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
Let the Flows Tell: Solving Graph Combinatorial Problems with GFlowNets
Symmetries have been leveraged to improve the generalization of neural networks through different mechanisms from data augmentation to equiv… (voir plus)ariant architectures. However, despite their potential, their integration into neural solvers for partial differential equations (PDEs) remains largely unexplored. We explore the integration of PDE symmetries, known as Lie point symmetries, in a major family of neural solvers known as physics-informed neural networks (PINNs). We propose a loss function that informs the network about Lie point symmetries in the same way that PINN models try to enforce the underlying PDE through a loss function. Intuitively, our symmetry loss ensures that the infinitesimal generators of the Lie group conserve the PDE solutions.. Effectively, this means that once the network learns a solution, it also learns the neighbouring solutions generated by Lie point symmetries.
Empirical evaluations indicate that the inductive bias introduced by the Lie point symmetries of the PDEs greatly boosts the sample efficiency of PINNs.
Animals have a developed ability to explore that aids them in important tasks such as locating food, exploring for shelter, and finding misp… (voir plus)laced items. These exploration skills necessarily track where they have been so that they can plan for finding items with relative efficiency. Contemporary exploration algorithms often learn a less efficient exploration strategy because they either condition only on the current state or simply rely on making random open-loop exploratory moves. In this work, we propose
Parameter-efficient fine-tuning (PEFT) for cross-task generalization consists in pre-training adapters on a multi-task training set before f… (voir plus)ew-shot adaptation to test tasks. Polytropon [Ponti et al., 2023] (
We consider the problem of solving stochastic monotone variational inequalities with a separable structure using a stochastic first-order or… (voir plus)acle. Building on standard extragradient for variational inequalities we propose a novel algorithm---stochastic \emph{accelerated gradient-extragradient} (AG-EG)---for strongly monotone variational inequalities (VIs). Our approach combines the strengths of extragradient and Nesterov acceleration. By showing that its iterates remain in a bounded domain and applying scheduled restarting, we prove that AG-EG has an optimal convergence rate for strongly monotone VIs. Furthermore, when specializing to the particular case of bilinearly coupled strongly-convex-strongly-concave saddle-point problems, including bilinear games, our algorithm achieves fine-grained convergence rates that match the respective lower bounds, with the stochasticity being characterized by an additive statistical error term that is optimal up to a constant prefactor.
We study offline model-based optimization to maximize a black-box objective function with a static dataset of designs and scores. These desi… (voir plus)gns encompass a variety of domains, including materials, robots, DNA sequences, and proteins. A common approach trains a proxy on the static dataset and performs gradient ascent to obtain new designs. However, this often results in poor designs due to the proxy inaccuracies for out-of-distribution designs. Recent studies indicate that (a) gradient ascent with a mean ensemble of proxies generally outperforms simple gradient ascent, and (b) a trained proxy provides weak ranking supervision signals for design selection. Motivated by (a) and (b), we propose
Deep reinforcement learning agents for continuous control are known to exhibit significant instability in their performance over time. In th… (voir plus)is work, we provide a fresh perspective on these behaviors by studying the return landscape: the mapping between a policy and a return. We find that popular algorithms traverse noisy neighborhoods of this landscape, in which a single update to the policy parameters leads to a wide range of returns. By taking a distributional view of these returns, we map the landscape, characterizing failure-prone regions of policy space and revealing a hidden dimension of policy quality. We show that the landscape exhibits surprising structure by finding simple paths in parameter space which improve the stability of a policy. To conclude, we develop a distribution-aware procedure which finds such paths, navigating away from noisy neighborhoods in order to improve the robustness of a policy. Taken together, our results provide new insight into the optimization, evaluation, and design of agents.
Temporal difference (TD) learning is often used to update the estimate of the value function which is used by RL agents to extract useful po… (voir plus)licies. In this paper, we focus on value function estimation in continual reinforcement learning. We propose to decompose the value function into two components which update at different timescales: a _permanent_ value function, which holds general knowledge that persists over time, and a _transient_ value function, which allows quick adaptation to new situations. We establish theoretical results showing that our approach is well suited for continual learning and draw connections to the complementary learning systems (CLS) theory from neuroscience. Empirically, this approach improves performance significantly on both prediction and control problems.
Self-supervised pre-training methods on proteins have recently gained attention, with most approaches focusing on either protein sequences o… (voir plus)r structures, neglecting the exploration of their joint distribution, which is crucial for a comprehensive understanding of protein functions by integrating co-evolutionary information and structural characteristics. In this work, inspired by the success of denoising diffusion models in generative tasks, we propose the DiffPreT approach to pre-train a protein encoder by sequence-structure joint diffusion modeling. DiffPreT guides the encoder to recover the native protein sequences and structures from the perturbed ones along the joint diffusion trajectory, which acquires the joint distribution of sequences and structures. Considering the essential protein conformational variations, we enhance DiffPreT by a method called Siamese Diffusion Trajectory Prediction (SiamDiff) to capture the correlation between different conformers of a protein. SiamDiff attains this goal by maximizing the mutual information between representations of diffusion trajectories of structurally-correlated conformers. We study the effectiveness of DiffPreT and SiamDiff on both atom- and residue-level structure-based protein understanding tasks. Experimental results show that the performance of DiffPreT is consistently competitive on all tasks, and SiamDiff achieves new state-of-the-art performance, considering the mean ranks on all tasks. Our implementation is available at https://github.com/DeepGraphLearning/SiamDiff.