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Large-scale knowledge bases have currently reached impressive sizes; however, these knowledge bases are still far from complete. In addition, most of the existing methods for knowledge base completion only consider the direct links between…

The temporal dynamics of a complex system such as a social network or a communication network can be studied by understanding the patterns of link appearance and disappearance over time. A critical task along this understanding is to…

Proteins are the major building blocks of life, and actuators of almost all chemical and biophysical events in living organisms. Their native structures in turn enable their biological functions which have a fundamental role in drug design.…

Deep learning has made significant progress in protein structure prediction, advancing the development of computational biology. However, despite the high accuracy achieved in predicting single-chain structures, a significant number of…

Link prediction, as a frontier task in complex network topology analysis, aims to infer the existence of latent links between node pairs based on observed nodes and structural information. We propose an ensemble link prediction model that…

Network representation learning (also known as information network embedding) has been the central piece of research in social and information network analysis for the last couple of years. An information network can be viewed as a linked…

Effective representation of data is crucial in various machine learning tasks, as it captures the underlying structure and context of the data. Embeddings have emerged as a powerful technique for data representation, but evaluating their…

Relational data mining is becoming ubiquitous in many fields of study. It offers insights into behaviour of complex, real-world systems which cannot be modeled directly using propositional learning. We propose Symbolic Graph Embedding…

Deep neural networks for machine comprehension typically utilizes only word or character embeddings without explicitly taking advantage of structured linguistic information such as constituency trees and dependency trees. In this paper, we…

Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein…

A popular testbed for deep learning has been multimodal recognition of human activity or gesture involving diverse inputs such as video, audio, skeletal pose and depth images. Deep learning architectures have excelled on such problems due…

We investigate compositional structures in data embeddings from pre-trained vision-language models (VLMs). Traditionally, compositionality has been associated with algebraic operations on embeddings of words from a pre-existing vocabulary.…

Complex networks represented as node adjacency matrices constrains the application of machine learning and parallel algorithms. To address this limitation, network embedding (i.e., graph representation) has been intensively studied to learn…

Convolutional neural networks (CNNs) have shown great success in computer vision, approaching human-level performance when trained for specific tasks via application-specific loss functions. In this paper, we propose a method for augmenting…

A formal description of the compositionality of neural networks is associated directly with the formal grammar-structure of the objects it seeks to represent. This formal grammar-structure specifies the kind of components that make up an…

Designing novel protein sequences for a desired 3D topological fold is a fundamental yet non-trivial task in protein engineering. Challenges exist due to the complex sequence--fold relationship, as well as the difficulties to capture the…

Empirical scoring functions based on either molecular force fields or cheminformatics descriptors are widely used, in conjunction with molecular docking, during the early stages of drug discovery to predict potency and binding affinity of a…

Kernel classifiers and regressors designed for structured data, such as sequences, trees and graphs, have significantly advanced a number of interdisciplinary areas such as computational biology and drug design. Typically, kernels are…

Link prediction is critical for the application of incomplete knowledge graph (KG) in the downstream tasks. As a family of effective approaches for link predictions, embedding methods try to learn low-rank representations for both entities…

Representation learning is central to graph machine learning, powering tasks such as link prediction and node classification. However, most graph embeddings are hard to interpret, offering limited insight into how learned features relate to…