Related papers: GFlowNets for Learning Better Drug-Drug Interactio…

Accurate drug response prediction (DRP) is a crucial yet challenging task in precision medicine. This paper presents a novel Attention-Guided Multi-omics Integration (AGMI) approach for DRP, which first constructs a Multi-edge Graph (MeG)…

Feature interaction is a core ingredient in ranking models for large-scale recommender systems, yet making it both expressive and efficiently scalable remains challenging. Exhaustive pairwise interaction is powerful but incurs quadratic…

Adverse drug-drug interactions~(DDIs) can compromise the effectiveness of concurrent drug administration, posing a significant challenge in healthcare. As the development of new drugs continues, the potential for unknown adverse effects…

Modeling the interactions between drugs, targets, and diseases is paramount in drug discovery and has significant implications for precision medicine and personalized treatments. Current approaches frequently consider drug-target or…

Generative Flow Networks (GFlowNets) excel at sampling diverse, high-reward objects. In many practical applications where active reward queries are infeasible, these models must be trained using static offline datasets. Prevailing training…

Background. Drug-drug interaction (DDI) is a major cause of morbidity and mortality. [...] Biomedical literature mining can aid DDI research by extracting relevant DDI signals from either the published literature or large clinical…

The application of generative models for experimental drug discovery campaigns is severely limited by the difficulty of designing molecules de novo that can be synthesized in practice. Previous works have leveraged Generative Flow Networks…

Characterizing interactions between drugs is important to avoid potentially harmful combinations, to reduce off-target effects of treatments and to fight antibiotic resistant pathogens, among others. Here we present a network inference…

The role of Artificial Intelligence (AI) is growing in every stage of drug development. Nevertheless, a major challenge in drug discovery AI remains: Drug pharmacokinetic (PK) and Drug-Target Interaction (DTI) datasets collected in…

Recent advancements in graph representation learning have shifted attention towards dynamic graphs, which exhibit evolving topologies and features over time. The increased use of such graphs creates a paramount need for generative models…

Predicting drug side-effects before they occur is a key task in keeping the number of drug-related hospitalizations low and to improve drug discovery processes. Automatic predictors of side-effects generally are not able to process the…

We present two novel generative geometric deep learning frameworks, termed Flow Matching PointNet and Diffusion PointNet, for predicting fluid flow variables on irregular geometries by incorporating PointNet into flow matching and diffusion…

Generative Flow Networks (GFlowNets) are amortized samplers that learn stochastic policies to sequentially generate compositional objects from a given unnormalized reward distribution. They can generate diverse sets of high-reward objects,…

Deep generative models (DGM) are neural networks with many hidden layers trained to approximate complicated, high-dimensional probability distributions using a large number of samples. When trained successfully, we can use the DGMs to…

Graph classification is a challenging research problem in many applications across a broad range of domains. In these applications, it is very common that class distribution is imbalanced. Recently, Graph Neural Network (GNN) models have…

Generative Flow Networks (GFlowNets) are a family of generative models that learn to sample objects from a given probability distribution, potentially known up to a normalizing constant. Instead of working in the object space, GFlowNets…

Traditional reinforcement learning often struggles to generate diverse, high-reward solutions, especially in domains like drug design and black-box function optimization. Markov Chain Monte Carlo (MCMC) methods provide an alternative method…

Recent years have witnessed great success in handling node classification tasks with Graph Neural Networks (GNNs). However, most existing GNNs are based on the assumption that node samples for different classes are balanced, while for many…

Flow matching and diffusion bridge models have emerged as leading paradigms in generative speech enhancement, modeling stochastic processes between paired noisy and clean speech signals based on principles such as flow matching, score…

We tackle the problem of sampling from intractable high-dimensional density functions, a fundamental task that often appears in machine learning and statistics. We extend recent sampling-based approaches that leverage controlled stochastic…