Emmanuel Bengio

Multi-Objective GFlowNets

Moksh J. Jain

Sharath Chandra Raparthy

Alex Hernandez-Garcia

Jarrid Rector-Brooks

Yoshua Bengio

Santiago Miret

We study the problem of generating diverse candidates in the context of Multi-Objective Optimization. In many applications of machine learni… (see more)ng such as drug discovery and material design, the goal is to generate candidates which simultaneously optimize a set of potentially conflicting objectives. Moreover, these objectives are often imperfect evaluations of some underlying property of interest, making it important to generate diverse candidates to have multiple options for expensive downstream evaluations. We propose Multi-Objective GFlowNets (MOGFNs), a novel method for generating diverse Pareto optimal solutions, based on GFlowNets. We introduce two variants of MOGFNs: MOGFN-PC, which models a family of independent sub-problems defined by a scalarization function, with reward-conditional GFlowNets, and MOGFN-AL, which solves a sequence of sub-problems defined by an acquisition function in an active learning loop. Our experiments on wide variety of synthetic and benchmark tasks demonstrate advantages of the proposed methods in terms of the Pareto performance and importantly, improved candidate diversity, which is the main contribution of this work.

2022-10-23

ArXiv (preprint)

Multi-Objective GFlowNets

Moksh J. Jain

Sharath Chandra Raparthy

Alex Hernandez-Garcia

Jarrid Rector-Brooks

Yoshua Bengio

Santiago Miret

We study the problem of generating diverse candidates in the context of Multi-Objective Optimization. In many applications of machine learni… (see more)ng such as drug discovery and material design, the goal is to generate candidates which simultaneously optimize a set of potentially conflicting objectives. Moreover, these objectives are often imperfect evaluations of some underlying property of interest, making it important to generate diverse candidates to have multiple options for expensive downstream evaluations. We propose Multi-Objective GFlowNets (MOGFNs), a novel method for generating diverse Pareto optimal solutions, based on GFlowNets. We introduce two variants of MOGFNs: MOGFN-PC, which models a family of independent sub-problems defined by a scalarization function, with reward-conditional GFlowNets, and MOGFN-AL, which solves a sequence of sub-problems defined by an acquisition function in an active learning loop. Our experiments on wide variety of synthetic and benchmark tasks demonstrate advantages of the proposed methods in terms of the Pareto performance and importantly, improved candidate diversity, which is the main contribution of this work.

2022-10-23

ArXiv (preprint)

Biological Sequence Design with GFlowNets

Moksh J. Jain

Alex Hernandez-Garcia

Jarrid Rector-Brooks

Bonaventure F. P. Dossou

Micheal Kilgour

Payel Das

2022-06-28

Proceedings of the 39th International Conference on Machine Learning (published)

E VALUATING G ENERALIZATION IN GF LOW N ETS FOR M OLECULE D ESIGN

Moksh J. Jain

Cheng-Hao Liu

Michael M. Bronstein

Deep learning bears promise for drug discovery problems such as de novo molecular design. Generating data to train such models is a costly a… (see more)nd time-consuming process, given the need for wet-lab experiments or expensive simulations. This problem is compounded by the notorious data-hungriness of machine learning algorithms. In small molecule generation the recently proposed GFlowNet method has shown good performance in generating diverse high-scoring candidates, and has the interesting advantage of being an off-policy offline method. Finding an appropriate generalization evaluation metric for such models, one predictive of the desired search performance (i.e. finding high-scoring diverse candidates), will help guide online data collection for such an algorithm. In this work, we develop techniques for evaluating GFlowNet performance on a test set, and identify the most promising metric for predicting generalization. We present empirical results on several small-molecule design tasks in drug discovery, for several GFlowNet training setups, and we find a metric strongly correlated with diverse high-scoring batch generation. This metric should be used to identify the best generative model from which to sample batches of molecules to be evaluated.

2022-04-05

ICLR.cc/2022/Workshop/MLDD (poster)

openreview.net

Trajectory Balance: Improved Credit Assignment in GFlowNets

Nikolay Malkin

Moksh J. Jain

Chen Sun

Yoshua Bengio

Generative flow networks (GFlowNets) are a method for learning a stochastic policy for generating compositional objects, such as graphs or s… (see more)trings, from a given unnormalized density by sequences of actions, where many possible action sequences may lead to the same object. We find previously proposed learning objectives for GFlowNets, flow matching and detailed balance, which are analogous to temporal difference learning, to be prone to inefficient credit propagation across long action sequences. We thus propose a new learning objective for GFlowNets, trajectory balance, as a more efficient alternative to previously used objectives. We prove that any global minimizer of the trajectory balance objective can define a policy that samples exactly from the target distribution. In experiments on four distinct domains, we empirically demonstrate the benefits of the trajectory balance objective for GFlowNet convergence, diversity of generated samples, and robustness to long action sequences and large action spaces.

GFlowNet Foundations

Edward J Hu

Mo Tiwari

2021-11-17

ArXiv (preprint)

GFlowNet Foundations

Edward J Hu

Mo Tiwari

2021-11-17

ArXiv (preprint)

GFlowNet Foundations

Edward J Hu

Mo Tiwari

Generative Flow Networks (GFlowNets) have been introduced as a method to sample a diverse set of candidates in an active learning context, w… (see more)ith a training objective that makes them approximately sample in proportion to a given reward function. In this paper, we show a number of additional theoretical properties of GFlowNets. They can be used to estimate joint probability distributions and the corresponding marginal distributions where some variables are unspecified and, of particular interest, can represent distributions over composite objects like sets and graphs. GFlowNets amortize the work typically done by computationally expensive MCMC methods in a single but trained generative pass. They could also be used to estimate partition functions and free energies, conditional probabilities of supersets (supergraphs) given a subset (subgraph), as well as marginal distributions over all supersets (supergraphs) of a given set (graph). We introduce variations enabling the estimation of entropy and mutual information, sampling from a Pareto frontier, connections to reward-maximizing policies, and extensions to stochastic environments, continuous actions and modular energy functions.

2021-11-17

ArXiv (preprint)

GFlowNet Foundations

Edward J Hu

Mo Tiwari

2021-11-17

ArXiv (preprint)

GFlowNet Foundations

Edward J Hu

Mo Tiwari

2021-11-17

ArXiv (preprint)

GFlowNet Foundations

Edward J Hu

Mo Tiwari

Generative Flow Networks (GFlowNets) have been introduced as a method to sample a diverse set of candidates in an active learning context, w… (see more)ith a training objective that makes them approximately sample in proportion to a given reward function. In this paper, we show a number of additional theoretical properties of GFlowNets. They can be used to estimate joint probability distributions and the corresponding marginal distributions where some variables are unspecified and, of particular interest, can represent distributions over composite objects like sets and graphs. GFlowNets amortize the work typically done by computationally expensive MCMC methods in a single but trained generative pass. They could also be used to estimate partition functions and free energies, conditional probabilities of supersets (supergraphs) given a subset (subgraph), as well as marginal distributions over all supersets (supergraphs) of a given set (graph). We introduce variations enabling the estimation of entropy and mutual information, sampling from a Pareto frontier, connections to reward-maximizing policies, and extensions to stochastic environments, continuous actions and modular energy functions.

2021-11-17

ArXiv (preprint)