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Publications
Inferring dynamic regulatory interaction graphs from time series data with perturbations
From physics to sentience: Deciphering the semantics of the free-energy principle and evaluating its claims: Comment on "Path integrals, particular kinds, and strange things" by Karl Friston et al.
The federated learning paradigm has motivated the development of methods for aggregating multiple client updates into a global server model,… (see more) without sharing client data. Many federated learning algorithms, including the canonical Federated Averaging (FedAvg), take a direct (possibly weighted) average of the client parameter updates, motivated by results in distributed optimization. In this work, we adopt a function space perspective and propose a new algorithm, FedFish, that aggregates local approximations to the functions learned by clients, using an estimate based on their Fisher information. We evaluate FedFish on realistic, large-scale cross-device benchmarks. While the performance of FedAvg can suffer as client models drift further apart, we demonstrate that FedFish is more robust to longer local training. Our evaluation across several settings in image and language benchmarks shows that FedFish outperforms FedAvg as local training epochs increase. Further, FedFish results in global networks that are more amenable to efficient personalization via local fine-tuning on the same or shifted data distributions. For instance, federated pretraining on the C4 dataset, followed by few-shot personalization on Stack Overflow, results in a 7% improvement in next-token prediction by FedFish over FedAvg.
In this paper we leverage self-supervised vision transformer models and their emergent semantic abilities to improve the generalization abil… (see more)ities of imitation learning policies. We introduce BC-ViT, an imitation learning algorithm that leverages rich DINO pre-trained Visual Transformer (ViT) patch-level embeddings to obtain better generalization when learning through demonstrations. Our learner sees the world by clustering appearance features into semantic concepts, forming stable keypoints that generalize across a wide range of appearance variations and object types. We show that this representation enables generalized behaviour by evaluating imitation learning across a diverse dataset of object manipulation tasks. Our method, data and evaluation approach are made available to facilitate further study of generalization in Imitation Learners.
The COVID-19 pandemic continues to pose a substantial threat to human lives and is likely to do so for years to come. Despite the availabili… (see more)ty of vaccines, searching for efficient small-molecule drugs that are widely available, including in low- and middle-income countries, is an ongoing challenge. In this work, we report the results of an open science community effort, the "Billion molecules against Covid-19 challenge", to identify small-molecule inhibitors against SARS-CoV-2 or relevant human receptors. Participating teams used a wide variety of computational methods to screen a minimum of 1 billion virtual molecules against 6 protein targets. Overall, 31 teams participated, and they suggested a total of 639,024 molecules, which were subsequently ranked to find 'consensus compounds'. The organizing team coordinated with various contract research organizations (CROs) and collaborating institutions to synthesize and test 878 compounds for biological activity against proteases (Nsp5, Nsp3, TMPRSS2), nucleocapsid N, RdRP (only the Nsp12 domain), and (alpha) spike protein S. Overall, 27 compounds with weak inhibition/binding were experimentally identified by binding-, cleavage-, and/or viral suppression assays and are presented here. Open science approaches such as the one presented here contribute to the knowledge base of future drug discovery efforts in finding better SARS-CoV-2 treatments.
