Care of terminally ill / Palliative care

Single-and double-strand circulating DNA fragmentomics for enhanced cancer detection performance

In early detection of cancer, the use of circulating cell-free DNA (cirDNA) obtained from blood samples is notable for its minimally invasive nature. We have developed an algorithm designed to discriminate cancer patients and healthy individuals based on cirDNA fragment end motif analysis assisted by machine learning, using data obtained from shallow whole genome sequencing (a method we call EMA)....

Intelligent Tool Orchestration for Rapid Mechanistic Model Prototyping: MCP Servers as AI-Biology Interfaces

The construction of multicellular mechanistic models in systems biology typically requires months of literature research, programming expertise, and deep knowledge of specialized computational tools. Here we present intelligent tool orchestration through Model Context Protocol (MCP) servers that enable Large Language Models (LLMs) agents to function as AI laboratory assistants for rapid model prot...

BioML-bench: Evaluation of AI Agents for End-to-End Biomedical ML

Large language model (LLM) agents hold promise for accelerating biomedical research and development (R&D). Several biomedical agents have recently bee...

PyCLM: programming-free, closed-loop microscopy for real-time measurement, segmentation, and optogenetic stimulation

In cell biology, optical techniques are increasingly used to measure cells’ internal states (biosensors) and to stimulate cellular responses (optogene...

JAX Animal Behavior System (JABS): A genetics informed, end-to-end advanced behavioral phenotyping platform for the laboratory mouse

Automated detection of complex animal behavior remains a challenge in neuroscience. Developments in computer vision have greatly advanced automated be...

Frequency-Aware Interpretable Deep Learning Framework for Alzheimer’s Disease Classification Using rs-fMRI

Gaining insight into the spectral and temporal alterations in brain connectivity associated with Alzheimer’s disease (AD) may offer pathways toward mo...

Pathologist-interpretable breast cancer subtyping and stratification from AI-inferred nuclear features

Artificial intelligence (AI) is making notable advances in digital pathology but faces challenges in human interpretability. Here we introduce EXPAND ...

RawBench: A Comprehensive Benchmarking Framework for Raw Nanopore Signal Analysis Techniques

Nanopore sequencing technologies continue to advance rapidly, offering critical benefits such as real-time analysis, the ability to sequence extremely...

Accurate and efficient phylogenetic inference through end-to-end deep learning

Accurate phylogenetic inference is crucial for understanding evolutionary relationships among species. Deep learning technique has been introduced for...

One-Class Bioacoustic Detector for Monitoring the Critically Endangered Pied Tamarin (Saguinus bicolor)

The pied tamarin (Saguinus bicolor) is a critically endangered primate with a small geographic range that includes fragmented urban forest mosaics in ...

Deciphering the Antigenic Evolution of Seasonal Influenza A Viruses with PREDAC-Transformer: From Antigenic Clustering to Key Site Identification

Seasonal influenza viruses undergo continuous antigenic drift due to mutations in the hemagglutinin (HA) protein, rendering vaccines ineffective and p...

PRSNet-2: End-to-end genotype-to-phenotype prediction via hierarchical graph neural networks

The emergence of large-scale biobanks has opened unprecedented opportunities for the development of data-driven approaches, especially deep learning-b...

Direct Training of Networks of Morris-Lecar Neurons with Backprop

Spiking Neural Networks (SNNs) have the potential to replicate the brain’s computational efficacy by explicitly incorporating action potentials or “sp...

Lab-in-the-loop therapeutic antibody design with deep learning

Therapeutic antibody design is a complex multi-property optimization problem with substantial promise for improvement with the application of machine-...

IRCAS: a novel end-to-end approach to identify, rectify and classify comprehensive alternative splicing events in a transcriptome without genome reference

Alternative splicing (AS) is a fundamental post-transcriptional mechanism that amplifies proteomic diversity and enables adaptive responses across euk...

Deep-Pose-Tracker: a unified model for behavioural studies of Caenorhabditis elegans

Tracking and analyzing animal behaviour is a crucial step in fields such as neuro-science and developmental biology. Behavioral studies in the nematod...

From Skin to Cortex: End-to-End Spiking Neural Network Simulation of Tactile Information Flow

Autonomous systems and neuroprosthetic devices demand real-time tactile processing under strict energy and latency constraints. Designing these system...

Closing the Sim-to-Real Gap: An End-to-End Robotic Ultrasound System Leveraging In Vivo Reinforcement Learning and 3D-Prior Guided Hybrid Control

Abdominal ultrasound is a crucial first-line diagnostic tool, yet its efficacy is inherently constrained by a strong dependency on operator skill, lea...

MS4MS: LLMs-driven Multi-agent System for Small-molecule Identification via LC-MS/MS

Small molecule identification is central to research fields such as drug discovery, but in complex systems like Traditional Chinese Medicine (TCM), tr...

End-to-end prediction of clinical outcomes in head and neck squamous cell carcinoma with foundation model-based multiple instance learning

Foundation models (FMs) show promise in medical AI by learning flexible features from large datasets, potentially surpassing handcrafted radiomics. Ou...