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Clinical practice in psychiatry is burdened with the increased demand for healthcare services and the scarce resources available. New paradigms of health data powered with machine learning techniques could open the possibility to improve…

Rare diseases (RDs) are collectively common and affect 300 million people worldwide. Accurate phenotyping is critical for informing diagnosis and treatment, but RD phenotypes are often embedded in unstructured text and time-consuming to…

RNA-sequencing (RNA-seq) has become an exemplar technology in modern biology and clinical applications over the past decade. It has gained immense popularity in the recent years driven by continuous efforts of the bioinformatics community…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

Human placenta is a complex and heterogeneous organ interfacing between the mother and the fetus that supports fetal development. Alterations to placental structural components are associated with various pregnancy complications. To reveal…

A key property of neural networks (both biological and artificial) is how they learn to represent and manipulate input information in order to solve a task. Different types of representations may be suited to different types of tasks,…

Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical…

Single-cell RNA-Sequencing (scRNA-Seq) has undergone major technological advances in recent years, enabling the conception of various organism-level cell atlassing projects. With increasing numbers of datasets being deposited in public…

Large language models excel at interpreting complex natural language instructions, enabling them to perform a wide range of tasks. In the life sciences, single-cell RNA sequencing (scRNA-seq) data serves as the "language of cellular…

Predicting the impact of genomic and drug perturbations in cellular function is crucial for understanding gene functions and drug effects, ultimately leading to improved therapies. To this end, Causal Representation Learning (CRL)…

Single-cell RNA sequencing (scRNA-seq) data is a potent tool for comprehending the "language of life" and can provide insights into various downstream biomedical tasks. Large-scale language models (LLMs) are starting to be used for cell…

Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. The analysis of scRNA-seq data poses…

The one-shot Person Re-ID scenario faces two kinds of uncertainties when constructing the prediction model from $X$ to $Y$. The first is model uncertainty, which captures the noise of the parameters in DNNs due to a lack of training data.…

In practical scenarios, the effectiveness of sequential recommendation systems is hindered by the user cold-start problem, which arises due to limited interactions for accurately determining user preferences. Previous studies have attempted…

Despite the success of deep learning in dermoscopy image analysis, its inherent black-box nature hinders clinical trust, motivating the use of prototypical networks for case-based visual transparency. However, inevitable selection bias in…

Background: Small interfering RNA (siRNA) is a promising therapeutic agent due to its ability to silence disease-related genes via RNA interference. While traditional machine learning and early deep learning methods have made progress in…

While single-cell RNA sequencing provides an understanding of the transcriptome of individual cells, its high sparsity, often termed dropout, hampers the capture of significant cell-cell relationships. Here, we propose scFP (single-cell…

Generating high-fidelity and biologically plausible synthetic single-cell RNA sequencing (scRNA-seq) data, especially with conditional control, is challenging due to its high dimensionality, sparsity, and complex biological variations.…

Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…

Single-cell RNA-seq foundation models achieve strong performance on downstream tasks but remain black boxes, limiting their utility for biological discovery. Recent work has shown that sparse dictionary learning can extract concepts from…