Jarrid Rector-Brooks

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.

2025-03-06

ICLR.cc/2025/Workshop/DeLTa (poster)

Adaptive teachers for amortized samplers

Minsu Kim

Sungsoo Ahn

Jinkyoo Park

Nikolay Malkin

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) by prioritizing high-loss regions. The Teacher, an auxiliary behavior model, is trained to sample high-error 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.

2025-01-22

ICLR.cc/2025/Conference (poster)

Integrating Generative and Experimental Platforms for Biomolecular Design

Cheng-Hao Liu

Soojung Yang

Sidney L Lisanza

Francesca-Zhoufan Li

Hannes Stärk

Jacob Gershon

Lauren Hong

Pranam Chatterjee

Tommi Jaakkola

Regina Barzilay

David Baker

Frances H. Arnold

Biomolecular design, through artificial engineering of proteins, ligands, and nucleic acids, holds immense promise in addressing pressing me… (see more)dical, industrial, and environmental challenges. While generative machine learning has shown significant potential in this area, a palpable disconnect exists with experimental biology: many ML research efforts prioritize static benchmark performance, potentially sidelining impactful biological applications. This workshop seeks to bridge this gap by bringing computationalists and experimentalists together, catalyzing a deeper interdisciplinary discourse. Together, we will explore the strengths and challenges of generative ML in biology, experimental integration of generative ML, and biological problems ready for ML. To attract high-quality and diverse research, we partnered with Nature Biotechnology for a special collection, and we created dedicated tracks for in-silico ML research and hybrid ML-experimental biology research. Our lineup features emerging leaders as speakers and renowned scientists as panelists, encapsulating a spectrum from high-throughput experimentation and computational biology to generative ML. With a diverse organizing team and backed by industry sponsors, we dedicate the workshop to pushing the boundaries of ML's role in biology.

2025-01-01

ICLR.cc/2025/Workshop_Proposals (published)

Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction

Mohsin Hasan

Zhangzhi Peng

Zachary Quinn

Cheng-Hao Liu

Sarthak Mittal

Nouha Dziri

Michael M. Bronstein

Pranam Chatterjee

Alexander Tong

Joey Bose

2025-01-01

ICLR (published)

Steering Masked Discrete Diffusion Models via Discrete Denoising Posterior Prediction

Mohsin Hasan

Zhangzhi Peng

Zachary Quinn

Cheng-Hao Liu

Sarthak Mittal

Nouha Dziri

Michael M. Bronstein

Pranam Chatterjee

Alexander Tong

Joey Bose

Generative modeling of discrete data underlies important applications spanning text-based agents like ChatGPT to the design of the very buil… (see more)ding blocks of life in protein sequences. However, application domains need to exert control over the generated data by steering the generative process - typically via RLHF - to satisfy a specified property, reward, or affinity metric. In this paper, we study the problem of steering Masked Diffusion Models (MDMs), a recent class of discrete diffusion models that offer a compelling alternative to traditional autoregressive models. We introduce Discrete Denoising Posterior Prediction (DDPP), a novel framework that casts the task of steering pre-trained MDMs as a problem of probabilistic inference by learning to sample from a target Bayesian posterior. Our DDPP framework leads to a family of three novel objectives that are all simulation-free, and thus scalable while applying to general non-differentiable reward functions. Empirically, we instantiate DDPP by steering MDMs to perform class-conditional pixel-level image modeling, RLHF-based alignment of MDMs using text-based rewards, and finetuning protein language models to generate more diverse secondary structures and shorter proteins. We substantiate our designs via wet-lab validation, where we observe transient expression of reward-optimized protein sequences.

2024-10-10

ArXiv (preprint)

Amortizing intractable inference in diffusion models for vision, language, and control

Moksh J. Jain

Minsu Kim

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,

2024-09-25

NeurIPS.cc/2024/Conference (poster)

Improved off-policy training of diffusion samplers

Minsu Kim

We study the problem of training diffusion models to sample from a distribution with a given unnormalized density or energy function. We ben… (see more)chmark several diffusion-structured inference methods, including simulation-based variational approaches and off-policy methods (continuous generative flow networks). Our results shed light on the relative advantages of existing algorithms while bringing into question some claims from past work. We also propose a novel exploration strategy for off-policy methods, based on local search in the target space with the use of a replay buffer, and show that it improves the quality of samples on a variety of target distributions. Our code for the sampling methods and benchmarks studied is made public at [this link](https://github.com/GFNOrg/gfn-diffusion) as a base for future work on diffusion models for amortized inference.

2024-09-25

NeurIPS.cc/2024/Conference (poster)

Amortizing intractable inference in diffusion models for vision, language, and control

Moksh J. Jain

Minsu Kim

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,

2024-05-31

ArXiv (preprint)

Amortizing intractable inference in diffusion models for vision, language, and control

Moksh J. Jain

Minsu Kim

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,

2024-05-31

ArXiv (preprint)

Amortizing intractable inference in diffusion models for vision, language, and control

Moksh J. Jain

Minsu Kim

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,

2024-05-31

ArXiv (preprint)

Generative Active Learning for the Search of Small-molecule Protein Binders

Maksym Korablyov

Cheng-Hao Liu

Moksh J. Jain

Almer M. van der Sloot

Eric Jolicoeur

Edward Ruediger

Andrei Cristian Nica

Emmanuel Bengio

Kostiantyn Lapchevskyi

Daniel St-Cyr

Doris Alexandra Schuetz

Victor I Butoi

Simon R. Blackburn

Leo Feng

Hadi Nekoei

Sai Krishna Gottipati

Priyesh Vijayan

Prateek Gupta

Ladislav Rampášek … (see 14 more)

Sasikanth Avancha

Pierre-Luc Bacon

William L. Hamilton

Brooks Paige

Sanchit Misra

Stanisław Jastrzębski

Bharat Kaul

Doina Precup

José Miguel Hernández-Lobato

Marwin Segler

Michael M. Bronstein

Anne Marinier

Mike Tyers

Despite substantial progress in machine learning for scientific discovery in recent years, truly de novo design of small molecules which exh… (see more)ibit a property of interest remains a significant challenge. We introduce LambdaZero, a generative active learning approach to search for synthesizable molecules. Powered by deep reinforcement learning, LambdaZero learns to search over the vast space of molecules to discover candidates with a desired property. We apply LambdaZero with molecular docking to design novel small molecules that inhibit the enzyme soluble Epoxide Hydrolase 2 (sEH), while enforcing constraints on synthesizability and drug-likeliness. LambdaZero provides an exponential speedup in terms of the number of calls to the expensive molecular docking oracle, and LambdaZero de novo designed molecules reach docking scores that would otherwise require the virtual screening of a hundred billion molecules. Importantly, LambdaZero discovers novel scaffolds of synthesizable, drug-like inhibitors for sEH. In in vitro experimental validation, a series of ligands from a generated quinazoline-based scaffold were synthesized, and the lead inhibitor N-(4,6-di(pyrrolidin-1-yl)quinazolin-2-yl)-N-methylbenzamide (UM0152893) displayed sub-micromolar enzyme inhibition of sEH.

2024-05-02

ArXiv (preprint)

Iterated Denoising Energy Matching for Sampling from Boltzmann Densities

Cheng-Hao Liu

Alexander Tong

Efficiently generating statistically independent samples from an unnormalized probability distribution, such as equilibrium samples of many-… (see more)body systems, is a foundational problem in science. In this paper, we propose Iterated Denoising Energy Matching (iDEM), an iterative algorithm that uses a novel stochastic score matching objective leveraging solely the energy function and its gradient---and no data samples---to train a diffusion-based sampler. Specifically, iDEM alternates between (I) sampling regions of high model density from a diffusion-based sampler and (II) using these samples in our stochastic matching objective to further improve the sampler. iDEM is scalable to high dimensions as the inner matching objective, is *simulation-free*, and requires no MCMC samples. Moreover, by leveraging the fast mode mixing behavior of diffusion, iDEM smooths out the energy landscape enabling efficient exploration and learning of an amortized sampler. We evaluate iDEM on a suite of tasks ranging from standard synthetic energy functions to invariant

2024-05-01

ICML.cc/2024/Conference (poster)