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Modern disease classification often overlooks molecular commonalities hidden beneath divergent clinical presentations. This study introduces a transcriptomics-driven framework for discovering disease relationships by analyzing over 1300…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Large language models (LLMs) have been demonstrated to possess the capabilities to understand fundamental graph properties and address various graph reasoning tasks. Existing methods fine-tune LLMs to understand and execute graph reasoning…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
Interrogation of biological pathways is an integral part of omics data analysis. Large language models (LLMs) enable the generation of custom pathways and gene sets tailored to specific scientific questions. These targeted sets are…
Even more interesting than the intricate organization of complex networks are the dynamical behavior of systems which such structures underly. Among the many types of dynamics, one particularly interesting category involves the evolution of…
The inspection of the Public Right of Way (PROW) for accessibility barriers is necessary for monitoring and maintaining the built environment for communities' walkability, rollability, safety, active transportation, and sustainability.…
The computer-aided detection (CADe) systems are developed to assist pathologists in slide assessment, increasing diagnosis efficiency and reducing missing inspections. Many studies have shown such a CADe system with deep learning approaches…
Purpose: Tracking the 3D motion of the surgical tool and the patient anatomy is a fundamental requirement for computer-assisted skull-base surgery. The estimated motion can be used both for intra-operative guidance and for downstream skill…
Background: Metabolomics datasets are becoming increasingly large and complex, with multiple types of algorithms and workflows needed to process and analyse the data. A cloud infrastructure with portable software tools can provide much…
Whole Slide Image (WSI) analysis plays a crucial role in modern digital pathology, enabling large-scale feature extraction from tissue samples. However, traditional feature extraction pipelines based on tools like CellProfiler often involve…
Cancer is a highly heterogeneous disease with significant variability in molecular features and clinical outcomes, making diagnosis and treatment challenging. In recent years, high-throughput omic technologies have facilitated the discovery…
Pathology foundation models (PFMs) have emerged as a core approach for learning transferable representations from whole slide images (WSIs), and they are typically benchmarked through downstream clinical endpoints. While such task level…
One essential component in the construction of patent landscapes in biomedical research and development (R&D) is identifying the most seminal patents. Hitherto, the identification of seminal patents required subject matter experts within…
Quantitative characterization of cellular spatial organization is critical for understanding tumor progression and immune response. Recent advances in artificial intelligence (AI) enable large-scale segmentation and classification of nuclei…
Motion planning algorithms often leverage topological information about the environment to improve planner performance. However, these methods often focus only on the environment's connectivity while ignoring other properties such as…
Developing and training deep learning models is expensive, so software engineers have begun to reuse pre-trained deep learning models (PTMs) and fine-tune them for downstream tasks. Despite the wide-spread use of PTMs, we know little about…
Background: To understand protein function, it is important to study protein- protein interaction networks. These networks can be represented in network diagrams called protein interaction maps that can lead to better understanding by…
We introduce PATHWAYS, a benchmark of 250 multi-step decision tasks that test whether web-based agents can discover and correctly use hidden contextual information. Across both closed and open models, agents typically navigate to relevant…
Diagnosing a whole-slide image is an interactive, multi-stage process of changing magnification and moving between fields. Although recent pathology foundation models demonstrated superior performances, practical agentic systems that decide…