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Exploiting Pretrained Biochemical Language Models for Targeted Drug Design

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

Efficient Online Reinforcement Learning Fine-Tuning Need Not Retain Offline Data

The modern paradigm in machine learning involves pre-training on diverse data, followed by task-specific fine-tuning. In reinforcement learning (RL), this translates to learning via offline RL on a diverse historical dataset, followed by rapid online RL fine-tuning using interaction data. Most RL fine-tuning methods require continued training on offline data for stability and performance. However, this is undesirable because training on diverse offline data is slow and expensive for large datasets, and in principle, also limit the performance improvement possible because of constraints or pessimism on offline data. In this paper, we show that retaining offline data is unnecessary as long as we use a properly-designed online RL approach for fine-tuning offline RL initializations. To build this approach, we start by analyzing the role of retaining offline data in online fine-tuning. We find that continued training on offline data is mostly useful for preventing a sudden divergence in the value function at the onset of fine-tuning, caused by a distribution mismatch between the offline data and online rollouts. This divergence typically results in unlearning and forgetting the benefits of offline pre-training. Our approach, Warm-start RL (WSRL), mitigates the catastrophic forgetting of pre-trained initializations using a very simple idea. WSRL employs a warmup phase that seeds the online RL run with a very small number of rollouts from the pre-trained policy to do fast online RL. The data collected during warmup helps ``recalibrate'' the offline Q-function to the online distribution, allowing us to completely discard offline data without destabilizing the online RL fine-tuning. We show that WSRL is able to fine-tune without retaining any offline data, and is able to learn faster and attains higher performance than existing algorithms irrespective of whether they retain offline data or not.

A Mixture-of-Expert Approach to RL-based Dialogue Management

Despite recent advancements in language models (LMs), their application to dialogue management (DM) problems and ability to carry on rich conversations remain a challenge. We use reinforcement learning (RL) to develop a dialogue agent that avoids being short-sighted (outputting generic utterances) and maximizes overall user satisfaction. Most existing RL approaches to DM train the agent at the word-level, and thus, have to deal with a combinatorially complex action space even for a medium-size vocabulary. As a result, they struggle to produce a successful and engaging dialogue even if they are warm-started with a pre-trained LM. To address this issue, we develop a RL-based DM using a novel mixture of expert language model (MoE-LM) that consists of (i) a LM capable of learning diverse semantics for conversation histories, (ii) a number of {\em specialized} LMs (or experts) capable of generating utterances corresponding to a particular attribute or personality, and (iii) a RL-based DM that performs dialogue planning with the utterances generated by the experts. Our MoE approach provides greater flexibility to generate sensible utterances with different intents and allows RL to focus on conversational-level DM. We compare it with SOTA baselines on open-domain dialogues and demonstrate its effectiveness both in terms of the diversity and sensibility of the generated utterances and the overall DM performance.

GaLore: Memory-Efficient LLM Training by Gradient Low-Rank Projection

Training Large Language Models (LLMs) presents significant memory challenges, predominantly due to the growing size of weights and optimizer states. Common memory-reduction approaches, such as low-rank adaptation (LoRA), add a trainable low-rank matrix to the frozen pre-trained weight in each layer, reducing trainable parameters and optimizer states. However, such approaches typically underperform training with full-rank weights in both pre-training and fine-tuning stages since they limit the parameter search to a low-rank subspace and alter the training dynamics, and further, may require full-rank warm start. In this work, we propose Gradient Low-Rank Projection (GaLore), a training strategy that allows full-parameter learning but is more memory-efficient than common low-rank adaptation methods such as LoRA. Our approach reduces memory usage by up to 65.5% in optimizer states while maintaining both efficiency and performance for pre-training on LLaMA 1B and 7B architectures with C4 dataset with up to 19.7B tokens, and on fine-tuning RoBERTa on GLUE tasks. Our 8-bit GaLore further reduces optimizer memory by up to 82.5% and total training memory by 63.3%, compared to a BF16 baseline. Notably, we demonstrate, for the first time, the feasibility of pre-training a 7B model on consumer GPUs with 24GB memory (e.g., NVIDIA RTX 4090) without model parallel, checkpointing, or offloading strategies.

Natural GaLore: Accelerating GaLore for memory-efficient LLM Training and Fine-tuning

Training LLMs presents significant memory challenges due to growing size of data, weights, and optimizer states. Techniques such as data and model parallelism, gradient checkpointing, and offloading strategies address this issue but are often infeasible due to hardware constraints. To mitigate memory usage, alternative methods like Parameter-Efficient-Fine-Tuning (PEFT) and GaLore approximate weights or optimizer states. PEFT methods, such as LoRA, have gained popularity for fine-tuning LLMs, though they require a full-rank warm start. In contrast, GaLore allows full-parameter learning while being more memory-efficient. This work introduces Natural GaLore, a simple drop in replacement for AdamW, which efficiently applies the inverse Empirical Fisher Information Matrix to low-rank gradients using Woodbury's Identity. We demonstrate that incorporating second-order information speeds up optimization significantly, especially when the iteration budget is limited. Empirical pretraining on 60M, 130M, 350M, and 1.1B parameter Llama models on C4 data demonstrate significantly lower perplexity over GaLore without additional memory overhead. By fine-tuning RoBERTa on the GLUE benchmark using Natural GaLore, we demonstrate significant reduction in gap 86.05% vs 86.28% for full-finetuning. Furthermore, fine-tuning the TinyLlama 1.1B model for function calling using the TinyAgent framework shows that Natural GaLore achieving 83.09% accuracy on the TinyAgent dataset, significantly outperforms 16-bit LoRA at 80.06% and even surpasses GPT4-Turbo by 4%, all while using 30% less memory. All code to reproduce the results are available at: https://github.com/selfsupervised-ai/Natural-GaLore.git

Self-Supervised Bot Play for Conversational Recommendation with Justifications

Conversational recommender systems offer the promise of interactive, engaging ways for users to find items they enjoy. We seek to improve conversational recommendation via three dimensions: 1) We aim to mimic a common mode of human interaction for recommendation: experts justify their suggestions, a seeker explains why they don't like the item, and both parties iterate through the dialog to find a suitable item. 2) We leverage ideas from conversational critiquing to allow users to flexibly interact with natural language justifications by critiquing subjective aspects. 3) We adapt conversational recommendation to a wider range of domains where crowd-sourced ground truth dialogs are not available. We develop a new two-part framework for training conversational recommender systems. First, we train a recommender system to jointly suggest items and justify its reasoning with subjective aspects. We then fine-tune this model to incorporate iterative user feedback via self-supervised bot-play. Experiments on three real-world datasets demonstrate that our system can be applied to different recommendation models across diverse domains to achieve superior performance in conversational recommendation compared to state-of-the-art methods. We also evaluate our model on human users, showing that systems trained under our framework provide more useful, helpful, and knowledgeable recommendations in warm- and cold-start settings.

Large Language Models to Enhance Bayesian Optimization

Bayesian optimization (BO) is a powerful approach for optimizing complex and expensive-to-evaluate black-box functions. Its importance is underscored in many applications, notably including hyperparameter tuning, but its efficacy depends on efficiently balancing exploration and exploitation. While there has been substantial progress in BO methods, striking this balance remains a delicate process. In this light, we present LLAMBO, a novel approach that integrates the capabilities of Large Language Models (LLM) within BO. At a high level, we frame the BO problem in natural language, enabling LLMs to iteratively propose and evaluate promising solutions conditioned on historical evaluations. More specifically, we explore how combining contextual understanding, few-shot learning proficiency, and domain knowledge of LLMs can improve model-based BO. Our findings illustrate that LLAMBO is effective at zero-shot warmstarting, and enhances surrogate modeling and candidate sampling, especially in the early stages of search when observations are sparse. Our approach is performed in context and does not require LLM finetuning. Additionally, it is modular by design, allowing individual components to be integrated into existing BO frameworks, or function cohesively as an end-to-end method. We empirically validate LLAMBO's efficacy on the problem of hyperparameter tuning, highlighting strong empirical performance across a range of diverse benchmarks, proprietary, and synthetic tasks.