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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…

In the treatment of complex diseases, treatment regimens using a single drug often yield limited efficacy and can lead to drug resistance. In contrast, combination drug therapies can significantly improve therapeutic outcomes through…

Recommender systems are designed to predict user preferences over collections of items. These systems process users' previous interactions to decide which items should be ranked higher to satisfy their desires. An ensemble recommender…

Hypergraphs effectively model higher-order relationships in natural phenomena, capturing complex interactions beyond pairwise connections. We introduce a novel hypergraph message passing framework inspired by interacting particle systems,…

Higher-order information is crucial for relational learning in many domains where relationships extend beyond pairwise interactions. Hypergraphs provide a natural framework for modeling such relationships, which has motivated recent…

Many empirical systems contain complex interactions of arbitrary size, representing, for example, chemical reactions, social groups, co-authorship relationships, and ecological dependencies. These interactions are known as higher-order…

Transformer architectures, capable of capturing sequential dependencies in the history of user interactions, have become the dominant approach in sequential recommender systems. Despite their success, such models consider sequence elements…

Drug-drug interactions (DDIs) are a major concern in clinical practice, as they can lead to reduced therapeutic efficacy or severe adverse effects. Traditional computational approaches often struggle to capture the complex relationships…

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…

Inferring the unseen attribute-object composition is critical to make machines learn to decompose and compose complex concepts like people. Most existing methods are limited to the composition recognition of single-attribute-object, and can…

Comparing networks is essential for a number of downstream tasks, from clustering to anomaly detection. Despite higher-order interactions being critical for understanding the dynamics of complex systems, traditional approaches for network…

Inferring objects and their relationships from an image in the form of a scene graph is useful in many applications at the intersection of vision and language. We consider a challenging problem of compositional generalization that emerges…

We introduce the hierarchical compositional network (HCN), a directed generative model able to discover and disentangle, without supervision, the building blocks of a set of binary images. The building blocks are binary features defined…

Graphs are the most ubiquitous data structures for representing relational datasets and performing inferences in them. They model, however, only pairwise relations between nodes and are not designed for encoding the higher-order relations.…

The widespread application of machine learning techniques to biomedical data has produced many new insights into disease progression and improving clinical care. Inspired by the flexibility and interpretability of graphs (networks), as well…

Recent advances and achievements of artificial intelligence (AI) as well as deep and graph learning models have established their usefulness in biomedical applications, especially in drug-drug interactions (DDIs). DDIs refer to a change in…

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without…

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically…

Numerous networked systems feature a structure of nontrivial communities, which often correspond to their functional modules. Such communities have been detected in real-world biological, social and technological systems, as well as in…

Networks are frequently used to model complex systems comprised of interacting elements. While edges capture the topology of direct interactions, the true complexity of many systems originates from higher-order patterns in paths by which…