Publications

Challenges for impact evaluation of WHO’s normative output
Catherine Régis
Gaëlle Foucault
Jean-Louis Denis
Pierre Larouche
Miriam Cohen
2024-10-01
Bulletin of the World Health Organization (publié)
doi.org
Doob's Lagrangian: A Sample-Efficient Variational Approach to Transition Path Sampling
Yuanqi Du
Michael Plainer
Rob Brekelmans
Chenru Duan
Frank No'e
Carla P. Gomes
Alan Aspuru-Guzik
Kirill Neklyudov
Rare event sampling in dynamical systems is a fundamental problem arising in the natural sciences, which poses significant computational cha… (voir plus)llenges due to an exponentially large space of trajectories. For settings where the dynamical system of interest follows a Brownian motion with known drift, the question of conditioning the process to reach a given endpoint or desired rare event is definitively answered by Doob's h-transform. However, the naive estimation of this transform is infeasible, as it requires simulating sufficiently many forward trajectories to estimate rare event probabilities. In this work, we propose a variational formulation of Doob's h-transform as an optimization problem over trajectories between a given initial point and the desired ending point. To solve this optimization, we propose a simulation-free training objective with a model parameterization that imposes the desired boundary conditions by design. Our approach significantly reduces the search space over trajectories and avoids expensive trajectory simulation and inefficient importance sampling estimators which are required in existing methods. We demonstrate the ability of our method to find feasible transition paths on real-world molecular simulation and protein folding tasks.
2024-10-01
arXiv (publié)
doi.org
arxiv.org
Efficient line search for optimizing Area Under the ROC Curve in gradient descent
Jadon Fowler
Toby Dylan Hocking
Receiver Operating Characteristic (ROC) curves are useful for evaluation in binary classification and changepoint detection, but difficult t… (voir plus)o use for learning since the Area Under the Curve (AUC) is piecewise constant (gradient zero almost everywhere). Recently the Area Under Min (AUM) of false positive and false negative rates has been proposed as a differentiable surrogate for AUC. In this paper we study the piecewise linear/constant nature of the AUM/AUC, and propose new efficient path-following algorithms for choosing the learning rate which is optimal for each step of gradient descent (line search), when optimizing a linear model. Remarkably, our proposed line search algorithm has the same log-linear asymptotic time complexity as gradient descent with constant step size, but it computes a complete representation of the AUM/AUC as a function of step size. In our empirical study of binary classification problems, we verify that our proposed algorithm is fast and exact; in changepoint detection problems we show that the proposed algorithm is just as accurate as grid search, but faster.
2024-10-01
arXiv (publié)
doi.org
arxiv.org
Finite Sample Complexity Analysis of Binary Segmentation
Toby Dylan Hocking
Binary segmentation is the classic greedy algorithm which recursively splits a sequential data set by optimizing some loss or likelihood fun… (voir plus)ction. Binary segmentation is widely used for changepoint detection in data sets measured over space or time, and as a sub-routine for decision tree learning. In theory it should be extremely fast for
2024-10-01
arXiv (publié)
doi.org
arxiv.org
Inferring electric vehicle charging patterns from smart meter data for impact studies
Feng Li
Élodie Campeau
Ilhan Kocar
Antoine Lesage-Landry
2024-10-01
Electric power systems research (publié)
doi.org
Inferring electric vehicle charging patterns from smart meter data for impact studies
Feng Li
Élodie Campeau
Ilhan Kocar
Antoine Lesage-Landry
2024-10-01
Electric power systems research (publié)
doi.org
Inferring electric vehicle charging patterns from smart meter data for impact studies
Feng Li
Élodie Campeau
Ilhan Kocar
Antoine Lesage-Landry
2024-10-01
Electric power systems research (publié)
doi.org
Innovative transfusion strategies for blood deserts in disaster settings
Shreenik Kundu
Ayla Gerk
Robert Glatter
Dan Poenaru
2024-10-01
BMJ Global Health (publié)
doi.org
Long-term outcomes of critically ill patients with hematological malignancies: what is the impact of the coronavirus disease 2019 pandemic? Author's reply
Laveena Munshi
Guillaume Dumas
Sangeeta Mehta
2024-10-01
Intensive Care Medicine (publié)
doi.org
MAP: Model Merging with Amortized Pareto Front Using Limited Computation
Li Li
Tianyu Zhang
Zhiqi Bu
Suyuchen Wang
Huan He
Jie Fu
Yonghui Wu
Jiang Bian
Yong Chen
Yoshua Bengio
2024-10-01
NeurIPS.cc/2024/Workshop/Federated_Learning (présentation orale)
openreview.net
openreview.net
ProtSCAPE: Mapping the landscape of protein conformations in molecular dynamics
Siddharth Viswanath
Dhananjay Bhaskar
David R. Johnson
João Felipe Rocha
Egbert Castro
Jackson Grady
Alex T. Grigas
Michael Perlmutter
Corey S. O'Hern
Smita Krishnaswamy
Understanding the dynamic nature of protein structures is essential for comprehending their biological functions. While significant progress… (voir plus) has been made in predicting static folded structures, modeling protein motions on microsecond to millisecond scales remains challenging. To address these challenges, we introduce a novel deep learning architecture, Protein Transformer with Scattering, Attention, and Positional Embedding (ProtSCAPE), which leverages the geometric scattering transform alongside transformer-based attention mechanisms to capture protein dynamics from molecular dynamics (MD) simulations. ProtSCAPE utilizes the multi-scale nature of the geometric scattering transform to extract features from protein structures conceptualized as graphs and integrates these features with dual attention structures that focus on residues and amino acid signals, generating latent representations of protein trajectories. Furthermore, ProtSCAPE incorporates a regression head to enforce temporally coherent latent representations.
2024-10-01
arXiv (publié)
doi.org
arxiv.org
Robust Guided Diffusion for Offline Black-Box Optimization
Can Chen
Christopher Beckham
Zixuan Liu
Xue (Steve) Liu
Chris Pal
Offline black-box optimization aims to maximize a black-box function using an offline dataset of designs and their measured properties. Two … (voir plus)main approaches have emerged: the forward approach, which learns a mapping from input to its value, thereby acting as a proxy to guide optimization, and the inverse approach, which learns a mapping from value to input for conditional generation. (a) Although proxy-free~(classifier-free) diffusion shows promise in robustly modeling the inverse mapping, it lacks explicit guidance from proxies, essential for generating high-performance samples beyond the training distribution. Therefore, we propose \textit{proxy-enhanced sampling} which utilizes the explicit guidance from a trained proxy to bolster proxy-free diffusion with enhanced sampling control. (b) Yet, the trained proxy is susceptible to out-of-distribution issues. To address this, we devise the module \textit{diffusion-based proxy refinement}, which seamlessly integrates insights from proxy-free diffusion back into the proxy for refinement. To sum up, we propose \textit{\textbf{R}obust \textbf{G}uided \textbf{D}iffusion for Offline Black-box Optimization}~(\textbf{RGD}), combining the advantages of proxy~(explicit guidance) and proxy-free diffusion~(robustness) for effective conditional generation. RGD achieves state-of-the-art results on various design-bench tasks, underscoring its efficacy. Our code is at https://github.com/GGchen1997/RGD.
2024-10-01
ArXiv (prépublication)
doi.org
arxiv.org