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Graph embedding maps a graph into a convenient vector-space representation for graph analysis and machine learning applications. Many graph embedding methods hinge on a sampling of context nodes based on random walks. However, random walks…

In traditional software programs, it is easy to trace program logic from variables back to input, apply assertion statements to block erroneous behavior, and compose programs together. Although deep learning programs have demonstrated…

Neural networks have become an increasingly popular tool for solving many real-world problems. They are a general framework for differentiable optimization which includes many other machine learning approaches as special cases. In this…

Recently, there has been an interest in embedding networks in hyperbolic space, since hyperbolic space has been shown to work well in capturing graph/network structure as it can naturally reflect some properties of complex networks.…

Deep learning has revolutionized many industries by enabling models to automatically learn complex patterns from raw data, reducing dependence on manual feature engineering. However, deep learning algorithms are sensitive to input data, and…

Network embeddings, which learn low-dimensional representations for each vertex in a large-scale network, have received considerable attention in recent years. For a wide range of applications, vertices in a network are typically…

Network embedding has attracted an increasing attention over the past few years. As an effective approach to solve graph mining problems, network embedding aims to learn a low-dimensional feature vector representation for each node of a…

Recent advances in machine learning offer new ways to represent and study scholarly works and the space of knowledge. Graph and text embeddings provide a convenient vector representation of scholarly works based on citations and text. Yet,…

Proteins are essential for life, and their structure determines their function. The protein secondary structure is formed by the folding of the protein primary structure, and the protein tertiary structure is formed by the bending and…

In graph representation learning, it is important that the complex geometric structure of the input graph, e.g. hidden relations among nodes, is well captured in embedding space. However, standard Euclidean embedding spaces have a limited…

Topological representations are rapidly becoming a popular way to capture and encode higher-order interactions in complex systems. They have found applications in disciplines as different as cancer genomics, brain function, and…

This paper investigates how the compositional structure of neural networks shapes their optimization landscape and training dynamics. We analyze the gradient flow associated with overparameterized optimization problems, which can be…

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered…

Learning the distance metric between pairs of examples is of great importance for learning and visual recognition. With the remarkable success from the state of the art convolutional neural networks, recent works have shown promising…

Modern deep learning-based recommendation systems exploit hundreds to thousands of different categorical features, each with millions of different categories ranging from clicks to posts. To respect the natural diversity within the…

In this paper, we show that high-performing embedding models organize their embedding spaces in a consistent way. We evaluate 25 contemporary embedding models on five MTEB tasks spanning four diverse task categories (retrieval, bitext…

The characterization of drug-protein interactions is crucial in the high-throughput screening for drug discovery. The deep learning-based approaches have attracted attention because they can predict drug-protein interactions without…

Text word embeddings that encode distributional semantics work by modeling contextual similarities of frequently occurring words. Acoustic word embeddings, on the other hand, typically encode low-level phonetic similarities. Semantic…

Though modern neural networks have achieved impressive performance in both vision and language tasks, we know little about the functions that they implement. One possibility is that neural networks implicitly break down complex tasks into…

Since proteins carry out biological processes by interacting with other proteins, analyzing the structure of protein-protein interaction (PPI) networks could explain complex biological mechanisms, evolution, and disease. Similarly, studying…