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Mar 12

REX: Revisiting Budgeted Training with an Improved Schedule

Deep learning practitioners often operate on a computational and monetary budget. Thus, it is critical to design optimization algorithms that perform well under any budget. The linear learning rate schedule is considered the best budget-aware schedule, as it outperforms most other schedules in the low budget regime. On the other hand, learning rate schedules -- such as the 30-60-90 step schedule -- are known to achieve high performance when the model can be trained for many epochs. Yet, it is often not known a priori whether one's budget will be large or small; thus, the optimal choice of learning rate schedule is made on a case-by-case basis. In this paper, we frame the learning rate schedule selection problem as a combination of i) selecting a profile (i.e., the continuous function that models the learning rate schedule), and ii) choosing a sampling rate (i.e., how frequently the learning rate is updated/sampled from this profile). We propose a novel profile and sampling rate combination called the Reflected Exponential (REX) schedule, which we evaluate across seven different experimental settings with both SGD and Adam optimizers. REX outperforms the linear schedule in the low budget regime, while matching or exceeding the performance of several state-of-the-art learning rate schedules (linear, step, exponential, cosine, step decay on plateau, and OneCycle) in both high and low budget regimes. Furthermore, REX requires no added computation, storage, or hyperparameters.

When, Why and How Much? Adaptive Learning Rate Scheduling by Refinement

Learning rate schedules used in practice bear little resemblance to those recommended by theory. We close much of this theory/practice gap, and as a consequence are able to derive new problem-adaptive learning rate schedules. Our key technical contribution is a refined analysis of learning rate schedules for a wide class of optimization algorithms (including SGD). In contrast to most prior works that study the convergence of the average iterate, we study the last iterate, which is what most people use in practice. When considering only worst-case analysis, our theory predicts that the best choice is the linear decay schedule: a popular choice in practice that sets the stepsize proportionally to 1 - t/T, where t is the current iteration and T is the total number of steps. To go beyond this worst-case analysis, we use the observed gradient norms to derive schedules refined for any particular task. These refined schedules exhibit learning rate warm-up and rapid learning rate annealing near the end of training. Ours is the first systematic approach to automatically yield both of these properties. We perform the most comprehensive evaluation of learning rate schedules to date, evaluating across 10 diverse deep learning problems, a series of LLMs, and a suite of logistic regression problems. We validate that overall, the linear-decay schedule matches or outperforms all commonly used default schedules including cosine annealing, and that our schedule refinement method gives further improvements.

AutoLRS: Automatic Learning-Rate Schedule by Bayesian Optimization on the Fly

The learning rate (LR) schedule is one of the most important hyper-parameters needing careful tuning in training DNNs. However, it is also one of the least automated parts of machine learning systems and usually costs significant manual effort and computing. Though there are pre-defined LR schedules and optimizers with adaptive LR, they introduce new hyperparameters that need to be tuned separately for different tasks/datasets. In this paper, we consider the question: Can we automatically tune the LR over the course of training without human involvement? We propose an efficient method, AutoLRS, which automatically optimizes the LR for each training stage by modeling training dynamics. AutoLRS aims to find an LR applied to every tau steps that minimizes the resulted validation loss. We solve this black-box optimization on the fly by Bayesian optimization (BO). However, collecting training instances for BO requires a system to evaluate each LR queried by BO's acquisition function for tau steps, which is prohibitively expensive in practice. Instead, we apply each candidate LR for only tau'lltau steps and train an exponential model to predict the validation loss after tau steps. This mutual-training process between BO and the loss-prediction model allows us to limit the training steps invested in the BO search. We demonstrate the advantages and the generality of AutoLRS through extensive experiments of training DNNs for tasks from diverse domains using different optimizers. The LR schedules auto-generated by AutoLRS lead to a speedup of 1.22times, 1.43times, and 1.5times when training ResNet-50, Transformer, and BERT, respectively, compared to the LR schedules in their original papers, and an average speedup of 1.31times over state-of-the-art heavily-tuned LR schedules.

High-performance symbolic-numerics via multiple dispatch

As mathematical computing becomes more democratized in high-level languages, high-performance symbolic-numeric systems are necessary for domain scientists and engineers to get the best performance out of their machine without deep knowledge of code optimization. Naturally, users need different term types either to have different algebraic properties for them, or to use efficient data structures. To this end, we developed Symbolics.jl, an extendable symbolic system which uses dynamic multiple dispatch to change behavior depending on the domain needs. In this work we detail an underlying abstract term interface which allows for speed without sacrificing generality. We show that by formalizing a generic API on actions independent of implementation, we can retroactively add optimized data structures to our system without changing the pre-existing term rewriters. We showcase how this can be used to optimize term construction and give a 113x acceleration on general symbolic transformations. Further, we show that such a generic API allows for complementary term-rewriting implementations. We demonstrate the ability to swap between classical term-rewriting simplifiers and e-graph-based term-rewriting simplifiers. We showcase an e-graph ruleset which minimizes the number of CPU cycles during expression evaluation, and demonstrate how it simplifies a real-world reaction-network simulation to halve the runtime. Additionally, we show a reaction-diffusion partial differential equation solver which is able to be automatically converted into symbolic expressions via multiple dispatch tracing, which is subsequently accelerated and parallelized to give a 157x simulation speedup. Together, this presents Symbolics.jl as a next-generation symbolic-numeric computing environment geared towards modeling and simulation.

EHRMamba: Towards Generalizable and Scalable Foundation Models for Electronic Health Records

Transformers have significantly advanced the modeling of Electronic Health Records (EHR), yet their deployment in real-world healthcare is limited by several key challenges. Firstly, the quadratic computational cost and insufficient context length of these models pose significant obstacles for hospitals in processing the extensive medical histories typical in EHR data. Additionally, existing models employ separate finetuning for each clinical task, complicating maintenance in healthcare environments. Moreover, these models focus exclusively on either clinical prediction or EHR forecasting, lacking the flexibility to perform well across both. To overcome these limitations, we introduce EHRMamba, a robust foundation model built on the Mamba architecture. EHRMamba can process sequences up to four times longer than previous models due to its linear computational cost. We also introduce a novel approach to Multitask Prompted Finetuning (MTF) for EHR data, which enables EHRMamba to simultaneously learn multiple clinical tasks in a single finetuning phase, significantly enhancing deployment and cross-task generalization. Furthermore, our model leverages the HL7 FHIR data standard to simplify integration into existing hospital systems. Alongside EHRMamba, we open-source Odyssey, a toolkit designed to support the development and deployment of EHR foundation models, with an emphasis on data standardization and interpretability. Our evaluations on the MIMIC-IV dataset demonstrate that EHRMamba advances state-of-the-art performance across 6 major clinical tasks and excels in EHR forecasting, marking a significant leap forward in the field.

AutoNumerics-Zero: Automated Discovery of State-of-the-Art Mathematical Functions

Computers calculate transcendental functions by approximating them through the composition of a few limited-precision instructions. For example, an exponential can be calculated with a Taylor series. These approximation methods were developed over the centuries by mathematicians, who emphasized the attainability of arbitrary precision. Computers, however, operate on few limited precision types, such as the popular float32. In this study, we show that when aiming for limited precision, existing approximation methods can be outperformed by programs automatically discovered from scratch by a simple evolutionary algorithm. In particular, over real numbers, our method can approximate the exponential function reaching orders of magnitude more precision for a given number of operations when compared to previous approaches. More practically, over float32 numbers and constrained to less than 1 ULP of error, the same method attains a speedup over baselines by generating code that triggers better XLA/LLVM compilation paths. In other words, in both cases, evolution searched a vast space of possible programs, without knowledge of mathematics, to discover previously unknown optimized approximations to high precision, for the first time. We also give evidence that these results extend beyond the exponential. The ubiquity of transcendental functions suggests that our method has the potential to reduce the cost of scientific computing applications.

Fine-Tuning Discrete Diffusion Models via Reward Optimization with Applications to DNA and Protein Design

Recent studies have demonstrated the strong empirical performance of diffusion models on discrete sequences across domains from natural language to biological sequence generation. For example, in the protein inverse folding task, conditional diffusion models have achieved impressive results in generating natural-like sequences that fold back into the original structure. However, practical design tasks often require not only modeling a conditional distribution but also optimizing specific task objectives. For instance, we may prefer protein sequences with high stability. To address this, we consider the scenario where we have pre-trained discrete diffusion models that can generate natural-like sequences, as well as reward models that map sequences to task objectives. We then formulate the reward maximization problem within discrete diffusion models, analogous to reinforcement learning (RL), while minimizing the KL divergence against pretrained diffusion models to preserve naturalness. To solve this RL problem, we propose a novel algorithm, DRAKES, that enables direct backpropagation of rewards through entire trajectories generated by diffusion models, by making the originally non-differentiable trajectories differentiable using the Gumbel-Softmax trick. Our theoretical analysis indicates that our approach can generate sequences that are both natural-like and yield high rewards. While similar tasks have been recently explored in diffusion models for continuous domains, our work addresses unique algorithmic and theoretical challenges specific to discrete diffusion models, which arise from their foundation in continuous-time Markov chains rather than Brownian motion. Finally, we demonstrate the effectiveness of DRAKES in generating DNA and protein sequences that optimize enhancer activity and protein stability, respectively, important tasks for gene therapies and protein-based therapeutics.