Computational systems biology is empowering the study of drug action. Studies on biological effects of chemical compounds have increased in scale and accessibility, allowing integration with other large-scale experimental data types. Here, we review computational approaches for elucidating the mechanisms of both intended and undesirable effects of drugs, with the collective potential to change the nature of drug discovery and pharmacological therapy.
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http://dx.doi.org/10.1074/jbc.R110.174797 | DOI Listing |
Biomed Phys Eng Express
January 2025
Department of Ophthalmology, Hospital Universitario de Canarias, Carretera Ofra S/N, La Laguna, Santa Cruz de Tenerife, 38320, SPAIN.
This paper systematically evaluates saliency methods as explainability tools for convolutional neural networks trained to diagnose glaucoma using simplified eye fundus images that contain only disc and cup outlines. These simplified images, a methodological novelty, were used to relate features highlighted in the saliency maps to the geometrical clues that experts consider in glaucoma diagnosis. Despite their simplicity, these images retained sufficient information for accurate classification, with balanced accuracies ranging from 0.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139.
Protein language models (PLMs) have demonstrated impressive success in modeling proteins. However, general-purpose "foundational" PLMs have limited performance in modeling antibodies due to the latter's hypervariable regions, which do not conform to the evolutionary conservation principles that such models rely on. In this study, we propose a transfer learning framework called Antibody Mutagenesis-Augmented Processing (AbMAP), which fine-tunes foundational models for antibody-sequence inputs by supervising on antibody structure and binding specificity examples.
View Article and Find Full Text PDFProc Natl Acad Sci U S A
January 2025
Centre for Ecological Dynamics in a Novel Biosphere, Section of EcoInformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus 8000, Denmark.
PLoS One
January 2025
North China Institute of Aerospace Engineering, Langfang, China.
As the global economy expands, waterway transportation has become increasingly crucial to the logistics sector. This growth presents both significant challenges and opportunities for enhancing the accuracy of ship detection and tracking through the application of artificial intelligence. This article introduces a multi-object tracking system designed for unmanned aerial vehicles (UAVs), utilizing the YOLOv7 and Deep SORT algorithms for detection and tracking, respectively.
View Article and Find Full Text PDFPLoS One
January 2025
Department of Neonatology/Neonatal Intensive Care Unit, University Hospital of Heraklion, School of Medicine, University of Crete, Heraklion, Crete, Greece.
Preterm births constitute a major public health issue and a chronic, cross-generational condition globally. Psychological and biological factors interact in a way that women from low socio-economic status (SES) are disproportionally affected by preterm delivery and at increased risk for the development of perinatal mental health problems. Low SES constitutes one of the most evident contributors to poor neurodevelopment of preterm infants.
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