Portrait of Emmanuel Bengio

Emmanuel Bengio

Associate Industry Member
Staff Machine Learning Scientist, Recursion
Research Topics
Deep Learning
Generative Models
GFlowNets
Molecular Modeling
Reinforcement Learning

Biography

Emmanuel Bengio is an ML Scientist at Valence Labs/Recursion, working on the intersection of GFlowNets and drug discovery. He did his PhD under Joelle Pineau and Doina Precup at McGill/Mila - Quebec Artificial Intelligence Institute, focusing on understanding generalization in deep RL.

Publications

Improved Off-policy Reinforcement Learning in Biological Sequence Design
Hyeonah Kim
Minsu Kim
Taeyoung YUN
Sanghyeok Choi
Emmanuel Bengio
Alex Hernandez-Garcia
Jinkyoo Park
Designing biological sequences with desired properties is challenging due to vast search spaces and limited evaluation budgets. Although rei… (see more)nforcement learning methods use proxy models for rapid reward evaluation, insufficient training data can cause proxy misspecification on out-of-distribution inputs. To address this, we propose a novel off-policy search,
2025-10-05
Proceedings of the 42nd International Conference on Machine Learning (published)
doi.org
proceedings.mlr.press
Pretraining Generative Flow Networks with Inexpensive Rewards for Molecular Graph Generation
Mohit Pandey
Gopeshh Subbaraj
Artem Cherkasov
Martin Ester
Emmanuel Bengio
2025-10-05
Proceedings of the 42nd International Conference on Machine Learning (published)
doi.org
proceedings.mlr.press
Random Policy Evaluation Uncovers Policies of Generative Flow Networks
Haoran He
Emmanuel Bengio
Qingpeng Cai 0001
Ling Pan
2025-10-05
Proceedings of the 42nd International Conference on Machine Learning (published)
proceedings.mlr.press
proceedings.mlr.press
Torsional-GFN: a conditional conformation generator for small molecules
Alexandra Volokhova
Lena Nehale Ezzine
Piotr Gainski
Luca Scimeca
Emmanuel Bengio
Prudencio Tossou
Yoshua Bengio
Alex Hernandez-Garcia
2025-06-10
ICML.cc/2025/Workshop/GenBio (poster)
doi.org
openreview.net
Virtual Cells: Predict, Explain, Discover
Emmanuel Noutahi
Jason Hartford
Prudencio Tossou
Shawn Whitfield
Ali Denton
Cas Wognum
Kristina Ulicna
Michael Craig
Jonathan Hsu
Michael Cuccarese
Emmanuel Bengio
Dominique Beaini
Christopher Gibson
Daniel Cohen
Berton Earnshaw
2025-04-30
arXiv (published)
doi.org
arxiv.org
Solving Bayesian Inverse Problems with Diffusion Priors and Off-Policy RL
Luca Scimeca
Siddarth Venkatraman
Moksh Jain
Minsu Kim
Marcin Sendera
Mohsin Hasan
Luke Rowe
Sarthak Mittal
Pablo Lemos
Emmanuel Bengio
Alexandre Adam
Jarrid Rector-Brooks
Yashar Hezaveh
Laurence Perreault-Levasseur
Yoshua Bengio
Glen Berseth
Nikolay Malkin
This paper presents a practical application of Relative Trajectory Balance (RTB), a recently introduced off-policy reinforcement learning (R… (see more)L) objective that can asymptotically solve Bayesian inverse problems optimally. We extend the original work by using RTB to train conditional diffusion model posteriors from pretrained unconditional priors for challenging linear and non-linear inverse problems in vision, and science. We use the objective alongside techniques such as off-policy backtracking exploration to improve training. Importantly, our results show that existing training-free diffusion posterior methods struggle to perform effective posterior inference in latent space due to inherent biases.
2025-03-05
ICLR.cc/2025/Workshop/DeLTa (poster)
doi.org
openreview.net
Action Abstractions for Amortized Sampling
Oussama Boussif
Lena Nehale Ezzine
Joseph Viviano
Michał Koziarski
Moksh Jain
Nikolay Malkin
Emmanuel Bengio
Rim Assouel
Yoshua Bengio
As trajectories sampled by policies used by reinforcement learning (RL) and generative flow networks (GFlowNets) grow longer, credit assignm… (see more)ent and exploration become more challenging, and the long planning horizon hinders mode discovery and generalization. The challenge is particularly pronounced in entropy-seeking RL methods, such as generative flow networks, where the agent must learn to sample from a structured distribution and discover multiple high-reward states, each of which take many steps to reach. To tackle this challenge, we propose an approach to incorporate the discovery of action abstractions, or high-level actions, into the policy optimization process. Our approach involves iteratively extracting action subsequences commonly used across many high-reward trajectories and `chunking' them into a single action that is added to the action space. In empirical evaluation on synthetic and real-world environments, our approach demonstrates improved sample efficiency performance in discovering diverse high-reward objects, especially on harder exploration problems. We also observe that the abstracted high-order actions are interpretable, capturing the latent structure of the reward landscape of the action space. This work provides a cognitively motivated approach to action abstraction in RL and is the first demonstration of hierarchical planning in amortized sequential sampling.
2025-01-21
ICLR.cc/2025/Conference (poster)
doi.org
openreview.net
Adaptive Teachers for Amortized Samplers
Minsu Kim
Sanghyeok Choi
Taeyoung YUN
Emmanuel Bengio
Leo Feng
Jarrid Rector-Brooks
Sungsoo Ahn
Jinkyoo Park
Nikolay Malkin
Yoshua Bengio
Amortized inference is the task of training a parametric model, such as a neural network, to approximate a distribution with a given unnorma… (see more)lized density where exact sampling is intractable. When sampling is implemented as a sequential decision-making process, reinforcement learning (RL) methods, such as generative flow networks, can be used to train the sampling policy. Off-policy RL training facilitates the discovery of diverse, high-reward candidates, but existing methods still face challenges in efficient exploration. We propose to use an adaptive training distribution (the \teacher) to guide the training of the primary amortized sampler (the \student). The \teacher, an auxiliary behavior model, is trained to sample high-loss regions of the \student and can generalize across unexplored modes, thereby enhancing mode coverage by providing an efficient training curriculum. We validate the effectiveness of this approach in a synthetic environment designed to present an exploration challenge, two diffusion-based sampling tasks, and four biochemical discovery tasks demonstrating its ability to improve sample efficiency and mode coverage. Source code is available at https://github.com/alstn12088/adaptive-teacher.
2025-01-21
ICLR.cc/2025/Conference (poster)
doi.org
openreview.net
Towards Improving Exploration Through Sibling Augmented GFlowNets
Kanika Madan
Alex Lamb
Emmanuel Bengio
Glen Berseth
Yoshua Bengio
2025-01-21
ICLR.cc/2025/Conference (poster)
openreview.net
openreview.net
Investigating Generalization Behaviours of Generative Flow Networks
Lazar Atanackovic
Emmanuel Bengio
Generative Flow Networks (GFlowNets, GFNs) are a generative framework for learning unnormalized probability mass functions over discrete spa… (see more)ces. Since their inception, GFlowNets have proven to be useful for learning generative models in applications where the majority of the discrete space is unvisited during training. This has inspired some to hypothesize that GFlowNets, when paired with deep neural networks (DNNs), have favourable generalization properties. In this work, we empirically verify some of the hypothesized mechanisms of generalization of GFlowNets. In particular, we find that the functions that GFlowNets learn to approximate have an implicit underlying structure which facilitate generalization. We also find that GFlowNets are sensitive to being trained offline and off-policy; however, the reward implicitly learned by GFlowNets is robust to changes in the training distribution.
2024-12-31
Trans. Mach. Learn. Res. (published)
doi.org
arxiv.org
Efficient Biological Data Acquisition through Inference Set Design
Ihor Neporozhnii
Julien Roy
Emmanuel Bengio
Jason Hartford
In drug discovery, highly automated high-throughput laboratories are used to screen a large number of compounds in search of effective drugs… (see more). These experiments are expensive, so one might hope to reduce their cost by only experimenting on a subset of the compounds, and predicting the outcomes of the remaining experiments. In this work, we model this scenario as a sequential subset selection problem: we aim to select the smallest set of candidates in order to achieve some desired level of accuracy for the system as a whole. Our key observation is that, if there is heterogeneity in the difficulty of the prediction problem across the input space, selectively obtaining the labels for the hardest examples in the acquisition pool will leave only the relatively easy examples to remain in the inference set, leading to better overall system performance. We call this mechanism inference set design, and propose the use of a confidence-based active learning solution to prune out these challenging examples. Our algorithm includes an explicit stopping criterion that interrupts the acquisition loop when it is sufficiently confident that the system has reached the target performance. Our empirical studies on image and molecular datasets, as well as a real-world large-scale biological assay, show that active learning for inference set design leads to significant reduction in experimental cost while retaining high system performance.
2024-10-24
ArXiv (preprint)
doi.org
arxiv.org
Amortizing intractable inference in diffusion models for vision, language, and control
Siddarth Venkatraman
Moksh Jain
Luca Scimeca
Minsu Kim
Marcin Sendera
Mohsin Hasan
Luke Rowe
Sarthak Mittal
Pablo Lemos
Emmanuel Bengio
Alexandre Adam
Jarrid Rector-Brooks
Yoshua Bengio
Glen Berseth
Nikolay Malkin
Diffusion models have emerged as effective distribution estimators in vision, language, and reinforcement learning, but their use as priors … (see more)in downstream tasks poses an intractable posterior inference problem. This paper studies amortized sampling of the posterior over data,
2024-09-24
Neural Information Processing Systems (poster)
doi.org
openreview.net