Portrait of Pablo Lemos

Pablo Lemos

Postdoctorate - Université de Montréal
Supervisor
Laurence Perreault-Levasseur
Co-supervisor
Yashar Hezaveh
Research Topics
Computational Biology
Generative Models
Probabilistic Models
Website
Google Scholar
GitHub

Publications

Towards equilibrium molecular conformation generation with GFlowNets
Alexandra Volokhova
Michał Koziarski
Alex Hernández-García
Cheng-Hao Liu
Santiago Miret
Pablo Lemos
Luca Thiede
Zichao Yan
Alán Aspuru-Guzik
Yoshua Bengio
Sampling diverse, thermodynamically feasible molecular conformations plays a crucial role in predicting properties of a molecule. In this pa… (see more)per we propose to use GFlowNet for sampling conformations of small molecules from the Boltzmann distribution, as determined by the molecule's energy. The proposed approach can be used in combination with energy estimation methods of different fidelity and discovers a diverse set of low-energy conformations for highly flexible drug-like molecules. We demonstrate that GFlowNet can reproduce molecular potential energy surfaces by sampling proportionally to the Boltzmann distribution.
2023-10-26
NeurIPS.cc/2023/Workshop/AI4Mat (poster)
doi.org
openreview.net
Posterior Sampling of the Initial Conditions of the Universe from Non-linear Large Scale Structures using Score-Based Generative Models
Ronan Legin
Matthew Ho
Pablo Lemos
Laurence Perreault-Levasseur
Shirley Ho
Yashar Hezaveh
Benjamin Wandelt
Reconstructing the initial conditions of the universe is a key problem in cosmology. Methods based on simulating the forward evolution of th… (see more)e universe have provided a way to infer initial conditions consistent with present-day observations. However, due to the high complexity of the inference problem, these methods either fail to sample a distribution of possible initial density fields or require significant approximations in the simulation model to be tractable, potentially leading to biased results. In this work, we propose the use of score-based generative models to sample realizations of the early universe given present-day observations. We infer the initial density field of full high-resolution dark matter N-body simulations from the present-day density field and verify the quality of produced samples compared to the ground truth based on summary statistics. The proposed method is capable of providing plausible realizations of the early universe density field from the initial conditions posterior distribution marginalized over cosmological parameters and can sample orders of magnitude faster than current state-of-the-art methods.
2023-10-03
Monthly Notices of the Royal Astronomical Society: Letters (published)
doi.org
arxiv.org
Sampling-Based Accuracy Testing of Posterior Estimators for General Inference
Pablo Lemos
Adam Coogan
Yashar Hezaveh
Laurence Perreault-Levasseur
Parameter inference, i.e. inferring the posterior distribution of the parameters of a statistical model given some data, is a central proble… (see more)m to many scientific disciplines. Generative models can be used as an alternative to Markov Chain Monte Carlo methods for conducting posterior inference, both in likelihood-based and simulation-based problems. However, assessing the accuracy of posteriors encoded in generative models is not straightforward. In this paper, we introduce `Tests of Accuracy with Random Points' (TARP) coverage testing as a method to estimate coverage probabilities of generative posterior estimators. Our method differs from previously-existing coverage-based methods, which require posterior evaluations. We prove that our approach is necessary and sufficient to show that a posterior estimator is accurate. We demonstrate the method on a variety of synthetic examples, and show that TARP can be used to test the results of posterior inference analyses in high-dimensional spaces. We also show that our method can detect inaccurate inferences in cases where existing methods fail.
2023-07-02
Proceedings of the 40th International Conference on Machine Learning (published)
doi.org
proceedings.mlr.press
A Theory of Continuous Generative Flow Networks
Salem Lahlou
Tristan Deleu
Pablo Lemos
Dinghuai Zhang
Alexandra Volokhova
Alex Hernández-García
Lena Nehale Ezzine
Yoshua Bengio
Nikolay Malkin
Generative flow networks (GFlowNets) are amortized variational inference algorithms that are trained to sample from unnormalized target dist… (see more)ributions over compositional objects. A key limitation of GFlowNets until this time has been that they are restricted to discrete spaces. We present a theory for generalized GFlowNets, which encompasses both existing discrete GFlowNets and ones with continuous or hybrid state spaces, and perform experiments with two goals in mind. First, we illustrate critical points of the theory and the importance of various assumptions. Second, we empirically demonstrate how observations about discrete GFlowNets transfer to the continuous case and show strong results compared to non-GFlowNet baselines on several previously studied tasks. This work greatly widens the perspectives for the application of GFlowNets in probabilistic inference and various modeling settings.
2022-12-31
ICML (published)
doi.org
proceedings.mlr.press