Genetics

RNAElectra: An ELECTRA-Style RNA Foundation Model for RNA Regulatory Inference

RNA regulation governs gene expression through sequence-encoded mechanisms such as RNA structure formation, protein binding, chemical modification, and RNA-RNA targeting, with regulatory rules spanning both nucleotide-scale motifs and longer-range context. RNA foundation models seek to learn transferable representations from large RNA corpora, but most existing approaches rely on masked language m...

A network-based deep learning model integrating subclonal architecture for therapy response prediction in cancer

Predicting treatment response remains challenging in oncology, particularly given the growing diversity of therapeutic options. Despite efforts using gene expression signatures, or integrative multi-omics frameworks, robust and interpretable biomarkers remain limited. We present SubNetDL, a deep learning framework that integrates subclonal mutation profiles and protein-protein interaction networks...

Identification of compounds that repress DUX4 expression in facioscapulohumeral muscular dystrophy

Facioscapulohumeral muscular dystrophy (FSHD) is caused by epigenetic dysregulation of the disease locus, leading to pathogenic misexpression of DUX4 ...

ChromBERT: Uncovering Chromatin State Motifs in the Human Genome Using a BERT-based Approach

Chromatin states, which are defined by specific combinations of histone post-translational modifications, are fundamental to gene regulation and cellu...

CompDiff: Hierarchical Compositional Diffusion for Fair and Zero-Shot Intersectional Medical Image Generation

Generative models are increasingly used to augment medical imaging datasets for fairer AI. Yet a key assumption often goes unexamined: that generators...

HistoAtlas: A Pan-Cancer Morphology Atlas Linking Histomics to Molecular Programs and Clinical Outcomes

We present HistoAtlas, a pan-cancer computational atlas that extracts 38 interpretable histomic features from 6,745 diagnostic H&E slides across 21 TC...

pertTF: context-aware AI modeling for genome-scale and cross-system perturbation prediction

Predicting genetic perturbation responses at a single-cell level is central to building models for cell state and disease. However, existing approache...

Longitudinal Risk Prediction in Mammography with Privileged History Distillation

Breast cancer remains a leading cause of cancer-related mortality worldwide. Longitudinal mammography risk prediction models improve multi-year breast...

Multi-Task Genetic Algorithm with Multi-Granularity Encoding for Protein-Nucleotide Binding Site Prediction

Accurate identification of protein-nucleotide binding sites is fundamental to deciphering molecular mechanisms and accelerating drug discovery. Howeve...

From Artefact to Insight: Efficient Low-Rank Adaptation of BrushNet for Scanning Probe Microscopy Image Restoration

Scanning Probe Microscopy or SPM offers nanoscale resolution but is frequently marred by structured artefacts such as line scan dropout, gain induced ...

Autonomous Agents Coordinating Distributed Discovery Through Emergent Artifact Exchange

We present ScienceClaw + Infinite, a framework for autonomous scientific investigation in which independent agents conduct research without central co...

Distilling Latent Manifolds: Resolution Extrapolation by Variational Autoencoders

Variational Autoencoder (VAE) encoders play a critical role in modern generative models, yet their computational cost often motivates the use of knowl...

A Heterogeneous Ensemble for Multi-Center COVID-19 Classification from Chest CT Scans

The COVID-19 pandemic exposed critical limitations in diagnostic workflows: RT-PCR tests suffer from slow turnaround times and high false-negative rat...

A Closed-Form Solution for Debiasing Vision-Language Models with Utility Guarantees Across Modalities and Tasks

While Vision-Language Models (VLMs) have achieved remarkable performance across diverse downstream tasks, recent studies have shown that they can inhe...

Generative AI-based design of hybrid transcriptional activator proteins with new DNA-binding specificity

Transcriptional control arises from the specific recognition of promoter DNA by transcription factors (TFs), forming the basis of cellular information...

Facilitating genome annotation using ANNEXA and long-read RNA sequencing

With the advent of complete genome assemblies, genome annotation has become essential for the functional interpretation of genomic data. Long-read RNA...

mnDINO: Accurate and robust segmentation of micronuclei with vision transformer networks

Recent advances in cell segmentation successfully produce models that generalize across various cell-lines and imaging types. However, these methods s...

A DNA foundation model predicts osteoporosis risk genes without proximity bias

Targets supported by human genetic associations are more than twice as likely to progress from clinical development to approval. Genome-wide associati...

Application of large language models to the annotation of cell lines and mouse strains in genomics data

Accurate, consistent and comprehensive metadata are essential for the reuse of functional genomics data deposited in repositories such as the Gene Exp...

Predicting targeted- and immunotherapeutic response outcomes in melanoma with single-cell Raman Spectroscopy and AI

Identifying predictive biomarkers of immunotherapeutic response in melanoma remains an outstanding challenge. Existing transcriptomic and proteomic pr...