Related papers: A Comparison of the Pathway Tools Software with th…
Based on the data of the NIH-funded Human Connectome Project, we have computed structural connectomes of 426 human subjects in five different resolutions of 83, 129, 234, 463 and 1015 nodes and several edge weights. The graphs are given in…
Multimodal survival methods combining gigapixel histology whole-slide images (WSIs) and transcriptomic profiles are particularly promising for patient prognostication and stratification. Current approaches involve tokenizing the WSIs into…
The effective visualization of genomic data is crucial for exploring and interpreting complex relationships within and across genes and genomes. Despite advances in developing dedicated bioinformatics software, common visualization tools…
Medical image computing software is essential for identifying imaging biomarkers that can support diagnosis, prognosis, treatment planning, and clinical research. However, the lack of standardized, user-friendly, and reproducible software…
Large language models (LLMs) have garnered significant attention due to their impressive natural language processing (NLP) capabilities. Recently, many studies have focused on the tool utilization ability of LLMs. They primarily…
AI tools in pathology have improved screening throughput, standardized quantification, and revealed prognostic patterns that inform treatment. However, adoption remains limited because most systems still lack the human-readable reasoning…
The metabolic wiring of patient cells is altered drastically in many diseases, including cancer. Understanding the nature of such changes may pave the way for new therapeutic opportunities, as well as the development of personalized…
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep…
Recent advances in computational pathology have led to the emergence of numerous foundation models. These models typically rely on general-purpose encoders with multi-instance learning for whole slide image (WSI) classification or apply…
Background: In silico drug-target interaction (DTI) prediction plays an integral role in drug repositioning: the discovery of new uses for existing drugs. One popular method of drug repositioning is network-based DTI prediction, which uses…
Honeytokens, decoy digital assets planted to detect and attribute unauthorised access, are a well-established primitive in cyber deception. Existing generation tools produce static, template-based tokens that lack organisational specificity…
Melanoma diagnosed and treated in its early stages can increase the survival rate. A projected increase in skin cancer incidents and a dearth of dermatopathologists have emphasized the need for computational pathology (CPATH) systems. CPATH…
The development and training of deep learning models have become increasingly costly and complex. Consequently, software engineers are adopting pre-trained models (PTMs) for their downstream applications. The dynamics of the PTM supply…
High-throughput "pathomic" analysis of Whole Slide Images (WSIs) offers new opportunities to study tissue characteristics and for biomarker discovery. However, the clinical relevance of the tissue characteristics at the micro- and…
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since,…
The use of generative artificial intelligence (AI) models is becoming ubiquitous in many fields. Though progress continues to be made, general purpose large language AI models (LLM) show a tendency to deliver creative answers, often called…
Many database resources, such as Reactome, collect manually annotated reactions, interactions, and pathways from peer-reviewed publications. The interactors (e.g., a protein), interactions, and pathways in these data resources are often…
Information on protein-protein interactions (PPIs) not only advances our understanding of molecular biology but also provides important clues for target selection in drug discovery and the design of PPI inhibitors. One of the techniques…
The vast amount of sequencing data presently available allow the scientific community to explore a range of genetic variables that may drive and progress cancer. A myriad of predictive tools has been proposed, allowing researchers and…
Tool-calling agents are increasingly deployed in real-world customer-facing workflows. Yet most studies on tool-calling agents focus on idealized settings with general, fixed, and well-specified tasks. In real-world applications, user…