Reactzyme: A Benchmark for Enzyme-Reaction Prediction

Enzymes, with their specific catalyzed reactions, are necessary for all aspects of life, enabling diverse biological processes and adaptations. Predicting enzyme functions is essential for understanding biological pathways, guiding drug development, enhancing bioproduct yields, and facilitating evolutionary studies. Addressing the inherent complexities, we introduce a new approach to annotating enzymes based on their catalyzed reactions. This method provides detailed insights into specific reactions and is adaptable to newly discovered reactions, diverging from traditional classifications by protein family or expert-derived reaction classes. We employ machine learning algorithms to analyze enzyme reaction datasets, delivering a much more refined view on the functionality of enzymes. Our evaluation leverages the largest enzyme-reaction dataset to date, derived from the SwissProt and Rhea databases with entries up to January 8, 2024. We frame the enzyme-reaction prediction as a retrieval problem, aiming to rank enzymes by their catalytic ability for specific reactions. With our model, we can recruit proteins for novel reactions and predict reactions in novel proteins, facilitating enzyme discovery and function annotation.

Functional Acceleration for Policy Mirror Descent

We apply functional acceleration to the Policy Mirror Descent (PMD) general family of algorithms, which cover a wide range of novel and fundamental methods in Reinforcement Learning (RL). Leveraging duality, we propose a momentum-based PMD update. By taking the functional route, our approach is independent of the policy parametrization and applicable to large-scale optimization, covering previous applications of momentum at the level of policy parameters as a special case. We theoretically analyze several properties of this approach and complement with a numerical ablation study, which serves to illustrate the policy optimization dynamics on the value polytope, relative to different algorithmic design choices in this space. We further characterize numerically several features of the problem setting relevant for functional acceleration, and lastly, we investigate the impact of approximation on their learning mechanics.

The Heterophilic Graph Learning Handbook: Benchmarks, Models, Theoretical Analysis, Applications and Challenges

Homophily principle, \ie{} nodes with the same labels or similar attributes are more likely to be connected, has been commonly believed to be the main reason for the superiority of Graph Neural Networks (GNNs) over traditional Neural Networks (NNs) on graph-structured data, especially on node-level tasks. However, recent work has identified a non-trivial set of datasets where GNN's performance compared to the NN's is not satisfactory. Heterophily, i.e. low homophily, has been considered the main cause of this empirical observation. People have begun to revisit and re-evaluate most existing graph models, including graph transformer and its variants, in the heterophily scenario across various kinds of graphs, e.g. heterogeneous graphs, temporal graphs and hypergraphs. Moreover, numerous graph-related applications are found to be closely related to the heterophily problem. In the past few years, considerable effort has been devoted to studying and addressing the heterophily issue. In this survey, we provide a comprehensive review of the latest progress on heterophilic graph learning, including an extensive summary of benchmark datasets and evaluation of homophily metrics on synthetic graphs, meticulous classification of the most updated supervised and unsupervised learning methods, thorough digestion of the theoretical analysis on homophily/heterophily, and broad exploration of the heterophily-related applications. Notably, through detailed experiments, we are the first to categorize benchmark heterophilic datasets into three sub-categories: malignant, benign and ambiguous heterophily. Malignant and ambiguous datasets are identified as the real challenging datasets to test the effectiveness of new models on the heterophily challenge. Finally, we propose several challenges and future directions for heterophilic graph representation learning.

More Efficient Randomized Exploration for Reinforcement Learning via Approximate Sampling

Thompson sampling (TS) is one of the most popular exploration techniques in reinforcement learning (RL). However, most TS algorithms with theoretical guarantees are difficult to implement and not generalizable to Deep RL. While the emerging approximate sampling-based exploration schemes are promising, most existing algorithms are specific to linear Markov Decision Processes (MDP) with suboptimal regret bounds, or only use the most basic samplers such as Langevin Monte Carlo. In this work, we propose an algorithmic framework that incorporates different approximate sampling methods with the recently proposed Feel-Good Thompson Sampling (FGTS) approach (Zhang, 2022; Dann et al., 2021), which was previously known to be computationally intractable in general. When applied to linear MDPs, our regret analysis yields the best known dependency of regret on dimensionality, surpassing existing randomized algorithms. Additionally, we provide explicit sampling complexity for each employed sampler. Empirically, we show that in tasks where deep exploration is necessary, our proposed algorithms that combine FGTS and approximate sampling perform significantly better compared to other strong baselines. On several challenging games from the Atari 57 suite, our algorithms achieve performance that is either better than or on par with other strong baselines from the deep RL literature.

On the Limits of Multi-modal Meta-Learning with Auxiliary Task Modulation Using Conditional Batch Normalization

Few-shot learning aims to learn representations that can tackle novel tasks given a small number of examples. Recent studies show that cross-modal learning can improve representations for few-shot classification. More specifically, language is a rich modality that can be used to guide visual learning. In this work, we experiment with a multi-modal architecture for few-shot learning that consists of three components: a classifier, an auxiliary network, and a bridge network. While the classifier performs the main classification task, the auxiliary network learns to predict language representations from the same input, and the bridge network transforms high-level features of the auxiliary network into modulation parameters for layers of the few-shot classifier using conditional batch normalization. The bridge should encourage a form of lightweight semantic alignment between language and vision which could be useful for the classifier. However, after evaluating the proposed approach on two popular few-shot classification benchmarks we find that a) the improvements do not reproduce across benchmarks, and b) when they do, the improvements are due to the additional compute and parameters introduced by the bridge network. We contribute insights and recommendations for future work in multi-modal meta-learning, especially when using language representations.

Partial Models for Building Adaptive Model-Based Reinforcement Learning Agents

In neuroscience, one of the key behavioral tests for determining whether a subject of study exhibits model-based behavior is to study its adaptiveness to local changes in the environment. In reinforcement learning, however, recent studies have shown that modern model-based agents display poor adaptivity to such changes. The main reason for this is that modern agents are typically designed to improve sample efficiency in single task settings and thus do not take into account the challenges that can arise in other settings. In local adaptation settings, one particularly important challenge is in quickly building and maintaining a sufficiently accurate model after a local change. This is challenging for deep model-based agents as their models and replay buffers are monolithic structures lacking distribution shift handling capabilities. In this study, we show that the conceptually simple idea of partial models can allow deep model-based agents to overcome this challenge and thus allow for building locally adaptive model-based agents. By modeling the different parts of the state space through different models, the agent can not only maintain a model that is accurate across the state space, but it can also quickly adapt it in the presence of a local change in the environment. We demonstrate this by showing that the use of partial models in agents such as deep Dyna-Q, PlaNet and Dreamer can allow for them to effectively adapt to the local changes in their environments.

Adaptive Exploration for Data-Efficient General Value Function Evaluations

General Value Functions (GVFs) (Sutton et al, 2011) are an established way to represent predictive knowledge in reinforcement learning. Each GVF computes the expected return for a given policy, based on a unique pseudo-reward. Multiple GVFs can be estimated in parallel using off-policy learning from a single stream of data, often sourced from a fixed behavior policy or pre-collected dataset. This leaves an open question: how can behavior policy be chosen for data-efficient GVF learning? To address this gap, we propose GVFExplorer, which aims at learning a behavior policy that efficiently gathers data for evaluating multiple GVFs in parallel. This behavior policy selects actions in proportion to the total variance in the return across all GVFs, reducing the number of environmental interactions. To enable accurate variance estimation, we use a recently proposed temporal-difference-style variance estimator. We prove that each behavior policy update reduces the mean squared error in the summed predictions over all GVFs. We empirically demonstrate our method's performance in both tabular representations and nonlinear function approximation.

Generative Active Learning for the Search of Small-molecule Protein Binders

Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exhibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.

Offline Multitask Representation Learning for Reinforcement Learning

We study offline multitask representation learning in reinforcement learning (RL), where a learner is provided with an offline dataset from different tasks that share a common representation and is asked to learn the shared representation. We theoretically investigate offline multitask low-rank RL, and propose a new algorithm called MORL for offline multitask representation learning. Furthermore, we examine downstream RL in reward-free, offline and online scenarios, where a new task is introduced to the agent that shares the same representation as the upstream offline tasks. Our theoretical results demonstrate the benefits of using the learned representation from the upstream offline task instead of directly learning the representation of the low-rank model.

Discrete Probabilistic Inference as Control in Multi-path Environments

We consider the problem of sampling from a discrete and structured distribution as a sequential decision problem, where the objective is to find a stochastic policy such that objects are sampled at the end of this sequential process proportionally to some predefined reward. While we could use maximum entropy Reinforcement Learning (MaxEnt RL) to solve this problem for some distributions, it has been shown that in general, the distribution over states induced by the optimal policy may be biased in cases where there are multiple ways to generate the same object. To address this issue, Generative Flow Networks (GFlowNets) learn a stochastic policy that samples objects proportionally to their reward by approximately enforcing a conservation of flows across the whole Markov Decision Process (MDP). In this paper, we extend recent methods correcting the reward in order to guarantee that the marginal distribution induced by the optimal MaxEnt RL policy is proportional to the original reward, regardless of the structure of the underlying MDP. We also prove that some flow-matching objectives found in the GFlowNet literature are in fact equivalent to well-established MaxEnt RL algorithms with a corrected reward. Finally, we study empirically the performance of multiple MaxEnt RL and GFlowNet algorithms on multiple problems involving sampling from discrete distributions.