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Embedding network data into a low-dimensional vector space has shown promising performance for many real-world applications, such as node classification and entity retrieval. However, most existing methods focused only on leveraging network…

Genetic mutations frequently disrupt protein structure, stability, and solubility, acting as primary drivers for a wide spectrum of diseases. Despite the critical importance of these molecular alterations, existing computational models…

Recent advances in high-resolution sequencing have paved the way for population-scale analysis in single-cell RNA-sequencing (scRNA-seq) data. scRNA-seq data, in particular, have proven to be extremely powerful in profiling a variety of…

Motivation: High-throughput sequencing enables expression analysis at the level of individual transcripts. The analysis of transcriptome expression levels and differential expression estimation requires a probabilistic approach to properly…

Hierarchical clustering is a fundamental machine-learning technique for grouping data points into dendrograms. However, existing hierarchical clustering methods encounter two primary challenges: 1) Most methods specify dendrograms without a…

Heterogeneous information network (HIN) embedding aims to embed multiple types of nodes into a low-dimensional space. Although most existing HIN embedding methods consider heterogeneous relations in HINs, they usually employ one single…

A robust and informative local shape descriptor plays an important role in mesh registration. In this regard, spectral descriptors that are based on the spectrum of the Laplace-Beltrami operator have been a popular subject of research for…

Single-cell RNA sequencing technologies have revolutionized our understanding of cellular heterogeneity, yet computational methods often struggle to balance performance with biological interpretability. Embedded topic models have been…

Deep learning models have achieved promising disease prediction performance of the Electronic Health Records (EHR) of patients. However, most models developed under the I.I.D. hypothesis fail to consider the agnostic distribution shifts,…

Estimating the probability of rare failure events is an essential step in the reliability assessment of engineering systems. Computing this failure probability for complex non-linear systems is challenging, and has recently spurred the…

Existing Masked Image Modeling methods apply fixed mask patterns to guide the self-supervised training. As those mask patterns resort to different criteria to depict image contents, sticking to a fixed pattern leads to a limited vision cues…

Reasoning from sequences of raw sensory data is a ubiquitous problem across fields ranging from medical devices to robotics. These problems often involve using long sequences of raw sensor data (e.g. magnetometers, piezoresistors) to…

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…

We introduce a spectral embedding algorithm for finding proximal relationships between nodes in signed graphs, where edges can take either positive or negative weights. Adopting a physical perspective, we construct a Hamiltonian which is…

Histology imaging is an important tool in medical diagnosis and research, enabling the examination of tissue structure and composition at the microscopic level. Understanding the underlying molecular mechanisms of tissue architecture is…

Persistent homology (PH) is one of the most popular tools in topological data analysis (TDA), while graph theory has had a significant impact on data science. Our earlier work introduced the persistent spectral graph (PSG) theory as a…

Graph-based methods are known to be successful in many machine learning and pattern classification tasks. These methods consider semi-structured data as graphs where nodes correspond to primitives (parts, interest points, segments, etc.)…

We present a systematic evaluation framework - thirty-seven analyses, 153 statistical tests, four cell types, two perturbation modalities - for assessing mechanistic interpretability in single-cell foundation models. Applying this framework…

t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a…

Network embedding represents nodes in a continuous vector space and preserves structure information from the Network. Existing methods usually adopt a "one-size-fits-all" approach when concerning multi-scale structure information, such as…