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Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational biology. Recently, Large Language Models have shown great promise in solving certain biological tasks but current approaches are limited to a single sequence modality (DNA, RNA, or protein). Key problems in genomics intrinsically involve multiple modalities, but it remains unclear how to adapt general-purpose sequence models to those cases. In this work we propose a multi-modal model that connects DNA, RNA, and proteins by leveraging information from different pre-trained modality-specific encoders. We demonstrate its capabilities by applying it to the largely unsolved problem of predicting how multiple RNA transcript isoforms originate from the same gene (i.e. same DNA sequence) and map to different transcription expression levels across various human tissues. We show that our model, dubbed IsoFormer, is able to accurately predict differential transcript expression, outperforming existing methods and leveraging the use of multiple modalities. Our framework also achieves efficient transfer knowledge from the encoders pre-training as well as in between modalities. We open-source our model, paving the way for new multi-modal gene expression approaches.

Representation learning and \emph{de novo} generation of proteins are pivotal computational biology tasks. Whilst natural language processing (NLP) techniques have proven highly effective for protein sequence modelling, structure modelling presents a complex challenge, primarily due to its continuous and three-dimensional nature. Motivated by this discrepancy, we introduce an approach using a vector-quantized autoencoder that effectively tokenizes protein structures into discrete representations. This method transforms the continuous, complex space of protein structures into a manageable, discrete format with a codebook ranging from 4096 to 64000 tokens, achieving high-fidelity reconstructions with backbone root mean square deviations (RMSD) of approximately 1-5 \AA. To demonstrate the efficacy of our learned representations, we show that a simple GPT model trained on our codebooks can generate novel, diverse, and designable protein structures. Our approach not only provides representations of protein structure, but also mitigates the challenges of disparate modal representations and sets a foundation for seamless, multi-modal integration, enhancing the capabilities of computational methods in protein design.

Crystal structures are indispensable across various domains, from batteries to solar cells, and extensive research has been dedicated to predicting their properties based on their atomic configurations. However, prevailing Crystal Structure Prediction methods focus on identifying the most stable solutions that lie at the global minimum of the energy function. This approach overlooks other potentially interesting materials that lie in neighbouring local minima and have different material properties such as conductivity or resistance to deformation. By contrast, Quality-Diversity algorithms provide a promising avenue for Crystal Structure Prediction as they aim to find a collection of high-performing solutions that have diverse characteristics. However, it may also be valuable to optimise for the stability of crystal structures alongside other objectives such as magnetism or thermoelectric efficiency. Therefore, in this work, we harness the power of Multi-Objective Quality-Diversity algorithms in order to find crystal structures which have diverse features and achieve different trade-offs of objectives. We analyse our approach on 5 crystal systems and demonstrate that it is not only able to re-discover known real-life structures, but also find promising new ones. Moreover, we propose a method for illuminating the objective space to gain an understanding of what trade-offs can be achieved., Comment: Accepted GECCO 2024

QDax is an open-source library with a streamlined and modular API for Quality-Diversity (QD) optimization algorithms in Jax. The library serves as a versatile tool for optimization purposes, ranging from black-box optimization to continuous control. QDax offers implementations of popular QD, Neuroevolution, and Reinforcement Learning (RL) algorithms, supported by various examples. All the implementations can be just-in-time compiled with Jax, facilitating efficient execution across multiple accelerators, including GPUs and TPUs. These implementations effectively demonstrate the framework's flexibility and user-friendliness, easing experimentation for research purposes. Furthermore, the library is thoroughly documented and tested with 95\% coverage.

Self-supervised learning has brought about a revolutionary paradigm shift in various computing domains, including NLP, vision, and biology. Recent approaches involve pre-training transformer models on vast amounts of unlabeled data, serving as a starting point for efficiently solving downstream tasks. In reinforcement learning, researchers have recently adapted these approaches, developing models pre-trained on expert trajectories. This advancement enables the models to tackle a broad spectrum of tasks, ranging from robotics to recommendation systems. However, existing methods mostly rely on intricate pre-training objectives tailored to specific downstream applications. This paper conducts a comprehensive investigation of models, referred to as pre-trained action-state transformer agents (PASTA). Our study covers a unified methodology and covers an extensive set of general downstream tasks including behavioral cloning, offline RL, sensor failure robustness, and dynamics change adaptation. Our objective is to systematically compare various design choices and offer valuable insights that will aid practitioners in developing robust models. Key highlights of our study include tokenization at the component level for actions and states, the use of fundamental pre-training objectives such as next token prediction or masked language modeling, simultaneous training of models across multiple domains, and the application of various fine-tuning strategies. In this study, the developed models contain fewer than 7 million parameters allowing a broad community to use these models and reproduce our experiments. We hope that this study will encourage further research into the use of transformers with first principle design choices to represent RL trajectories and contribute to robust policy learning.

Quality Diversity (QD) algorithms have been proposed to search for a large collection of both diverse and high-performing solutions instead of a single set of local optima. While early QD algorithms view the objective and descriptor functions as black-box functions, novel tools have been introduced to use gradient information to accelerate the search and improve overall performance of those algorithms over continuous input spaces. However a broad range of applications involve discrete spaces, such as drug discovery or image generation. Exploring those spaces is challenging as they are combinatorially large and gradients cannot be used in the same manner as in continuous spaces. We introduce map-elites with a Gradient-Informed Discrete Emitter (ME-GIDE), which extends QD optimisation with differentiable functions over discrete search spaces. ME-GIDE leverages the gradient information of the objective and descriptor functions with respect to its discrete inputs to propose gradient-informed updates that guide the search towards a diverse set of high quality solutions. We evaluate our method on challenging benchmarks including protein design and discrete latent space illumination and find that our method outperforms state-of-the-art QD algorithms in all benchmarks.

In the context of neuroevolution, Quality-Diversity algorithms have proven effective in generating repertoires of diverse and efficient policies by relying on the definition of a behavior space. A natural goal induced by the creation of such a repertoire is trying to achieve behaviors on demand, which can be done by running the corresponding policy from the repertoire. However, in uncertain environments, two problems arise. First, policies can lack robustness and repeatability, meaning that multiple episodes under slightly different conditions often result in very different behaviors. Second, due to the discrete nature of the repertoire, solutions vary discontinuously. Here we present a new approach to achieve behavior-conditioned trajectory generation based on two mechanisms: First, MAP-Elites Low-Spread (ME-LS), which constrains the selection of solutions to those that are the most consistent in the behavior space. Second, the Quality-Diversity Transformer (QDT), a Transformer-based model conditioned on continuous behavior descriptors, which trains on a dataset generated by policies from a ME-LS repertoire and learns to autoregressively generate sequences of actions that achieve target behaviors. Results show that ME-LS produces consistent and robust policies, and that its combination with the QDT yields a single policy capable of achieving diverse behaviors on demand with high accuracy., Comment: 10+7 pages

Quality Diversity (QD) has emerged as a powerful alternative optimization paradigm that aims at generating large and diverse collections of solutions, notably with its flagship algorithm MAP-ELITES (ME) which evolves solutions through mutations and crossovers. While very effective for some unstructured problems, early ME implementations relied exclusively on random search to evolve the population of solutions, rendering them notoriously sample-inefficient for high-dimensional problems, such as when evolving neural networks. Follow-up works considered exploiting gradient information to guide the search in order to address these shortcomings through techniques borrowed from either Black-Box Optimization (BBO) or Reinforcement Learning (RL). While mixing RL techniques with ME unlocked state-of-the-art performance for robotics control problems that require a good amount of exploration, it also plagued these ME variants with limitations common among RL algorithms that ME was free of, such as hyperparameter sensitivity, high stochasticity as well as training instability, including when the population size increases as some components are shared across the population in recent approaches. Furthermore, existing approaches mixing ME with RL tend to be tied to a specific RL algorithm, which effectively prevents their use on problems where the corresponding RL algorithm fails. To address these shortcomings, we introduce a flexible framework that allows the use of any RL algorithm and alleviates the aforementioned limitations by evolving populations of agents (whose definition include hyperparameters and all learnable parameters) instead of just policies. We demonstrate the benefits brought about by our framework through extensive numerical experiments on a number of robotics control problems, some of which with deceptive rewards, taken from the QD-RL literature.

Quality-Diversity (QD) algorithms have recently gained traction as optimisation methods due to their effectiveness at escaping local optima and capability of generating wide-ranging and high-performing solutions. Recently, Multi-Objective MAP-Elites (MOME) extended the QD paradigm to the multi-objective setting by maintaining a Pareto front in each cell of a map-elites grid. MOME achieved a global performance that competed with NSGA-II and SPEA2, two well-established Multi-Objective Evolutionary Algorithms (MOEA), while also acquiring a diverse repertoire of solutions. However, MOME is limited by non-directed genetic search mechanisms which struggle in high-dimensional search spaces. In this work, we present Multi-Objective MAP-Elites with Policy-Gradient Assistance and Crowding-based Exploration (MOME-PGX): a new QD algorithm that extends MOME to improve its data efficiency and performance. MOME-PGX uses gradient-based optimisation to efficiently drive solutions towards higher performance. It also introduces crowding-based mechanisms to create an improved exploration strategy and to encourage uniformity across Pareto fronts. We evaluate MOME-PGX in four simulated robot locomotion tasks and demonstrate that it converges faster and to a higher performance than all other baselines. We show that MOME-PGX is between 4.3 and 42 times more data-efficient than MOME and doubles the performance of MOME, NSGA-II and SPEA2 in challenging environments., Comment: Accepted GECCO 2023

A fascinating aspect of nature lies in its ability to produce a collection of organisms that are all high-performing in their niche. Quality-Diversity (QD) methods are evolutionary algorithms inspired by this observation, that obtained great results in many applications, from wing design to robot adaptation. Recently, several works demonstrated that these methods could be applied to perform neuro-evolution to solve control problems in large search spaces. In such problems, diversity can be a target in itself. Diversity can also be a way to enhance exploration in tasks exhibiting deceptive reward signals. While the first aspect has been studied in depth in the QD community, the latter remains scarcer in the literature. Exploration is at the heart of several domains trying to solve control problems such as Reinforcement Learning and QD methods are promising candidates to overcome the challenges associated. Therefore, we believe that standardized benchmarks exhibiting control problems in high dimension with exploration difficulties are of interest to the QD community. In this paper, we highlight three candidate benchmarks and explain why they appear relevant for systematic evaluation of QD algorithms. We also provide open-source implementations in Jax allowing practitioners to run fast and numerous experiments on few compute resources., Comment: GECCO 2022 Workshop on Quality Diversity Algorithm Benchmarks

Deep Reinforcement Learning (RL) has emerged as a powerful paradigm for training neural policies to solve complex control tasks. However, these policies tend to be overfit to the exact specifications of the task and environment they were trained on, and thus do not perform well when conditions deviate slightly or when composed hierarchically to solve even more complex tasks. Recent work has shown that training a mixture of policies, as opposed to a single one, that are driven to explore different regions of the state-action space can address this shortcoming by generating a diverse set of behaviors, referred to as skills, that can be collectively used to great effect in adaptation tasks or for hierarchical planning. This is typically realized by including a diversity term - often derived from information theory - in the objective function optimized by RL. However these approaches often require careful hyperparameter tuning to be effective. In this work, we demonstrate that less widely-used neuroevolution methods, specifically Quality Diversity (QD), are a competitive alternative to information-theory-augmented RL for skill discovery. Through an extensive empirical evaluation comparing eight state-of-the-art algorithms (four flagship algorithms from each line of work) on the basis of (i) metrics directly evaluating the skills' diversity, (ii) the skills' performance on adaptation tasks, and (iii) the skills' performance when used as primitives for hierarchical planning; QD methods are found to provide equal, and sometimes improved, performance whilst being less sensitive to hyperparameters and more scalable. As no single method is found to provide near-optimal performance across all environments, there is a rich scope for further research which we support by proposing future directions and providing optimized open-source implementations., Comment: Camera ready version for ICLR2023 (spotlight)

Training populations of agents has demonstrated great promise in Reinforcement Learning for stabilizing training, improving exploration and asymptotic performance, and generating a diverse set of solutions. However, population-based training is often not considered by practitioners as it is perceived to be either prohibitively slow (when implemented sequentially), or computationally expensive (if agents are trained in parallel on independent accelerators). In this work, we compare implementations and revisit previous studies to show that the judicious use of compilation and vectorization allows population-based training to be performed on a single machine with one accelerator with minimal overhead compared to training a single agent. We also show that, when provided with a few accelerators, our protocols extend to large population sizes for applications such as hyperparameter tuning. We hope that this work and the public release of our code will encourage practitioners to use population-based learning more frequently for their research and applications.

In this work, we consider the problem of Quality-Diversity (QD) optimization with multiple objectives. QD algorithms have been proposed to search for a large collection of both diverse and high-performing solutions instead of a single set of local optima. Thriving for diversity was shown to be useful in many industrial and robotics applications. On the other hand, most real-life problems exhibit several potentially antagonist objectives to be optimized. Hence being able to optimize for multiple objectives with an appropriate technique while thriving for diversity is important to many fields. Here, we propose an extension of the MAP-Elites algorithm in the multi-objective setting: Multi-Objective MAP-Elites (MOME). Namely, it combines the diversity inherited from the MAP-Elites grid algorithm with the strength of multi-objective optimizations by filling each cell with a Pareto Front. As such, it allows to extract diverse solutions in the descriptor space while exploring different compromises between objectives. We evaluate our method on several tasks, from standard optimization problems to robotics simulations. Our experimental evaluation shows the ability of MOME to provide diverse solutions while providing global performances similar to standard multi-objective algorithms.

The SARS-CoV-2 pandemic has created a global race for a cure. One approach focuses on designing a novel variant of the human angiotensin-converting enzyme 2 (ACE2) that binds more tightly to the SARS-CoV-2 spike protein and diverts it from human cells. Here we formulate a novel protein design framework as a reinforcement learning problem. We generate new designs efficiently through the combination of a fast, biologically-grounded reward function and sequential action-space formulation. The use of Policy Gradients reduces the compute budget needed to reach consistent, high-quality designs by at least an order of magnitude compared to standard methods. Complexes designed by this method have been validated by molecular dynamics simulations, confirming their increased stability. This suggests that combining leading protein design methods with modern deep reinforcement learning is a viable path for discovering a Covid-19 cure and may accelerate design of peptide-based therapeutics for other diseases.

Offline Reinforcement Learning (RL) aims to turn large datasets into powerful decision-making engines without any online interactions with the environment. This great promise has motivated a large amount of research that hopes to replicate the success RL has experienced in simulation settings. This work ambitions to reflect upon these efforts from a practitioner viewpoint. We start by discussing the dataset properties that we hypothesise can characterise the type of offline methods that will be the most successful. We then verify these claims through a set of experiments and designed datasets generated from environments with both discrete and continuous action spaces. We experimentally validate that diversity and high-return examples in the data are crucial to the success of offline RL and show that behavioural cloning remains a strong contender compared to its contemporaries. Overall, this work stands as a tutorial to help people build their intuition on today's offline RL methods and their applicability., Comment: Accepted at NeurIPS 2020 Offline Reinforcement Learning Workshop. First two authors contributed equally. Authors three and four advised equally

We propose a novel solution to challenging sparse-reward, continuous control problems that require hierarchical planning at multiple levels of abstraction. Our solution, dubbed AlphaNPI-X, involves three separate stages of learning. First, we use off-policy reinforcement learning algorithms with experience replay to learn a set of atomic goal-conditioned policies, which can be easily repurposed for many tasks. Second, we learn self-models describing the effect of the atomic policies on the environment. Third, the self-models are harnessed to learn recursive compositional programs with multiple levels of abstraction. The key insight is that the self-models enable planning by imagination, obviating the need for interaction with the world when learning higher-level compositional programs. To accomplish the third stage of learning, we extend the AlphaNPI algorithm, which applies AlphaZero to learn recursive neural programmer-interpreters. We empirically show that AlphaNPI-X can effectively learn to tackle challenging sparse manipulation tasks, such as stacking multiple blocks, where powerful model-free baselines fail.

A fascinating aspect of nature lies in its ability to produce a large and diverse collection of organisms that are all high-performing in their niche. By contrast, most AI algorithms focus on finding a single efficient solution to a given problem. Aiming for diversity in addition to performance is a convenient way to deal with the exploration-exploitation trade-off that plays a central role in learning. It also allows for increased robustness when the returned collection contains several working solutions to the considered problem, making it well-suited for real applications such as robotics. Quality-Diversity (QD) methods are evolutionary algorithms designed for this purpose. This paper proposes a novel algorithm, QDPG, which combines the strength of Policy Gradient algorithms and Quality Diversity approaches to produce a collection of diverse and high-performing neural policies in continuous control environments. The main contribution of this work is the introduction of a Diversity Policy Gradient (DPG) that exploits information at the time-step level to drive policies towards more diversity in a sample-efficient manner. Specifically, QDPG selects neural controllers from a MAP-Elites grid and uses two gradient-based mutation operators to improve both quality and diversity. Our results demonstrate that QDPG is significantly more sample-efficient than its evolutionary competitors., Comment: Add several baselines (Policy Gradient assisted MAP Elites, DIAYN, AGAC) Change writing to take the point of view of the evo community Change style, writing, explanation, figures

We propose a novel reinforcement learning algorithm, AlphaNPI, that incorporates the strengths of Neural Programmer-Interpreters (NPI) and AlphaZero. NPI contributes structural biases in the form of modularity, hierarchy and recursion, which are helpful to reduce sample complexity, improve generalization and increase interpretability. AlphaZero contributes powerful neural network guided search algorithms, which we augment with recursion. AlphaNPI only assumes a hierarchical program specification with sparse rewards: 1 when the program execution satisfies the specification, and 0 otherwise. Using this specification, AlphaNPI is able to train NPI models effectively with RL for the first time, completely eliminating the need for strong supervision in the form of execution traces. The experiments show that AlphaNPI can sort as well as previous strongly supervised NPI variants. The AlphaNPI agent is also trained on a Tower of Hanoi puzzle with two disks and is shown to generalize to puzzles with an arbitrary number of disk

In this paper, we provide an overview of first-order and second-order variants of the gradient descent method that are commonly used in machine learning. We propose a general framework in which 6 of these variants can be interpreted as different instances of the same approach. They are the vanilla gradient descent, the classical and generalized Gauss-Newton methods, the natural gradient descent method, the gradient covariance matrix approach, and Newton's method. Besides interpreting these methods within a single framework, we explain their specificities and show under which conditions some of them coincide., Comment: 13 pages