identify that a key weakness of such models is their inability to perform content-based reasoning, and make several improvements. First, simply letting the SSM parameters be functions of the input addresses their weakness with discrete modalities, allowing the model to selectively propagate or forget information along the sequence length dimension depending on the current token. Second, even though this change prevents the use of efficient convolutions, we design a hardware-aware parallel algorithm in recurrent mode. We integrate these selective SSMs into a simplified end-to-end neural network architecture without attention or even MLP blocks (Mamba). Mamba enjoys fast inference (5times higher throughput than Transformers) and linear scaling in sequence length, and its performance improves on real data up to million-length sequences. As a general sequence model backbone, Mamba achieves state-of-the-art performance across several modalities such as language, audio, and genomics. On language modeling, our Mamba-3B model outperforms Transformers of the same size and matches Transformers twice its size, both in pretraining and downstream evaluation.

State-of-art NPUs are typically architected as a self-contained sub-system with multiple heterogeneous hardware computing modules, and a dataflow-driven programming model. There lacks well-established methodology and tools in the industry to evaluate and compare the performance of NPUs from different architectures. We present an event-based performance modeling framework, VPU-EM, targeting scalable performance evaluation of modern NPUs across diversified AI workloads. The framework adopts high-level event-based system-simulation methodology to abstract away design details for speed, while maintaining hardware pipelining, concurrency and interaction with software task scheduling. It is natively developed in Python and built to interface directly with AI frameworks such as Tensorflow, PyTorch, ONNX and OpenVINO, linking various in-house NPU graph compilers to achieve optimized full model performance. Furthermore, VPU-EM also provides the capability to model power characteristics of NPU in Power-EM mode to enable joint performance/power analysis. Using VPU-EM, we conduct performance/power analysis of models from representative neural network architecture. We demonstrate that even though this framework is developed for Intel VPU, an Intel in-house NPU IP technology, the methodology can be generalized for analysis of modern NPUs.

We study a family of distributed stochastic optimization algorithms where gradients are sampled by a token traversing a network of agents in random-walk fashion. Typically, these random-walks are chosen to be Markov chains that asymptotically sample from a desired target distribution, and play a critical role in the convergence of the optimization iterates. In this paper, we take a novel approach by replacing the standard linear Markovian token by one which follows a nonlinear Markov chain - namely the Self-Repellent Radom Walk (SRRW). Defined for any given 'base' Markov chain, the SRRW, parameterized by a positive scalar {\alpha}, is less likely to transition to states that were highly visited in the past, thus the name. In the context of MCMC sampling on a graph, a recent breakthrough in Doshi et al. (2023) shows that the SRRW achieves O(1/{\alpha}) decrease in the asymptotic variance for sampling. We propose the use of a 'generalized' version of the SRRW to drive token algorithms for distributed stochastic optimization in the form of stochastic approximation, termed SA-SRRW. We prove that the optimization iterate errors of the resulting SA-SRRW converge to zero almost surely and prove a central limit theorem, deriving the explicit form of the resulting asymptotic covariance matrix corresponding to iterate errors. This asymptotic covariance is always smaller than that of an algorithm driven by the base Markov chain and decreases at rate O(1/{\alpha}^2) - the performance benefit of using SRRW thereby amplified in the stochastic optimization context. Empirical results support our theoretical findings.

Large language model (LLM) training and finetuning are often bottlenecked by limited GPU memory. While existing projection-based optimization methods address this by projecting gradients into a lower-dimensional subspace to reduce optimizer state memory, they typically rely on dense projection matrices, which can introduce computational and memory overheads. In this work, we propose Grass (GRAdient Stuctured Sparsification), a novel approach that leverages sparse projections to transform gradients into structured sparse updates. This design not only significantly reduces memory usage for optimizer states but also minimizes gradient memory footprint, computation, and communication costs, leading to substantial throughput improvements. Extensive experiments on pretraining and finetuning tasks demonstrate that Grass achieves competitive performance to full-rank training and existing projection-based methods. Notably, Grass enables half-precision pretraining of a 13B parameter LLaMA model on a single 40GB A100 GPU--a feat infeasible for previous methods--and yields up to a 2times throughput improvement on an 8-GPU system. Code can be found at https://github.com/aashiqmuhamed/GRASS .

Graph mining workloads aim to extract structural properties of a graph by exploring its subgraph structures. General purpose graph mining systems provide a generic runtime to explore subgraph structures of interest with the help of user-defined functions that guide the overall exploration process. However, the state-of-the-art graph mining systems remain largely oblivious to the shape (or pattern) of the subgraphs that they mine. This causes them to: (a) explore unnecessary subgraphs; (b) perform expensive computations on the explored subgraphs; and, (c) hold intermediate partial subgraphs in memory; all of which affect their overall performance. Furthermore, their programming models are often tied to their underlying exploration strategies, which makes it difficult for domain users to express complex mining tasks. In this paper, we develop Peregrine, a pattern-aware graph mining system that directly explores the subgraphs of interest while avoiding exploration of unnecessary subgraphs, and simultaneously bypassing expensive computations throughout the mining process. We design a pattern-based programming model that treats "graph patterns" as first class constructs and enables Peregrine to extract the semantics of patterns, which it uses to guide its exploration. Our evaluation shows that Peregrine outperforms state-of-the-art distributed and single machine graph mining systems, and scales to complex mining tasks on larger graphs, while retaining simplicity and expressivity with its "pattern-first" programming approach.

We present two new classes of algorithms for efficient field integration on graphs encoding point clouds. The first class, SeparatorFactorization(SF), leverages the bounded genus of point cloud mesh graphs, while the second class, RFDiffusion(RFD), uses popular epsilon-nearest-neighbor graph representations for point clouds. Both can be viewed as providing the functionality of Fast Multipole Methods (FMMs), which have had a tremendous impact on efficient integration, but for non-Euclidean spaces. We focus on geometries induced by distributions of walk lengths between points (e.g., shortest-path distance). We provide an extensive theoretical analysis of our algorithms, obtaining new results in structural graph theory as a byproduct. We also perform exhaustive empirical evaluation, including on-surface interpolation for rigid and deformable objects (particularly for mesh-dynamics modeling), Wasserstein distance computations for point clouds, and the Gromov-Wasserstein variant.

We generalize the Hamiltonian Monte Carlo algorithm with a stack of neural network layers and evaluate its ability to sample from different topologies in a two dimensional lattice gauge theory. We demonstrate that our model is able to successfully mix between modes of different topologies, significantly reducing the computational cost required to generated independent gauge field configurations. Our implementation is available at https://github.com/saforem2/l2hmc-qcd .

We introduce Graph-Induced Sum-Product Networks (GSPNs), a new probabilistic framework for graph representation learning that can tractably answer probabilistic queries. Inspired by the computational trees induced by vertices in the context of message-passing neural networks, we build hierarchies of sum-product networks (SPNs) where the parameters of a parent SPN are learnable transformations of the a-posterior mixing probabilities of its children's sum units. Due to weight sharing and the tree-shaped computation graphs of GSPNs, we obtain the efficiency and efficacy of deep graph networks with the additional advantages of a probabilistic model. We show the model's competitiveness on scarce supervision scenarios, under missing data, and for graph classification in comparison to popular neural models. We complement the experiments with qualitative analyses on hyper-parameters and the model's ability to answer probabilistic queries.

Neural network pruning serves as a critical technique for enhancing the efficiency of deep learning models. Unlike unstructured pruning, which only sets specific parameters to zero, structured pruning eliminates entire channels, thus yielding direct computational and storage benefits. However, the diverse patterns for coupling parameters, such as residual connections and group convolutions, the diverse deep learning frameworks, and the various time stages at which pruning can be performed make existing pruning methods less adaptable to different architectures, frameworks, and pruning criteria. To address this, we introduce Structurally Prune Anything (SPA), a versatile structured pruning framework that can prune neural networks with any architecture, from any framework, and at any stage of training. SPA leverages a standardized computational graph and ONNX representation to prune diverse neural network architectures without the need for manual intervention. SPA employs a group-level importance estimation method, which groups dependent computational operators, estimates their importance, and prunes unimportant coupled channels. This enables the transfer of various existing pruning criteria into a structured group style. As a result, SPA supports pruning at any time, either before training, after training with fine-tuning, or after training without fine-tuning. In the context of the latter, we introduce Optimal Brain SPA (OBSPA), an algorithm that achieves state-of-the-art pruning results needing neither fine-tuning nor calibration data. In extensive experiments, SPA shows competitive to state-of-the-art pruning performance across various architectures, from popular frameworks, at different pruning times.

Sparse training is one of the promising techniques to reduce the computational cost of DNNs while retaining high accuracy. In particular, N:M fine-grained structured sparsity, where only N out of consecutive M elements can be nonzero, has attracted attention due to its hardware-friendly pattern and capability of achieving a high sparse ratio. However, the potential to accelerate N:M sparse DNN training has not been fully exploited, and there is a lack of efficient hardware supporting N:M sparse training. To tackle these challenges, this paper presents a computation-efficient training scheme for N:M sparse DNNs using algorithm, architecture, and dataflow co-design. At the algorithm level, a bidirectional weight pruning method, dubbed BDWP, is proposed to leverage the N:M sparsity of weights during both forward and backward passes of DNN training, which can significantly reduce the computational cost while maintaining model accuracy. At the architecture level, a sparse accelerator for DNN training, namely SAT, is developed to neatly support both the regular dense operations and the computation-efficient N:M sparse operations. At the dataflow level, multiple optimization methods ranging from interleave mapping, pre-generation of N:M sparse weights, and offline scheduling, are proposed to boost the computational efficiency of SAT. Finally, the effectiveness of our training scheme is evaluated on a Xilinx VCU1525 FPGA card using various DNN models and datasets. Experimental results show the SAT accelerator with the BDWP sparse training method under 2:8 sparse ratio achieves an average speedup of 1.75x over that with the dense training, accompanied by a negligible accuracy loss of 0.56% on average. Furthermore, our proposed training scheme significantly improves the training throughput by 2.97~25.22x and the energy efficiency by 1.36~3.58x over prior FPGA-based accelerators.

State space models (SSMs) have high performance on long sequence modeling but require sophisticated initialization techniques and specialized implementations for high quality and runtime performance. We study whether a simple alternative can match SSMs in performance and efficiency: directly learning long convolutions over the sequence. We find that a key requirement to achieving high performance is keeping the convolution kernels smooth. We find that simple interventions--such as squashing the kernel weights--result in smooth kernels and recover SSM performance on a range of tasks including the long range arena, image classification, language modeling, and brain data modeling. Next, we develop FlashButterfly, an IO-aware algorithm to improve the runtime performance of long convolutions. FlashButterfly appeals to classic Butterfly decompositions of the convolution to reduce GPU memory IO and increase FLOP utilization. FlashButterfly speeds up convolutions by 2.2times, and allows us to train on Path256, a challenging task with sequence length 64K, where we set state-of-the-art by 29.1 points while training 7.2times faster than prior work. Lastly, we introduce an extension to FlashButterfly that learns the coefficients of the Butterfly decomposition, increasing expressivity without increasing runtime. Using this extension, we outperform a Transformer on WikiText103 by 0.2 PPL with 30% fewer parameters.

This paper presents the design, implementation, and evaluation of the PyTorch distributed data parallel module. PyTorch is a widely-adopted scientific computing package used in deep learning research and applications. Recent advances in deep learning argue for the value of large datasets and large models, which necessitates the ability to scale out model training to more computational resources. Data parallelism has emerged as a popular solution for distributed training thanks to its straightforward principle and broad applicability. In general, the technique of distributed data parallelism replicates the model on every computational resource to generate gradients independently and then communicates those gradients at each iteration to keep model replicas consistent. Despite the conceptual simplicity of the technique, the subtle dependencies between computation and communication make it non-trivial to optimize the distributed training efficiency. As of v1.5, PyTorch natively provides several techniques to accelerate distributed data parallel, including bucketing gradients, overlapping computation with communication, and skipping gradient synchronization. Evaluations show that, when configured appropriately, the PyTorch distributed data parallel module attains near-linear scalability using 256 GPUs.

The emergence of large-scale Mixture of Experts (MoE) models has marked a significant advancement in artificial intelligence, offering enhanced model capacity and computational efficiency through conditional computation. However, the deployment and inference of these models present substantial challenges in terms of computational resources, latency, and energy efficiency. This comprehensive survey systematically analyzes the current landscape of inference optimization techniques for MoE models across the entire system stack. We first establish a taxonomical framework that categorizes optimization approaches into model-level, system-level, and hardware-level optimizations. At the model level, we examine architectural innovations including efficient expert design, attention mechanisms, various compression techniques such as pruning, quantization, and knowledge distillation, as well as algorithm improvement including dynamic routing strategies and expert merging methods. At the system level, we investigate distributed computing approaches, load balancing mechanisms, and efficient scheduling algorithms that enable scalable deployment. Furthermore, we delve into hardware-specific optimizations and co-design strategies that maximize throughput and energy efficiency. This survey not only provides a structured overview of existing solutions but also identifies key challenges and promising research directions in MoE inference optimization. Our comprehensive analysis serves as a valuable resource for researchers and practitioners working on large-scale deployment of MoE models in resource-constrained environments. To facilitate ongoing updates and the sharing of cutting-edge advances in MoE inference optimization research, we have established a repository accessible at https://github.com/MoE-Inf/awesome-moe-inference/.

Sequence Parallel (SP) serves as a prevalent strategy to handle long sequences that exceed the memory limit of a single GPU. However, existing SP methods do not take advantage of linear attention features, resulting in sub-optimal parallelism efficiency and usability for linear attention-based language models. In this paper, we introduce Linear Attention Sequence Parallel (LASP), an efficient SP method tailored to linear attention-based language models. Specifically, we design an efficient point-to-point communication mechanism to leverage the right-product kernel trick of linear attention, which sharply decreases the communication overhead of SP. We also enhance the practical efficiency of LASP by performing kernel fusion and intermediate state caching, making the implementation of LASP hardware-friendly on GPU clusters. Furthermore, we meticulously ensure the compatibility of sequence-level LASP with all types of batch-level data parallel methods, which is vital for distributed training on large clusters with long sequences and large batches. We conduct extensive experiments on two linear attention-based models with varying sequence lengths and GPU cluster sizes. LASP scales sequence length up to 4096K using 128 A100 80G GPUs on 1B models, which is 8 times longer than existing SP methods while being significantly faster. The code is available at https://github.com/OpenNLPLab/LASP.

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional architectures in a causal multi-headed graph mechanism, to realize a generative pretrained model. The model is applied to predict secondary structure content (per-residue level and overall content), protein solubility, and sequencing tasks. Further trained on inverse tasks, the model is rendered capable of designing proteins with these properties as target features. The model is formulated as a general framework, completely prompt-based, and can be adapted for a variety of downstream tasks. We find that adding additional tasks yields emergent synergies that the model exploits in improving overall performance, beyond what would be possible by training a model on each dataset alone. Case studies are presented to validate the method, yielding protein designs specifically focused on structural proteins, but also exploring the applicability in the design of soluble, antimicrobial biomaterials. While our model is trained to ultimately perform 8 distinct tasks, with available datasets it can be extended to solve additional problems. In a broader sense, this work illustrates a form of multiscale modeling that relates a set of ultimate building blocks (here, byte-level utf8 characters) to complex output. This materiomic scheme captures complex emergent relationships between universal building block and resulting properties via a synergizing learning capacity to express a set of potentialities embedded in the knowledge used in training, via the interplay of universality and diversity.

Large language models (LLMs) face a daunting challenge due to the excessive computational and memory requirements of the commonly used Transformer architecture. While state space model (SSM) is a new type of foundational network architecture offering lower computational complexity, their performance has yet to fully rival that of Transformers. This paper introduces DenseSSM, a novel approach to enhance the flow of hidden information between layers in SSMs. By selectively integrating shallowlayer hidden states into deeper layers, DenseSSM retains fine-grained information crucial for the final output. Dense connections enhanced DenseSSM still maintains the training parallelizability and inference efficiency. The proposed method can be widely applicable to various SSM types like RetNet and Mamba. With similar model size, DenseSSM achieves significant improvements, exemplified by DenseRetNet outperforming the original RetNet with up to 5% accuracy improvement on public benchmarks.

Active matter systems, from self-propelled colloids to motile bacteria, are characterized by the conversion of free energy into useful work at the microscopic scale. These systems generically involve physics beyond the reach of equilibrium statistical mechanics, and a persistent challenge has been to understand the nature of their nonequilibrium states. The entropy production rate and the magnitude of the steady-state probability current provide quantitative ways to do so by measuring the breakdown of time-reversal symmetry and the strength of nonequilibrium transport of measure. Yet, their efficient computation has remained elusive, as they depend on the system's unknown and high-dimensional probability density. Here, building upon recent advances in generative modeling, we develop a deep learning framework that estimates the score of this density. We show that the score, together with the microscopic equations of motion, gives direct access to the entropy production rate, the probability current, and their decomposition into local contributions from individual particles, spatial regions, and degrees of freedom. To represent the score, we introduce a novel, spatially-local transformer-based network architecture that learns high-order interactions between particles while respecting their underlying permutation symmetry. We demonstrate the broad utility and scalability of the method by applying it to several high-dimensional systems of interacting active particles undergoing motility-induced phase separation (MIPS). We show that a single instance of our network trained on a system of 4096 particles at one packing fraction can generalize to other regions of the phase diagram, including systems with as many as 32768 particles. We use this observation to quantify the spatial structure of the departure from equilibrium in MIPS as a function of the number of particles and the packing fraction.

Computation in a typical Transformer-based large language model (LLM) can be characterized by batch size, hidden dimension, number of layers, and sequence length. Until now, system works for accelerating LLM training have focused on the first three dimensions: data parallelism for batch size, tensor parallelism for hidden size and pipeline parallelism for model depth or layers. These widely studied forms of parallelism are not targeted or optimized for long sequence Transformer models. Given practical application needs for long sequence LLM, renewed attentions are being drawn to sequence parallelism. However, existing works in sequence parallelism are constrained by memory-communication inefficiency, limiting their scalability to long sequence large models. In this work, we introduce DeepSpeed-Ulysses, a novel, portable and effective methodology for enabling highly efficient and scalable LLM training with extremely long sequence length. DeepSpeed-Ulysses at its core partitions input data along the sequence dimension and employs an efficient all-to-all collective communication for attention computation. Theoretical communication analysis shows that whereas other methods incur communication overhead as sequence length increases, DeepSpeed-Ulysses maintains constant communication volume when sequence length and compute devices are increased proportionally. Furthermore, experimental evaluations show that DeepSpeed-Ulysses trains 2.5X faster with 4X longer sequence length than the existing method SOTA baseline.

Monolithic large language models (LLMs) like GPT-4 have paved the way for modern generative AI applications. Training, serving, and maintaining monolithic LLMs at scale, however, remains prohibitively expensive and challenging. The disproportionate increase in compute-to-memory ratio of modern AI accelerators have created a memory wall, necessitating new methods to deploy AI. Composition of Experts (CoE) is an alternative modular approach that lowers the cost and complexity of training and serving. However, this approach presents two key challenges when using conventional hardware: (1) without fused operations, smaller models have lower operational intensity, which makes high utilization more challenging to achieve; and (2) hosting a large number of models can be either prohibitively expensive or slow when dynamically switching between them. In this paper, we describe how combining CoE, streaming dataflow, and a three-tier memory system scales the AI memory wall. We describe Samba-CoE, a CoE system with 150 experts and a trillion total parameters. We deploy Samba-CoE on the SambaNova SN40L Reconfigurable Dataflow Unit (RDU) - a commercial dataflow accelerator architecture that has been co-designed for enterprise inference and training applications. The chip introduces a new three-tier memory system with on-chip distributed SRAM, on-package HBM, and off-package DDR DRAM. A dedicated inter-RDU network enables scaling up and out over multiple sockets. We demonstrate speedups ranging from 2x to 13x on various benchmarks running on eight RDU sockets compared with an unfused baseline. We show that for CoE inference deployments, the 8-socket RDU Node reduces machine footprint by up to 19x, speeds up model switching time by 15x to 31x, and achieves an overall speedup of 3.7x over a DGX H100 and 6.6x over a DGX A100.

Grid-based structures are commonly used to encode explicit features for graphics primitives such as images, signed distance functions (SDF), and neural radiance fields (NeRF) due to their simple implementation. However, in n-dimensional space, calculating the value of a sampled point requires interpolating the values of its 2^n neighboring vertices. The exponential scaling with dimension leads to significant computational overheads. To address this issue, we propose a simplex-based approach for encoding graphics primitives. The number of vertices in a simplex-based structure increases linearly with dimension, making it a more efficient and generalizable alternative to grid-based representations. Using the non-axis-aligned simplicial structure property, we derive and prove a coordinate transformation, simplicial subdivision, and barycentric interpolation scheme for efficient sampling, which resembles transformation procedures in the simplex noise algorithm. Finally, we use hash tables to store multiresolution features of all interest points in the simplicial grid, which are passed into a tiny fully connected neural network to parameterize graphics primitives. We implemented a detailed simplex-based structure encoding algorithm in C++ and CUDA using the methods outlined in our approach. In the 2D image fitting task, the proposed method is capable of fitting a giga-pixel image with 9.4% less time compared to the baseline method proposed by instant-ngp, while maintaining the same quality and compression rate. In the volumetric rendering setup, we observe a maximum 41.2% speedup when the samples are dense enough.

We study a new connection between a technical measure called mu-conductance that arises in the study of Markov chains for sampling convex bodies and the network community profile that characterizes size-resolved properties of clusters and communities in social and information networks. The idea of mu-conductance is similar to the traditional graph conductance, but disregards sets with small volume. We derive a sequence of optimization problems including a low-rank semi-definite program from which we can derive a lower bound on the optimal mu-conductance value. These ideas give the first theoretically sound bound on the behavior of the network community profile for a wide range of cluster sizes. The algorithm scales up to graphs with hundreds of thousands of nodes and we demonstrate how our framework validates the predicted structures of real-world graphs.

It is widely acknowledged that large models have the potential to deliver superior performance across a broad range of domains. Despite the remarkable progress made in the field of machine learning systems research, which has enabled the development and exploration of large models, such abilities remain confined to a small group of advanced users and industry leaders, resulting in an implicit technical barrier for the wider community to access and leverage these technologies. In this paper, we introduce PyTorch Fully Sharded Data Parallel (FSDP) as an industry-grade solution for large model training. FSDP has been closely co-designed with several key PyTorch core components including Tensor implementation, dispatcher system, and CUDA memory caching allocator, to provide non-intrusive user experiences and high training efficiency. Additionally, FSDP natively incorporates a range of techniques and settings to optimize resource utilization across a variety of hardware configurations. The experimental results demonstrate that FSDP is capable of achieving comparable performance to Distributed Data Parallel while providing support for significantly larger models with near-linear scalability in terms of TFLOPS.

Spider webs are incredible biological structures, comprising thin but strong silk filament and arranged into complex hierarchical architectures with striking mechanical properties (e.g., lightweight but high strength, achieving diverse mechanical responses). While simple 2D orb webs can easily be mimicked, the modeling and synthesis of 3D-based web structures remain challenging, partly due to the rich set of design features. Here we provide a detailed analysis of the heterogenous graph structures of spider webs, and use deep learning as a way to model and then synthesize artificial, bio-inspired 3D web structures. The generative AI models are conditioned based on key geometric parameters (including average edge length, number of nodes, average node degree, and others). To identify graph construction principles, we use inductive representation sampling of large experimentally determined spider web graphs, to yield a dataset that is used to train three conditional generative models: 1) An analog diffusion model inspired by nonequilibrium thermodynamics, with sparse neighbor representation, 2) a discrete diffusion model with full neighbor representation, and 3) an autoregressive transformer architecture with full neighbor representation. All three models are scalable, produce complex, de novo bio-inspired spider web mimics, and successfully construct graphs that meet the design objectives. We further propose algorithm that assembles web samples produced by the generative models into larger-scale structures based on a series of geometric design targets, including helical and parametric shapes, mimicking, and extending natural design principles towards integration with diverging engineering objectives. Several webs are manufactured using 3D printing and tested to assess mechanical properties.

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins)

The Mamba layer offers an efficient selective state space model (SSM) that is highly effective in modeling multiple domains including NLP, long-range sequences processing, and computer vision. Selective SSMs are viewed as dual models, in which one trains in parallel on the entire sequence via IO-aware parallel scan, and deploys in an autoregressive manner. We add a third view and show that such models can be viewed as attention-driven models. This new perspective enables us to compare the underlying mechanisms to that of the self-attention layers in transformers and allows us to peer inside the inner workings of the Mamba model with explainability methods. Our code is publicly available.

Many deep learning applications benefit from using large models with billions of parameters. Training these models is notoriously expensive due to the need for specialized HPC clusters. In this work, we consider alternative setups for training large models: using cheap "preemptible" instances or pooling existing resources from multiple regions. We analyze the performance of existing model-parallel algorithms in these conditions and find configurations where training larger models becomes less communication-intensive. Based on these findings, we propose SWARM parallelism, a model-parallel training algorithm designed for poorly connected, heterogeneous and unreliable devices. SWARM creates temporary randomized pipelines between nodes that are rebalanced in case of failure. We empirically validate our findings and compare SWARM parallelism with existing large-scale training approaches. Finally, we combine our insights with compression strategies to train a large Transformer language model with 1B shared parameters (approximately 13B before sharing) on preemptible T4 GPUs with less than 200Mb/s network.

With the fast growth of parameter size, it becomes increasingly challenging to deploy large generative models as they typically require large GPU memory consumption and massive computation. Unstructured model pruning has been a common approach to reduce both GPU memory footprint and the overall computation while retaining good model accuracy. However, the existing solutions do not provide a highly-efficient support for handling unstructured sparsity on modern GPUs, especially on the highly-structured Tensor Core hardware. Therefore, we propose Flash-LLM for enabling low-cost and highly-efficient large generative model inference with the sophisticated support of unstructured sparsity on high-performance but highly restrictive Tensor Cores. Based on our key observation that the main bottleneck of generative model inference is the several skinny matrix multiplications for which Tensor Cores would be significantly under-utilized due to low computational intensity, we propose a general Load-as-Sparse and Compute-as-Dense methodology for unstructured sparse matrix multiplication. The basic insight is to address the significant memory bandwidth bottleneck while tolerating redundant computations that are not critical for end-to-end performance on Tensor Cores. Based on this, we design an effective software framework for Tensor Core based unstructured SpMM, leveraging on-chip resources for efficient sparse data extraction and computation/memory-access overlapping. At SpMM kernel level, Flash-LLM significantly outperforms the state-of-the-art library, i.e., Sputnik and SparTA by an average of 2.9x and 1.5x, respectively. At end-to-end framework level on OPT-30B/66B/175B models, for tokens per GPU-second, Flash-LLM achieves up to 3.8x and 3.6x improvement over DeepSpeed and FasterTransformer, respectively, with significantly lower inference cost.

We present FastRP, a scalable and performant algorithm for learning distributed node representations in a graph. FastRP is over 4,000 times faster than state-of-the-art methods such as DeepWalk and node2vec, while achieving comparable or even better performance as evaluated on several real-world networks on various downstream tasks. We observe that most network embedding methods consist of two components: construct a node similarity matrix and then apply dimension reduction techniques to this matrix. We show that the success of these methods should be attributed to the proper construction of this similarity matrix, rather than the dimension reduction method employed. FastRP is proposed as a scalable algorithm for network embeddings. Two key features of FastRP are: 1) it explicitly constructs a node similarity matrix that captures transitive relationships in a graph and normalizes matrix entries based on node degrees; 2) it utilizes very sparse random projection, which is a scalable optimization-free method for dimension reduction. An extra benefit from combining these two design choices is that it allows the iterative computation of node embeddings so that the similarity matrix need not be explicitly constructed, which further speeds up FastRP. FastRP is also advantageous for its ease of implementation, parallelization and hyperparameter tuning. The source code is available at https://github.com/GTmac/FastRP.

In this paper, we present a new MTL framework that searches for structures optimized for multiple tasks with diverse graph topologies and shares features among tasks. We design a restricted DAG-based central network with read-in/read-out layers to build topologically diverse task-adaptive structures while limiting search space and time. We search for a single optimized network that serves as multiple task adaptive sub-networks using our three-stage training process. To make the network compact and discretized, we propose a flow-based reduction algorithm and a squeeze loss used in the training process. We evaluate our optimized network on various public MTL datasets and show ours achieves state-of-the-art performance. An extensive ablation study experimentally validates the effectiveness of the sub-module and schemes in our framework.

The emergence of Large Language Models (LLMs) has necessitated the adoption of parallel training techniques, involving the deployment of thousands of GPUs to train a single model. Unfortunately, we have found that the efficiency of current parallel training is often suboptimal, largely due to the following two main issues. Firstly, hardware failures are inevitable, leading to interruptions in the training tasks. The inability to quickly identify the faulty components results in a substantial waste of GPU resources. Secondly, since GPUs must wait for parameter synchronization to complete before proceeding to the next round of computation, network congestions can greatly increase the waiting time for GPUs. To address these challenges, this paper introduces a communication-driven solution, namely the C4. The key insights of C4 are two folds. First, in parallel training, collective communication exhibits periodic and homogeneous characteristics, so any anomalies are certainly due to some form of hardware malfunction. By leveraging this feature, C4 can rapidly identify the faulty components, swiftly isolate the anomaly, and restart the task, thereby avoiding resource wastage caused by delays in anomaly detection. Second, the predictable communication model of collective communication, involving few large flows, allows C4 to efficiently execute traffic planning, substantially reducing network congestion. C4 has been extensively implemented across our production systems, cutting error-induced overhead by roughly 30% and enhancing runtime performance by about 15% for certain applications with moderate communication costs.

Microprocessor architects are increasingly resorting to domain-specific customization in the quest for high-performance and energy-efficiency. As the systems grow in complexity, fine-tuning architectural parameters across multiple sub-systems (e.g., datapath, memory blocks in different hierarchies, interconnects, compiler optimization, etc.) quickly results in a combinatorial explosion of design space. This makes domain-specific customization an extremely challenging task. Prior work explores using reinforcement learning (RL) and other optimization methods to automatically explore the large design space. However, these methods have traditionally relied on single-agent RL/ML formulations. It is unclear how scalable single-agent formulations are as we increase the complexity of the design space (e.g., full stack System-on-Chip design). Therefore, we propose an alternative formulation that leverages Multi-Agent RL (MARL) to tackle this problem. The key idea behind using MARL is an observation that parameters across different sub-systems are more or less independent, thus allowing a decentralized role assigned to each agent. We test this hypothesis by designing domain-specific DRAM memory controller for several workload traces. Our evaluation shows that the MARL formulation consistently outperforms single-agent RL baselines such as Proximal Policy Optimization and Soft Actor-Critic over different target objectives such as low power and latency. To this end, this work opens the pathway for new and promising research in MARL solutions for hardware architecture search.

Structured state-space models (SSMs) such as S4, stemming from the seminal work of Gu et al., are gaining popularity as effective approaches for modeling sequential data. Deep SSMs demonstrate outstanding performance across a diverse set of domains, at a reduced training and inference cost compared to attention-based transformers. Recent developments show that if the linear recurrence powering SSMs allows for multiplicative interactions between inputs and hidden states (e.g. GateLoop, Mamba, GLA), then the resulting architecture can surpass in both in accuracy and efficiency attention-powered foundation models trained on text, at scales of billion parameters. In this paper, we give theoretical grounding to this recent finding using tools from Rough Path Theory: we show that when random linear recurrences are equipped with simple input-controlled transitions (selectivity mechanism), then the hidden state is provably a low-dimensional projection of a powerful mathematical object called the signature of the input -- capturing non-linear interactions between tokens at distinct timescales. Our theory not only motivates the success of modern selective state-space models such as Mamba but also provides a solid framework to understand the expressive power of future SSM variants.

Recent years have witnessed the rapid progress and broad application of diffusion probabilistic models (DPMs). Sampling from DPMs can be viewed as solving an ordinary differential equation (ODE). Despite the promising performance, the generation of DPMs usually consumes much time due to the large number of function evaluations (NFE). Though recent works have accelerated the sampling to around 20 steps with high-order solvers, the sample quality with less than 10 NFE can still be improved. In this paper, we propose a unified sampling framework (USF) to study the optional strategies for solver. Under this framework, we further reveal that taking different solving strategies at different timesteps may help further decrease the truncation error, and a carefully designed solver schedule has the potential to improve the sample quality by a large margin. Therefore, we propose a new sampling framework based on the exponential integral formulation that allows free choices of solver strategy at each step and design specific decisions for the framework. Moreover, we propose S^3, a predictor-based search method that automatically optimizes the solver schedule to get a better time-quality trade-off of sampling. We demonstrate that S^3 can find outstanding solver schedules which outperform the state-of-the-art sampling methods on CIFAR-10, CelebA, ImageNet, and LSUN-Bedroom datasets. Specifically, we achieve 2.69 FID with 10 NFE and 6.86 FID with 5 NFE on CIFAR-10 dataset, outperforming the SOTA method significantly. We further apply S^3 to Stable-Diffusion model and get an acceleration ratio of 2times, showing the feasibility of sampling in very few steps without retraining the neural network.

Most real-world graphs exhibit a hierarchical structure, which is often overlooked by existing graph generation methods. To address this limitation, we propose a novel graph generative network that captures the hierarchical nature of graphs and successively generates the graph sub-structures in a coarse-to-fine fashion. At each level of hierarchy, this model generates communities in parallel, followed by the prediction of cross-edges between communities using separate neural networks. This modular approach enables scalable graph generation for large and complex graphs. Moreover, we model the output distribution of edges in the hierarchical graph with a multinomial distribution and derive a recursive factorization for this distribution. This enables us to generate community graphs with integer-valued edge weights in an autoregressive manner. Empirical studies demonstrate the effectiveness and scalability of our proposed generative model, achieving state-of-the-art performance in terms of graph quality across various benchmark datasets. The code is available at https://github.com/Karami-m/HiGen_main.

Large language models have led to state-of-the-art accuracies across a range of tasks. However, training these models efficiently is challenging for two reasons: a) GPU memory capacity is limited, making it impossible to fit large models on even a multi-GPU server, and b) the number of compute operations required to train these models can result in unrealistically long training times. Consequently, new methods of model parallelism such as tensor and pipeline parallelism have been proposed. Unfortunately, naive usage of these methods leads to fundamental scaling issues at thousands of GPUs, e.g., due to expensive cross-node communication or devices spending significant time waiting on other devices to make progress. In this paper, we show how different types of parallelism methods (tensor, pipeline, and data parallelism) can be composed to scale to thousands of GPUs and models with trillions of parameters. We survey techniques for pipeline parallelism and propose a novel interleaved pipeline parallelism schedule that can improve throughput by 10+% with memory footprint comparable to existing approaches. We quantitatively study the trade-offs between tensor, pipeline, and data parallelism, and provide intuition as to how to configure distributed training of a large model. Our approach allows us to perform training iterations on a model with 1 trillion parameters at 502 petaFLOP/s on 3072 GPUs with achieved per-GPU throughput of 52% of theoretical peak. Our code is open sourced at https://github.com/nvidia/megatron-lm.

This paper presents ``Stim", a fast simulator for quantum stabilizer circuits. The paper explains how Stim works and compares it to existing tools. With no foreknowledge, Stim can analyze a distance 100 surface code circuit (20 thousand qubits, 8 million gates, 1 million measurements) in 15 seconds and then begin sampling full circuit shots at a rate of 1 kHz. Stim uses a stabilizer tableau representation, similar to Aaronson and Gottesman's CHP simulator, but with three main improvements. First, Stim improves the asymptotic complexity of deterministic measurement from quadratic to linear by tracking the {\em inverse} of the circuit's stabilizer tableau. Second, Stim improves the constant factors of the algorithm by using a cache-friendly data layout and 256 bit wide SIMD instructions. Third, Stim only uses expensive stabilizer tableau simulation to create an initial reference sample. Further samples are collected in bulk by using that sample as a reference for batches of Pauli frames propagating through the circuit.

Directed acyclic graphs (DAGs) encode a lot of information about a particular distribution in their structure. However, compute required to infer these structures is typically super-exponential in the number of variables, as inference requires a sweep of a combinatorially large space of potential structures. That is, until recent advances made it possible to search this space using a differentiable metric, drastically reducing search time. While this technique -- named NOTEARS -- is widely considered a seminal work in DAG-discovery, it concedes an important property in favour of differentiability: transportability. To be transportable, the structures discovered on one dataset must apply to another dataset from the same domain. We introduce D-Struct which recovers transportability in the discovered structures through a novel architecture and loss function while remaining fully differentiable. Because D-Struct remains differentiable, our method can be easily adopted in existing differentiable architectures, as was previously done with NOTEARS. In our experiments, we empirically validate D-Struct with respect to edge accuracy and structural Hamming distance in a variety of settings.

Graph Structure Learning (GSL) has recently garnered considerable attention due to its ability to optimize both the parameters of Graph Neural Networks (GNNs) and the computation graph structure simultaneously. Despite the proliferation of GSL methods developed in recent years, there is no standard experimental setting or fair comparison for performance evaluation, which creates a great obstacle to understanding the progress in this field. To fill this gap, we systematically analyze the performance of GSL in different scenarios and develop a comprehensive Graph Structure Learning Benchmark (GSLB) curated from 20 diverse graph datasets and 16 distinct GSL algorithms. Specifically, GSLB systematically investigates the characteristics of GSL in terms of three dimensions: effectiveness, robustness, and complexity. We comprehensively evaluate state-of-the-art GSL algorithms in node- and graph-level tasks, and analyze their performance in robust learning and model complexity. Further, to facilitate reproducible research, we have developed an easy-to-use library for training, evaluating, and visualizing different GSL methods. Empirical results of our extensive experiments demonstrate the ability of GSL and reveal its potential benefits on various downstream tasks, offering insights and opportunities for future research. The code of GSLB is available at: https://github.com/GSL-Benchmark/GSLB.

In this work, we propose a framework that constructs reduced order models for nonlinear structural mechanics in a nonintrusive fashion, and can handle large scale simulations. We identify three steps that are carried out separately in time, and possibly on different devices: (i) the production of high-fidelity solutions by a commercial software, (ii) the offline stage of the model reduction and (iii) the online stage where the reduced order model is exploited. The nonintrusivity assumes that only the displacement field solution is known, and relies on operations on simulation data during the offline phase by using an in-house code. The compatibility with a new commercial code only needs the implementation of a routine converting the mesh and result format into our in-house data format. The nonintrusive capabilities of the framework are demonstrated on numerical experiments using commercial versions of the finite element softwares Zset and Ansys Mechanical. The nonlinear constitutive equations are evaluated by using the same external plugins as for Zset or Ansys Mechanical. The large scale simulations are handled using domain decomposition and parallel computing with distributed memory. The features and performances of the framework are evaluated on two numerical applications involving elastoviscoplastic materials: the second one involves a model of high-pressure blade, where the framework is used to extrapolate cyclic loadings in 6.5 hours, whereas the reference high-fidelity computation would take 9.5 days.

With the advent of smart devices that support 4K and 8K resolution, Single Image Super Resolution (SISR) has become an important computer vision problem. However, most super resolution deep networks are computationally very expensive. In this paper, we propose Super-Efficient Super Resolution (SESR) networks that establish a new state-of-the-art for efficient super resolution. Our approach is based on linear overparameterization of CNNs and creates an efficient model architecture for SISR. With theoretical analysis, we uncover the limitations of existing overparameterization methods and show how the proposed method alleviates them. Detailed experiments across six benchmark datasets demonstrate that SESR achieves similar or better image quality than state-of-the-art models while requiring 2x to 330x fewer Multiply-Accumulate (MAC) operations. As a result, SESR can be used on constrained hardware to perform x2 (1080p to 4K) and x4 (1080p to 8K) SISR. Towards this, we estimate hardware performance numbers for a commercial Arm mobile-Neural Processing Unit (NPU) for 1080p to 4K (x2) and 1080p to 8K (x4) SISR. Our results highlight the challenges faced by super resolution on AI accelerators and demonstrate that SESR is significantly faster (e.g., 6x-8x higher FPS) than existing models on mobile-NPU. Finally, SESR outperforms prior models by 1.5x-2x in latency on Arm CPU and GPU when deployed on a real mobile device. The code for this work is available at https://github.com/ARM-software/sesr.

Various common deep learning architectures, such as LSTMs, GRUs, Resnets and Highway Networks, employ state passthrough connections that support training with high feed-forward depth or recurrence over many time steps. These "Passthrough Networks" architectures also enable the decoupling of the network state size from the number of parameters of the network, a possibility has been studied by Sak2014 with their low-rank parametrization of the LSTM. In this work we extend this line of research, proposing effective, low-rank and low-rank plus diagonal matrix parametrizations for Passthrough Networks which exploit this decoupling property, reducing the data complexity and memory requirements of the network while preserving its memory capacity. This is particularly beneficial in low-resource settings as it supports expressive models with a compact parametrization less susceptible to overfitting. We present competitive experimental results on several tasks, including language modeling and a near state of the art result on sequential randomly-permuted MNIST classification, a hard task on natural data.

With the increasing diversity of ML infrastructures nowadays, distributed training over heterogeneous computing systems is desired to facilitate the production of big models. Mixture-of-Experts (MoE) models have been proposed to lower the cost of training subject to the overall size of models/data through gating and parallelism in a divide-and-conquer fashion. While DeepSpeed has made efforts in carrying out large-scale MoE training over heterogeneous infrastructures, the efficiency of training and inference could be further improved from several system aspects, including load balancing, communication/computation efficiency, and memory footprint limits. In this work, we present SE-MoE that proposes Elastic MoE training with 2D prefetch and Fusion communication over Hierarchical storage, so as to enjoy efficient parallelisms in various types. For scalable inference in a single node, especially when the model size is larger than GPU memory, SE-MoE forms the CPU-GPU memory jointly into a ring of sections to load the model, and executes the computation tasks across the memory sections in a round-robin manner for efficient inference. We carried out extensive experiments to evaluate SE-MoE, where SE-MoE successfully trains a Unified Feature Optimization (UFO) model with a Sparsely-Gated Mixture-of-Experts model of 12B parameters in 8 days on 48 A100 GPU cards. The comparison against the state-of-the-art shows that SE-MoE outperformed DeepSpeed with 33% higher throughput (tokens per second) in training and 13% higher throughput in inference in general. Particularly, under unbalanced MoE Tasks, e.g., UFO, SE-MoE achieved 64% higher throughput with 18% lower memory footprints. The code of the framework will be released on: https://github.com/PaddlePaddle/Paddle.

Decoder-only Transformer models such as GPT have demonstrated superior performance in text generation, by autoregressively predicting the next token. However, the performance of GPT is bounded by low compute-to-memory-ratio and high memory access. Throughput-oriented architectures such as GPUs target parallel processing rather than sequential token generation, and are not efficient for GPT acceleration, particularly on-device inference applications. Process-in-memory (PIM) architectures can significantly reduce data movement and provide high computation parallelism, and are promising candidates to accelerate GPT inference. In this work, we propose PIM-GPT that aims to achieve high throughput, high energy efficiency and end-to-end acceleration of GPT inference. PIM-GPT leverages DRAM-based PIM solutions to perform multiply-accumulate (MAC) operations on the DRAM chips, greatly reducing data movement. A compact application-specific integrated chip (ASIC) is designed and synthesized to initiate instructions to PIM chips and support data communication along with necessary arithmetic computations. At the software level, the mapping scheme is designed to maximize data locality and computation parallelism by partitioning a matrix among DRAM channels and banks to utilize all in-bank computation resources concurrently. We develop an event-driven clock-cycle accurate simulator to validate the efficacy of the proposed PIM-GPT architecture. Overall, PIM-GPT achieves 41-137times, 631-1074times speedup and 339-1085times, 890-1632times energy efficiency over GPU and CPU baseline, respectively, on 8 GPT models with up to 1.4 billion parameters.

Neural graphics primitives are faster and achieve higher quality when their neural networks are augmented by spatial data structures that hold trainable features arranged in a grid. However, existing feature grids either come with a large memory footprint (dense or factorized grids, trees, and hash tables) or slow performance (index learning and vector quantization). In this paper, we show that a hash table with learned probes has neither disadvantage, resulting in a favorable combination of size and speed. Inference is faster than unprobed hash tables at equal quality while training is only 1.2-2.6x slower, significantly outperforming prior index learning approaches. We arrive at this formulation by casting all feature grids into a common framework: they each correspond to a lookup function that indexes into a table of feature vectors. In this framework, the lookup functions of existing data structures can be combined by simple arithmetic combinations of their indices, resulting in Pareto optimal compression and speed.

The increasing usage of Large Language Models (LLMs) has resulted in a surging demand for planet-scale serving systems, where tens of thousands of GPUs continuously serve hundreds of millions of users. Consequently, throughput (under reasonable latency constraints) has emerged as a key metric that determines serving systems' performance. To boost throughput, various methods of inter-device parallelism (e.g., data, tensor, pipeline) have been explored. However, existing methods do not consider overlapping the utilization of different resources within a single device, leading to underutilization and sub-optimal performance. We propose NanoFlow, a novel serving framework that exploits intra-device parallelism, which overlaps the usage of resources including compute, memory, and network within a single device through operation co-scheduling. To exploit intra-device parallelism, NanoFlow introduces two key innovations: First, NanoFlow splits requests into nano-batches at the granularity of operations, which breaks the dependency of sequential operations in LLM inference and enables overlapping; then, to get benefit from overlapping, NanoFlow uses an operation-level pipeline with execution unit scheduling, which partitions the device's functional units and simultaneously executes different operations in each unit. NanoFlow automates the pipeline setup using a parameter search algorithm, which enables easily porting NanoFlow to different models. We implement NanoFlow on NVIDIA GPUs and evaluate end-to-end serving throughput on several popular models such as LLaMA-2-70B, Mixtral 8x7B, LLaMA-3-8B, etc.. With practical workloads, NanoFlow provides 1.91x throughput boost compared to state-of-the-art serving systems achieving 59% to 72% of optimal throughput across ported models.

Based on the theory of homogeneous spaces we derive geometrically optimal edge attributes to be used within the flexible message-passing framework. We formalize the notion of weight sharing in convolutional networks as the sharing of message functions over point-pairs that should be treated equally. We define equivalence classes of point-pairs that are identical up to a transformation in the group and derive attributes that uniquely identify these classes. Weight sharing is then obtained by conditioning message functions on these attributes. As an application of the theory, we develop an efficient equivariant group convolutional network for processing 3D point clouds. The theory of homogeneous spaces tells us how to do group convolutions with feature maps over the homogeneous space of positions R^3, position and orientations R^3 {times} S^2, and the group SE(3) itself. Among these, R^3 {times} S^2 is an optimal choice due to the ability to represent directional information, which R^3 methods cannot, and it significantly enhances computational efficiency compared to indexing features on the full SE(3) group. We support this claim with state-of-the-art results -- in accuracy and speed -- on five different benchmarks in 2D and 3D, including interatomic potential energy prediction, trajectory forecasting in N-body systems, and generating molecules via equivariant diffusion models.

A modern challenge of Artificial Intelligence is learning multiple patterns at once (i.e.parallel learning). While this can not be accomplished by standard Hebbian associative neural networks, in this paper we show how the Multitasking Hebbian Network (a variation on theme of the Hopfield model working on sparse data-sets) is naturally able to perform this complex task. We focus on systems processing in parallel a finite (up to logarithmic growth in the size of the network) amount of patterns, mirroring the low-storage level of standard associative neural networks at work with pattern recognition. For mild dilution in the patterns, the network handles them hierarchically, distributing the amplitudes of their signals as power-laws w.r.t. their information content (hierarchical regime), while, for strong dilution, all the signals pertaining to all the patterns are raised with the same strength (parallel regime). Further, confined to the low-storage setting (i.e., far from the spin glass limit), the presence of a teacher neither alters the multitasking performances nor changes the thresholds for learning: the latter are the same whatever the training protocol is supervised or unsupervised. Results obtained through statistical mechanics, signal-to-noise technique and Monte Carlo simulations are overall in perfect agreement and carry interesting insights on multiple learning at once: for instance, whenever the cost-function of the model is minimized in parallel on several patterns (in its description via Statistical Mechanics), the same happens to the standard sum-squared error Loss function (typically used in Machine Learning).

Large-scale distributed training in production datacenters constitutes a challenging workload bottlenecked by network communication. In response, both major industry players (e.g., Ultra Ethernet Consortium) and parts of academia have surprisingly, and almost unanimously, agreed that packet spraying is necessary to improve the performance of large-scale distributed training workloads. In this paper, we challenge this prevailing belief and pose the question: How close can a singlepath transport approach an optimal multipath transport? We demonstrate that singlepath transport (from a NIC's perspective) is sufficient and can perform nearly as well as an ideal multipath transport with packet spraying, particularly in the context of distributed training in leaf-spine topologies. Our assertion is based on four key observations about workloads driven by collective communication patterns: (i) flows within a collective start almost simultaneously, (ii) flow sizes are nearly equal, (iii) the completion time of a collective is more crucial than individual flow completion times, and (iv) flows can be split upon arrival. We analytically prove that singlepath transport, using minimal flow splitting (at the application layer), is equivalent to an ideal multipath transport with packet spraying in terms of maximum congestion. Our preliminary evaluations support our claims. This paper suggests an alternative agenda for developing next-generation transport protocols tailored for large-scale distributed training.

Understanding the glassy nature of neural networks is pivotal both for theoretical and computational advances in Machine Learning and Theoretical Artificial Intelligence. Keeping the focus on dense associative Hebbian neural networks, the purpose of this paper is two-fold: at first we develop rigorous mathematical approaches to address properly a statistical mechanical picture of the phenomenon of {\em replica symmetry breaking} (RSB) in these networks, then -- deepening results stemmed via these routes -- we aim to inspect the {\em glassiness} that they hide. In particular, regarding the methodology, we provide two techniques: the former is an adaptation of the transport PDE to the case, while the latter is an extension of Guerra's interpolation breakthrough. Beyond coherence among the results, either in replica symmetric and in the one-step replica symmetry breaking level of description, we prove the Gardner's picture and we identify the maximal storage capacity by a ground-state analysis in the Baldi-Venkatesh high-storage regime. In the second part of the paper we investigate the glassy structure of these networks: in contrast with the replica symmetric scenario (RS), RSB actually stabilizes the spin-glass phase. We report huge differences w.r.t. the standard pairwise Hopfield limit: in particular, it is known that it is possible to express the free energy of the Hopfield neural network as a linear combination of the free energies of an hard spin glass (i.e. the Sherrington-Kirkpatrick model) and a soft spin glass (the Gaussian or "spherical" model). This is no longer true when interactions are more than pairwise (whatever the level of description, RS or RSB): for dense networks solely the free energy of the hard spin glass survives, proving a huge diversity in the underlying glassiness of associative neural networks.

The widespread of Large Language Models (LLMs) marks a significant milestone in generative AI. Nevertheless, the increasing context length and batch size in offline LLM inference escalate the memory requirement of the key-value (KV) cache, which imposes a huge burden on the GPU VRAM, especially for resource-constraint scenarios (e.g., edge computing and personal devices). Several cost-effective solutions leverage host memory or SSDs to reduce storage costs for offline inference scenarios and improve the throughput. Nevertheless, they suffer from significant performance penalties imposed by intensive KV cache accesses due to limited PCIe bandwidth. To address these issues, we propose InstInfer, a novel LLM inference system that offloads the most performance-critical computation (i.e., attention in decoding phase) and data (i.e., KV cache) parts to Computational Storage Drives (CSDs), which minimize the enormous KV transfer overheads. InstInfer designs a dedicated flash-aware in-storage attention engine with KV cache management mechanisms to exploit the high internal bandwidths of CSDs instead of being limited by the PCIe bandwidth. The optimized P2P transmission between GPU and CSDs further reduces data migration overheads. Experimental results demonstrate that for a 13B model using an NVIDIA A6000 GPU, InstInfer improves throughput for long-sequence inference by up to 11.1times, compared to existing SSD-based solutions such as FlexGen.

Superconducting Digital (SCD) technology offers significant potential for enhancing the performance of next generation large scale compute workloads. By leveraging advanced lithography and a 300 mm platform, SCD devices can reduce energy consumption and boost computational power. This paper presents a cross-layer modeling approach to evaluate the system-level performance benefits of SCD architectures for Large Language Model (LLM) training and inference. Our findings, based on experimental data and Pulse Conserving Logic (PCL) design principles, demonstrate substantial performance gain in both training and inference. We are, thus, able to convincingly show that the SCD technology can address memory and interconnect limitations of present day solutions for next-generation compute systems.

Hyperdimensional computing (HD), also known as vector symbolic architectures (VSA), is a framework for computing with distributed representations by exploiting properties of random high-dimensional vector spaces. The commitment of the scientific community to aggregate and disseminate research in this particularly multidisciplinary area has been fundamental for its advancement. Joining these efforts, we present Torchhd, a high-performance open source Python library for HD/VSA. Torchhd seeks to make HD/VSA more accessible and serves as an efficient foundation for further research and application development. The easy-to-use library builds on top of PyTorch and features state-of-the-art HD/VSA functionality, clear documentation, and implementation examples from well-known publications. Comparing publicly available code with their corresponding Torchhd implementation shows that experiments can run up to 100x faster. Torchhd is available at: https://github.com/hyperdimensional-computing/torchhd.

Iterative improvement of model architectures is fundamental to deep learning: Transformers first enabled scaling, and recent advances in model hybridization have pushed the quality-efficiency frontier. However, optimizing architectures remains challenging and expensive. Current automated or manual approaches fall short, largely due to limited progress in the design of search spaces and due to the simplicity of resulting patterns and heuristics. In this work, we propose a new approach for the synthesis of tailored architectures (STAR). Our approach combines a novel search space based on the theory of linear input-varying systems, supporting a hierarchical numerical encoding into architecture genomes. STAR genomes are automatically refined and recombined with gradient-free, evolutionary algorithms to optimize for multiple model quality and efficiency metrics. Using STAR, we optimize large populations of new architectures, leveraging diverse computational units and interconnection patterns, improving over highly-optimized Transformers and striped hybrid models on the frontier of quality, parameter size, and inference cache for autoregressive language modeling.

Stochastic gradient Markov Chain Monte Carlo (SGMCMC) is considered the gold standard for Bayesian inference in large-scale models, such as Bayesian neural networks. Since practitioners face speed versus accuracy tradeoffs in these models, variational inference (VI) is often the preferable option. Unfortunately, VI makes strong assumptions on both the factorization and functional form of the posterior. In this work, we propose a new non-parametric variational approximation that makes no assumptions about the approximate posterior's functional form and allows practitioners to specify the exact dependencies the algorithm should respect or break. The approach relies on a new Langevin-type algorithm that operates on a modified energy function, where parts of the latent variables are averaged over samples from earlier iterations of the Markov chain. This way, statistical dependencies can be broken in a controlled way, allowing the chain to mix faster. This scheme can be further modified in a "dropout" manner, leading to even more scalability. We test our scheme for ResNet-20 on CIFAR-10, SVHN, and FMNIST. In all cases, we find improvements in convergence speed and/or final accuracy compared to SG-MCMC and VI.

It has been shown that a message passing neural networks (MPNNs), a popular family of neural networks for graph-structured data, are at most as expressive as the first-order Weisfeiler-Leman (1-WL) graph isomorphism test, which has motivated the development of more expressive architectures. In this work, we analyze if the limited expressiveness is actually a limiting factor for MPNNs and other WL-based models in standard graph datasets. Interestingly, we find that the expressiveness of WL is sufficient to identify almost all graphs in most datasets. Moreover, we find that the classification accuracy upper bounds are often close to 100\%. Furthermore, we find that simple WL-based neural networks and several MPNNs can be fitted to several datasets. In sum, we conclude that the performance of WL/MPNNs is not limited by their expressiveness in practice.

Recently, 3D Gaussian Splatting, as a novel 3D representation, has garnered attention for its fast rendering speed and high rendering quality. However, this comes with high memory consumption, e.g., a well-trained Gaussian field may utilize three million Gaussian primitives and over 700 MB of memory. We credit this high memory footprint to the lack of consideration for the relationship between primitives. In this paper, we propose a memory-efficient Gaussian field named SUNDAE with spectral pruning and neural compensation. On one hand, we construct a graph on the set of Gaussian primitives to model their relationship and design a spectral down-sampling module to prune out primitives while preserving desired signals. On the other hand, to compensate for the quality loss of pruning Gaussians, we exploit a lightweight neural network head to mix splatted features, which effectively compensates for quality losses while capturing the relationship between primitives in its weights. We demonstrate the performance of SUNDAE with extensive results. For example, SUNDAE can achieve 26.80 PSNR at 145 FPS using 104 MB memory while the vanilla Gaussian splatting algorithm achieves 25.60 PSNR at 160 FPS using 523 MB memory, on the Mip-NeRF360 dataset. Codes are publicly available at https://runyiyang.github.io/projects/SUNDAE/.

Albeit being a prevalent architecture searching approach, differentiable architecture search (DARTS) is largely hindered by its substantial memory cost since the entire supernet resides in the memory. This is where the single-path DARTS comes in, which only chooses a single-path submodel at each step. While being memory-friendly, it also comes with low computational costs. Nonetheless, we discover a critical issue of single-path DARTS that has not been primarily noticed. Namely, it also suffers from severe performance collapse since too many parameter-free operations like skip connections are derived, just like DARTS does. In this paper, we propose a new algorithm called RObustifying Memory-Efficient NAS (ROME) to give a cure. First, we disentangle the topology search from the operation search to make searching and evaluation consistent. We then adopt Gumbel-Top2 reparameterization and gradient accumulation to robustify the unwieldy bi-level optimization. We verify ROME extensively across 15 benchmarks to demonstrate its effectiveness and robustness.

The Cambrian explosion of easily accessible pre-trained diffusion models suggests a demand for methods that combine multiple different pre-trained diffusion models without incurring the significant computational burden of re-training a larger combined model. In this paper, we cast the problem of combining multiple pre-trained diffusion models at the generation stage under a novel proposed framework termed superposition. Theoretically, we derive superposition from rigorous first principles stemming from the celebrated continuity equation and design two novel algorithms tailor-made for combining diffusion models in SuperDiff. SuperDiff leverages a new scalable It\^o density estimator for the log likelihood of the diffusion SDE which incurs no additional overhead compared to the well-known Hutchinson's estimator needed for divergence calculations. We demonstrate that SuperDiff is scalable to large pre-trained diffusion models as superposition is performed solely through composition during inference, and also enjoys painless implementation as it combines different pre-trained vector fields through an automated re-weighting scheme. Notably, we show that SuperDiff is efficient during inference time, and mimics traditional composition operators such as the logical OR and the logical AND. We empirically demonstrate the utility of using SuperDiff for generating more diverse images on CIFAR-10, more faithful prompt conditioned image editing using Stable Diffusion, and improved unconditional de novo structure design of proteins. https://github.com/necludov/super-diffusion

Neural networks can be significantly compressed by pruning, yielding sparse models with reduced storage and computational demands while preserving predictive performance. Model soups (Wortsman et al., 2022) enhance generalization and out-of-distribution (OOD) performance by averaging the parameters of multiple models into a single one, without increasing inference time. However, achieving both sparsity and parameter averaging is challenging as averaging arbitrary sparse models reduces the overall sparsity due to differing sparse connectivities. This work addresses these challenges by demonstrating that exploring a single retraining phase of Iterative Magnitude Pruning (IMP) with varied hyperparameter configurations such as batch ordering or weight decay yields models suitable for averaging, sharing identical sparse connectivity by design. Averaging these models significantly enhances generalization and OOD performance over their individual counterparts. Building on this, we introduce Sparse Model Soups (SMS), a novel method for merging sparse models by initiating each prune-retrain cycle with the averaged model from the previous phase. SMS preserves sparsity, exploits sparse network benefits, is modular and fully parallelizable, and substantially improves IMP's performance. We further demonstrate that SMS can be adapted to enhance state-of-the-art pruning-during-training approaches.

Large-scale foundation models have demonstrated exceptional performance in language and vision tasks. However, the numerous dense matrix-vector operations involved in these large networks pose significant computational challenges during inference. To address these challenges, we introduce the Block-Level Adaptive STructured (BLAST) matrix, designed to learn and leverage efficient structures prevalent in the weight matrices of linear layers within deep learning models. Compared to existing structured matrices, the BLAST matrix offers substantial flexibility, as it can represent various types of structures that are either learned from data or computed from pre-existing weight matrices. We demonstrate the efficiency of using the BLAST matrix for compressing both language and vision tasks, showing that (i) for medium-sized models such as ViT and GPT-2, training with BLAST weights boosts performance while reducing complexity by 70% and 40%, respectively; and (ii) for large foundation models such as Llama-7B and DiT-XL, the BLAST matrix achieves a 2x compression while exhibiting the lowest performance degradation among all tested structured matrices. Our code is available at https://github.com/changwoolee/BLAST.

In this paper, we propose a highly parameter-efficient approach to scaling pre-trained language models (PLMs) to a deeper model depth. Unlike prior work that shares all parameters or uses extra blocks, we design a more capable parameter-sharing architecture based on matrix product operator (MPO). MPO decomposition can reorganize and factorize the information of a parameter matrix into two parts: the major part that contains the major information (central tensor) and the supplementary part that only has a small proportion of parameters (auxiliary tensors). Based on such a decomposition, our architecture shares the central tensor across all layers for reducing the model size and meanwhile keeps layer-specific auxiliary tensors (also using adapters) for enhancing the adaptation flexibility. To improve the model training, we further propose a stable initialization algorithm tailored for the MPO-based architecture. Extensive experiments have demonstrated the effectiveness of our proposed model in reducing the model size and achieving highly competitive performance.

The ever-growing complexity of reinforcement learning (RL) tasks demands a distributed RL system to efficiently generate and process a massive amount of data to train intelligent agents. However, existing open-source libraries suffer from various limitations, which impede their practical use in challenging scenarios where large-scale training is necessary. While industrial systems from OpenAI and DeepMind have achieved successful large-scale RL training, their system architecture and implementation details remain undisclosed to the community. In this paper, we present a novel abstraction on the dataflows of RL training, which unifies practical RL training across diverse applications into a general framework and enables fine-grained optimizations. Following this abstraction, we develop a scalable, efficient, and extensible distributed RL system called ReaLly Scalable RL (SRL). The system architecture of SRL separates major RL computation components and allows massively parallelized training. Moreover, SRL offers user-friendly and extensible interfaces for customized algorithms. Our evaluation shows that SRL outperforms existing academic libraries in both a single machine and a medium-sized cluster. In a large-scale cluster, the novel architecture of SRL leads to up to 3.7x speedup compared to the design choices adopted by the existing libraries. We also conduct a direct benchmark comparison to OpenAI's industrial system, Rapid, in the challenging hide-and-seek environment. SRL reproduces the same solution as reported by OpenAI with up to 5x speedup in wall-clock time. Furthermore, we also examine the performance of SRL in a much harder variant of the hide-and-seek environment and achieve substantial learning speedup by scaling SRL to over 15k CPU cores and 32 A100 GPUs. Notably, SRL is the first in the academic community to perform RL experiments at such a large scale.

Generative models trained on internet-scale data are capable of generating novel and realistic texts, images, and videos. A natural next question is whether these models can advance science, for example by generating novel stable materials. Traditionally, models with explicit structures (e.g., graphs) have been used in modeling structural relationships in scientific data (e.g., atoms and bonds in crystals), but generating structures can be difficult to scale to large and complex systems. Another challenge in generating materials is the mismatch between standard generative modeling metrics and downstream applications. For instance, common metrics such as the reconstruction error do not correlate well with the downstream goal of discovering stable materials. In this work, we tackle the scalability challenge by developing a unified crystal representation that can represent any crystal structure (UniMat), followed by training a diffusion probabilistic model on these UniMat representations. Our empirical results suggest that despite the lack of explicit structure modeling, UniMat can generate high fidelity crystal structures from larger and more complex chemical systems, outperforming previous graph-based approaches under various generative modeling metrics. To better connect the generation quality of materials to downstream applications, such as discovering novel stable materials, we propose additional metrics for evaluating generative models of materials, including per-composition formation energy and stability with respect to convex hulls through decomposition energy from Density Function Theory (DFT). Lastly, we show that conditional generation with UniMat can scale to previously established crystal datasets with up to millions of crystals structures, outperforming random structure search (the current leading method for structure discovery) in discovering new stable materials.

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based tasks, but their direct adaptation to tasks involving protein structures remains a challenge. In contrast, structure-based methods leverage 3D structural information with graph neural networks and geometric pre-training methods show potential in function prediction tasks, but still suffers from the limited number of available structures. To bridge this gap, our study undertakes a comprehensive exploration of joint protein representation learning by integrating a state-of-the-art PLM (ESM-2) with distinct structure encoders (GVP, GearNet, CDConv). We introduce three representation fusion strategies and explore different pre-training techniques. Our method achieves significant improvements over existing sequence- and structure-based methods, setting new state-of-the-art for function annotation. This study underscores several important design choices for fusing protein sequence and structure information. Our implementation is available at https://github.com/DeepGraphLearning/ESM-GearNet.

For a broad range of research, governmental and commercial applications it is important to understand the allegiances, communities and structure of key players in society. One promising direction towards extracting this information is to exploit the rich relational data in digital social networks (the social graph). As social media data sets are very large, most approaches make use of distributed computing systems for this purpose. Distributing graph processing requires solving many difficult engineering problems, which has lead some researchers to look at single-machine solutions that are faster and easier to maintain. In this article, we present a single-machine real-time system for large-scale graph processing that allows analysts to interactively explore graph structures. The key idea is that the aggregate actions of large numbers of users can be compressed into a data structure that encapsulates user similarities while being robust to noise and queryable in real-time. We achieve single machine real-time performance by compressing the neighbourhood of each vertex using minhash signatures and facilitate rapid queries through Locality Sensitive Hashing. These techniques reduce query times from hours using industrial desktop machines operating on the full graph to milliseconds on standard laptops. Our method allows exploration of strongly associated regions (i.e. communities) of large graphs in real-time on a laptop. It has been deployed in software that is actively used by social network analysts and offers another channel for media owners to monetise their data, helping them to continue to provide free services that are valued by billions of people globally.

Quantization is a widely-used compression technology to reduce the overhead of serving large language models (LLMs) on terminal devices and in cloud data centers. However, prevalent quantization methods, such as 8-bit weight-activation or 4-bit weight-only quantization, achieve limited performance improvements due to poor support for low-precision (e.g., 4-bit) activation. This work, for the first time, realizes practical W4A4KV4 serving for LLMs, fully utilizing the INT4 tensor cores on modern GPUs and reducing the memory bottleneck caused by the KV cache. Specifically, we propose a novel fine-grained mixed-precision quantization algorithm (FMPQ) that compresses most activations into 4-bit with negligible accuracy loss. To support mixed-precision matrix multiplication for W4A4 and W4A8, we develop a highly optimized W4Ax kernel. Our approach introduces a novel mixed-precision data layout to facilitate access and fast dequantization for activation and weight tensors, utilizing the GPU's software pipeline to hide the overhead of data loading and conversion. Additionally, we propose fine-grained streaming multiprocessor (SM) scheduling to achieve load balance across different SMs. We integrate the optimized W4Ax kernel into our inference framework, COMET, and provide efficient management to support popular LLMs such as LLaMA-3-70B. Extensive evaluations demonstrate that, when running LLaMA family models on a single A100-80G-SMX4, COMET achieves a kernel-level speedup of 2.88times over cuBLAS and a 2.02 times throughput improvement compared to TensorRT-LLM from an end-to-end framework perspective.

Neural Architecture Search (NAS) has gained significant popularity as an effective tool for designing high performance deep neural networks (DNNs). NAS can be performed via policy gradient, evolutionary algorithms, differentiable architecture search or tree-search methods. While significant progress has been made for both policy gradient and differentiable architecture search, tree-search methods have so far failed to achieve comparable accuracy or search efficiency. In this paper, we formulate NAS as a Combinatorial Multi-Armed Bandit (CMAB) problem (CMAB-NAS). This allows the decomposition of a large search space into smaller blocks where tree-search methods can be applied more effectively and efficiently. We further leverage a tree-based method called Nested Monte-Carlo Search to tackle the CMAB-NAS problem. On CIFAR-10, our approach discovers a cell structure that achieves a low error rate that is comparable to the state-of-the-art, using only 0.58 GPU days, which is 20 times faster than current tree-search methods. Moreover, the discovered structure transfers well to large-scale datasets such as ImageNet.

Consistency models (CMs) are a powerful class of diffusion-based generative models optimized for fast sampling. Most existing CMs are trained using discretized timesteps, which introduce additional hyperparameters and are prone to discretization errors. While continuous-time formulations can mitigate these issues, their success has been limited by training instability. To address this, we propose a simplified theoretical framework that unifies previous parameterizations of diffusion models and CMs, identifying the root causes of instability. Based on this analysis, we introduce key improvements in diffusion process parameterization, network architecture, and training objectives. These changes enable us to train continuous-time CMs at an unprecedented scale, reaching 1.5B parameters on ImageNet 512x512. Our proposed training algorithm, using only two sampling steps, achieves FID scores of 2.06 on CIFAR-10, 1.48 on ImageNet 64x64, and 1.88 on ImageNet 512x512, narrowing the gap in FID scores with the best existing diffusion models to within 10%.

Spiking Neural Networks (SNNs), known for their biologically plausible architecture, face the challenge of limited performance. The self-attention mechanism, which is the cornerstone of the high-performance Transformer and also a biologically inspired structure, is absent in existing SNNs. To this end, we explore the potential of leveraging both self-attention capability and biological properties of SNNs, and propose a novel Spiking Self-Attention (SSA) and Spiking Transformer (Spikformer). The SSA mechanism eliminates the need for softmax and captures the sparse visual feature employing spike-based Query, Key, and Value. This sparse computation without multiplication makes SSA efficient and energy-saving. Further, we develop a Spiking Convolutional Stem (SCS) with supplementary convolutional layers to enhance the architecture of Spikformer. The Spikformer enhanced with the SCS is referred to as Spikformer V2. To train larger and deeper Spikformer V2, we introduce a pioneering exploration of Self-Supervised Learning (SSL) within the SNN. Specifically, we pre-train Spikformer V2 with masking and reconstruction style inspired by the mainstream self-supervised Transformer, and then finetune the Spikformer V2 on the image classification on ImageNet. Extensive experiments show that Spikformer V2 outperforms other previous surrogate training and ANN2SNN methods. An 8-layer Spikformer V2 achieves an accuracy of 80.38% using 4 time steps, and after SSL, a 172M 16-layer Spikformer V2 reaches an accuracy of 81.10% with just 1 time step. To the best of our knowledge, this is the first time that the SNN achieves 80+% accuracy on ImageNet. The code will be available at Spikformer V2.

The design of novel protein structures remains a challenge in protein engineering for applications across biomedicine and chemistry. In this line of work, a diffusion model over rigid bodies in 3D (referred to as frames) has shown success in generating novel, functional protein backbones that have not been observed in nature. However, there exists no principled methodological framework for diffusion on SE(3), the space of orientation preserving rigid motions in R3, that operates on frames and confers the group invariance. We address these shortcomings by developing theoretical foundations of SE(3) invariant diffusion models on multiple frames followed by a novel framework, FrameDiff, for learning the SE(3) equivariant score over multiple frames. We apply FrameDiff on monomer backbone generation and find it can generate designable monomers up to 500 amino acids without relying on a pretrained protein structure prediction network that has been integral to previous methods. We find our samples are capable of generalizing beyond any known protein structure.

The Schr\"odinger Bridge (SB) problem offers a powerful framework for combining optimal transport and diffusion models. A promising recent approach to solve the SB problem is the Iterative Markovian Fitting (IMF) procedure, which alternates between Markovian and reciprocal projections of continuous-time stochastic processes. However, the model built by the IMF procedure has a long inference time due to using many steps of numerical solvers for stochastic differential equations. To address this limitation, we propose a novel Discrete-time IMF (D-IMF) procedure in which learning of stochastic processes is replaced by learning just a few transition probabilities in discrete time. Its great advantage is that in practice it can be naturally implemented using the Denoising Diffusion GAN (DD-GAN), an already well-established adversarial generative modeling technique. We show that our D-IMF procedure can provide the same quality of unpaired domain translation as the IMF, using only several generation steps instead of hundreds. We provide the code at https://github.com/Daniil-Selikhanovych/ASBM.

Hyperdimensional computing (HDC) is a biologically-inspired framework which represents symbols with high-dimensional vectors, and uses vector operations to manipulate them. The ensemble of a particular vector space and a prescribed set of vector operations (including one addition-like for "bundling" and one outer-product-like for "binding") form a *vector symbolic architecture* (VSA). While VSAs have been employed in numerous applications and have been studied empirically, many theoretical questions about VSAs remain open. We analyze the *representation capacities* of four common VSAs: MAP-I, MAP-B, and two VSAs based on sparse binary vectors. "Representation capacity' here refers to bounds on the dimensions of the VSA vectors required to perform certain symbolic tasks, such as testing for set membership i in S and estimating set intersection sizes |X cap Y| for two sets of symbols X and Y, to a given degree of accuracy. We also analyze the ability of a novel variant of a Hopfield network (a simple model of associative memory) to perform some of the same tasks that are typically asked of VSAs. In addition to providing new bounds on VSA capacities, our analyses establish and leverage connections between VSAs, "sketching" (dimensionality reduction) algorithms, and Bloom filters.