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Biology & Medicine · 10 stories · page 1 of 1

Machine Learning and Statistical Models for Genomic Selection of Phytophthora Fruit Rot Resistance in Watermelon
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Machine Learning and Statistical Models for Genomic Selection of Phytophthora Fruit Rot Resistance in Watermelon

Breeding for Phytophthora fruit rot (PFR) resistance caused by the devastating pathogen Phytophthora capsici remains challenging in watermelon mainly due to phenotyping constraints. To overcome these bottlenecks, we developed and validated genomic selection models using an interspecific recombinant inbred line (RIL, F 11 ) population derived from USVL531-MDR (resistant, Citrullus mucosospermus ) × USVL677-PMS (susceptible, Citrullus lanatus ) and a segregating F 2 population (USVL531-MDR × 'Calhoun Grey'). Matur…

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Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer
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Assessing scale and predictive diversity in models for single-cell transcriptomics based on Geneformer

Author summary Single-cell analysis helps researchers understand how genes work together inside individual cells, and recent artificial intelligence models have shown strong potential for uncovering these patterns. However, many existing approaches do not fully account for how this data is structured, and often assume that using more training data will always improve performance. In this study, we introduce GFCAB, a model designed to better match the way single-cell data are organized. By reducing repeated predi…

Integrating multi-layer perceptron and random forest in an ensemble framework for improved genomic prediction accuracy and SHAP-derived interpretability of residual feed intake in cattle
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Integrating multi-layer perceptron and random forest in an ensemble framework for improved genomic prediction accuracy and SHAP-derived interpretability of residual feed intake in cattle

Background Feed efficiency (FE) is recognized as a vital component of sustainable dairy production, with residual feed intake (RFI) serving as a key metabolic indicator of FE independent of production levels. However, the genetic improvement of this complex trait is limited by the inability of conventional genomic Best Linear Unbiased Prediction (gBLUP) model to capture complex, non-linear genetic architectures and epistatic interactions. To address these limitations, this study aims to compare the predictive pe…

Predicting Biomolecular Interactions in the Next Decade: Physics-Based Methods Meet AI-Driven Approaches
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Predicting Biomolecular Interactions in the Next Decade: Physics-Based Methods Meet AI-Driven Approaches

The quantitative prediction of biomolecular recognition is crucial to molecular science. The challenge is not merely structural determination but the prediction of (thermo)dynamic and kinetic observables arising from high-dimensional molecular ensembles, such as free energies, conformational distributions, and rate processes across different conditions. As the field shifts from structure-centric to ensemble-based descriptions, two complementary modeling strategies have matured: explicit energy-based approaches g…

Accurate prediction of protein structures and interactions using a three-track neural network
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Accurate prediction of protein structures and interactions using a three-track neural network

Deep learning takes on protein folding In 1972, Anfinsen won a Nobel prize for demonstrating a connection between a protein’s amino acid sequence and its three-dimensional structure. Since 1994, scientists have competed in the biannual Critical Assessment of Structure Prediction (CASP) protein-folding challenge. Deep learning methods took center stage at CASP14, with DeepMind’s Alphafold2 achieving remarkable accuracy. Baek et al . explored network architectures based on the DeepMind framework. They used a three…

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Integrating machine learning and multiscale modeling-perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences

Fueled by breakthrough technology developments, the biological, biomedical, and behavioral sciences are now collecting more data than ever before. There is a critical need for time- and cost-efficient strategies to analyze and interpret these data to advance human health. The recent rise of machine learning as a powerful technique to integrate multimodality, multifidelity data, and reveal correlations between intertwined phenomena presents a special opportunity in this regard. However, machine learning alone ign…

Integrating machine learning and multiscale modeling-perspectives, challenges, and opportunities in the biological, biomedical, and behavioral sciences
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Highly accurate protein structure prediction with AlphaFold

Proteins are essential to life, and understanding their structure can facilitate a mechanistic understanding of their function. Through an enormous experimental effort 1-4 , the structures of around 100,000 unique proteins have been determined 5 , but this represents a small fraction of the billions of known protein sequences 6,7 . Structural coverage is bottlenecked by the months to years of painstaking effort required to determine a single protein structure. Accurate computational approaches are needed to addr…

Highly accurate protein structure prediction with AlphaFold