AI Medical Compendium Journal:
PLoS computational biology

Showing 11 to 20 of 484 articles

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning.

PLoS computational biology
The design of proteins capable effectively binding to specific protein targets is crucial for developing therapies, diagnostics, and vaccine candidates for viral infections. Here, we introduce a complementarity-determining region (CDR) grafting appro...

Integrating multiple spatial transcriptomics data using community-enhanced graph contrastive learning.

PLoS computational biology
Due to the rapid development of spatial sequencing technologies, large amounts of spatial transcriptomic datasets have been generated across various technological platforms or different biological conditions (e.g., control vs. treatment). Spatial tra...

Anticancer drug response prediction integrating multi-omics pathway-based difference features and multiple deep learning techniques.

PLoS computational biology
Individualized prediction of cancer drug sensitivity is of vital importance in precision medicine. While numerous predictive methodologies for cancer drug response have been proposed, the precise prediction of an individual patient's response to drug...

Generative AI extracts ecological meaning from the complex three dimensional shapes of bird bills.

PLoS computational biology
Data on the three dimensional shape of organismal morphology is becoming increasingly available, and forms part of a new revolution in high-throughput phenomics that promises to help understand ecological and evolutionary processes that influence phe...

Predictive reward-prediction errors of climbing fiber inputs integrate modular reinforcement learning with supervised learning.

PLoS computational biology
Although the cerebellum is typically associated with supervised learning algorithms, it also exhibits extensive involvement in reward processing. In this study, we investigated the cerebellum's role in executing reinforcement learning algorithms, wit...

Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.

PLoS computational biology
Neutrophils, an essential innate immune cell type with a short lifespan, rely on continuous replenishment from bone marrow (BM) precursors. Although it is established that neutrophils are derived from the granulocyte-macrophage progenitor (GMP), the ...

Pre-training artificial neural networks with spontaneous retinal activity improves motion prediction in natural scenes.

PLoS computational biology
The ability to process visual stimuli rich with motion represents an essential skill for animal survival and is largely already present at the onset of vision. Although the exact mechanisms underlying its maturation remain elusive, spontaneous activi...

Predicting the diversity of photosynthetic light-harvesting using thermodynamics and machine learning.

PLoS computational biology
Oxygenic photosynthesis is responsible for nearly all biomass production on Earth, and may have been a prerequisite for establishing a complex biosphere rich in multicellular life. Life on Earth has evolved to perform photosynthesis in a wide range o...

Compression-enabled interpretability of voxelwise encoding models.

PLoS computational biology
Voxelwise encoding models based on convolutional neural networks (CNNs) are widely used as predictive models of brain activity evoked by natural movies. Despite their superior predictive performance, the huge number of parameters in CNN-based models ...

Using a multi-strain infectious disease model with physical information neural networks to study the time dependence of SARS-CoV-2 variants of concern.

PLoS computational biology
With the ongoing evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its increasing adaptation to humans, several variants of concern (VOCs) and variants of interest (VOIs) have been identified since late 2020. These include...