Peu importe la taille : démocratiser la découverte de protéines avec l'IA
Des chercheurs de Mila ont créé un puissant modèle de langage protéique à source ouverte plus compact et efficace afin de démocratiser la découverte de protéines.
La prochaine cohorte de notre programme, conçu pour fournir aux participant·e·s une compréhension fondamentale des technologies de l'IA, se déroulera à Ottawa les 28 et 29 novembre.
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Publications
Contrastive Retrospection: honing in on critical steps for rapid learning and generalization in RL
In real life, success is often contingent upon multiple critical steps that are distant in time from each other and from the final reward. T… (voir plus)hese critical steps are challenging to identify with traditional reinforcement learning (RL) methods that rely on the Bellman equation for credit assignment. Here, we present a new RL algorithm that uses offline contrastive learning to hone in on these critical steps. This algorithm, which we call Contrastive Retrospection (ConSpec), can be added to any existing RL algorithm. ConSpec learns a set of prototypes for the critical steps in a task by a novel contrastive loss and delivers an intrinsic reward when the current state matches one of the prototypes. The prototypes in ConSpec provide two key benefits for credit assignment: (i) They enable rapid identification of all the critical steps. (ii) They do so in a readily interpretable manner, enabling out-of-distribution generalization when sensory features are altered. Distinct from other contemporary RL approaches to credit assignment, ConSpec takes advantage of the fact that it is easier to retrospectively identify the small set of steps that success is contingent upon (and ignoring other states) than it is to prospectively predict reward at every taken step. ConSpec greatly improves learning in a diverse set of RL tasks. The code is available at the link: https://github.com/sunchipsster1/ConSpec
Actor-critic (AC) methods are widely used in reinforcement learning (RL) and benefit from the flexibility of using any policy gradient metho… (voir plus)d as the actor and value-based method as the critic. The critic is usually trained by minimizing the TD error, an objective that is potentially decorrelated with the true goal of achieving a high reward with the actor. We address this mismatch by designing a joint objective for training the actor and critic in a decision-aware fashion. We use the proposed objective to design a generic, AC algorithm that can easily handle any function approximation. We explicitly characterize the conditions under which the resulting algorithm guarantees monotonic policy improvement, regardless of the choice of the policy and critic parameterization. Instantiating the generic algorithm results in an actor that involves maximizing a sequence of surrogate functions (similar to TRPO, PPO) and a critic that involves minimizing a closely connected objective. Using simple bandit examples, we provably establish the benefit of the proposed critic objective over the standard squared error. Finally, we empirically demonstrate the benefit of our decision-aware actor-critic framework on simple RL problems.
Proteins play a critical role in carrying out biological functions, and their 3D structures are essential in determining their functions.
A… (voir plus)ccurately predicting the conformation of protein side-chains given their backbones is important for applications in protein structure prediction, design and protein-protein interactions. Traditional methods are computationally intensive and have limited accuracy, while existing machine learning methods treat the problem as a regression task and overlook the restrictions imposed by the constant covalent bond lengths and angles. In this work, we present DiffPack, a torsional diffusion model that learns the joint distribution of side-chain torsional angles, the only degrees of freedom in side-chain packing, by diffusing and denoising on the torsional space. To avoid issues arising from simultaneous perturbation of all four torsional angles, we propose autoregressively generating the four torsional angles from
Simulation of autonomous vehicle systems requires that simulated traffic participants exhibit diverse and realistic behaviors. The use of pr… (voir plus)erecorded real-world traffic scenarios in simulation ensures realism but the rarity of safety critical events makes large scale collection of driving scenarios expensive. In this paper, we present DJINN - a diffusion based method of generating traffic scenarios. Our approach jointly diffuses the trajectories of all agents, conditioned on a flexible set of state observations from the past, present, or future. On popular trajectory forecasting datasets, we report state of the art performance on joint trajectory metrics. In addition, we demonstrate how DJINN flexibly enables direct test-time sampling from a variety of valuable conditional distributions including goal-based sampling, behavior-class sampling, and scenario editing.
Equivariant networks are specifically designed to ensure consistent behavior with respect to a set of input transformations, leading to high… (voir plus)er sample efficiency and more accurate and robust predictions. However, redesigning each component of prevalent deep neural network architectures to achieve chosen equivariance is a difficult problem and can result in a computationally expensive network during both training and inference. A recently proposed alternative towards equivariance that removes the architectural constraints is to use a simple canonicalization network that transforms the input to a canonical form before feeding it to an unconstrained prediction network. We show here that this approach can effectively be used to make a large pretrained network equivariant. However, we observe that the produced canonical orientations can be misaligned with those of the training distribution, hindering performance. Using dataset-dependent priors to inform the canonicalization function, we are able to make large pretrained models equivariant while maintaining their performance. This significantly improves the robustness of these models to deterministic transformations of the data, such as rotations. We believe this equivariant adaptation of large pretrained models can help their domain-specific applications with known symmetry priors.
In the field of reinforcement learning (RL), representation learning is a proven tool for complex image-based tasks, but is often overlooked… (voir plus) for environments with low-level states, such as physical control problems. This paper introduces SALE, a novel approach for learning embeddings that model the nuanced interaction between state and action, enabling effective representation learning from low-level states. We extensively study the design space of these embeddings and highlight important design considerations. We integrate SALE and an adaptation of checkpoints for RL into TD3 to form the TD7 algorithm, which significantly outperforms existing continuous control algorithms. On OpenAI gym benchmark tasks, TD7 has an average performance gain of 276.7% and 50.7% over TD3 at 300k and 5M time steps, respectively, and works in both the online and offline settings.
We introduce GAUCHE, a library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine… (voir plus) learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to chemical representations however is nontrivial, necessitating kernels defined over structured inputs such as graphs, strings and bit vectors. By defining such kernels in GAUCHE, we seek to open the door to powerful tools for uncertainty quantification and Bayesian optimisation in chemistry. Motivated by scenarios frequently encountered in experimental chemistry, we showcase applications for GAUCHE in molecular discovery and chemical reaction optimisation. The codebase is made available at https://github.com/leojklarner/gauche