A key facet of both natural and artificial intelligence lies in their predictive potential. The last decade offered a mere glimpse of AI's revolutionary potential in predicting protein structures. AI's impact on predictability and understanding in biology is destined to expand towards phenomena such as intracellular protein sorting. We outline a roadmap for next-generation algorithms emphasizing the integration of evolutionary and experimental diversity in training data and model parameters inspired by evolutionary cell biology. With the prevalence of advanced machine learning increasing, our analyses exemplify how diversity can bridge AI and biology, fostering novel insights and breakthroughs. Gould et al
Image Credit: Parth K. Raval
Education
Eleven quick tips for properly handling tabular data
PLOS Computational Biology: published November 27, 2024 | https://doi.org/10.1371/journal.pcbi.1012604
Research Articles
A mechanistic model of in vitro plasma activation to evaluate therapeutic kallikrein-kinin system inhibitors
PLOS Computational Biology: published November 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012552
Harnessing the optimization of enzyme catalytic rates in engineering of metabolic phenotypes
PLOS Computational Biology: published November 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012576
Synapses learn to utilize stochastic pre-synaptic release for the prediction of postsynaptic dynamics
PLOS Computational Biology: published November 4, 2024 | https://doi.org/10.1371/journal.pcbi.1012531
A computational analysis of the oncogenic and anti-tumor immunity role of P4HA3 in human cancers
PLOS Computational Biology: published November 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012284
Assessing the effect of model specification and prior sensitivity on Bayesian tests of temporal signal
PLOS Computational Biology: published November 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012371
During haptic communication, the central nervous system compensates distinctly for delay and noise
PLOS Computational Biology: published November 6, 2024 | https://doi.org/10.1371/journal.pcbi.1012037
Beyond IC50—A computational dynamic model of drug resistance in enzyme inhibition treatment
PLOS Computational Biology: published November 7, 2024 | https://doi.org/10.1371/journal.pcbi.1012570
A deep learning model for prediction of autism status using whole-exome sequencing data
PLOS Computational Biology: published November 8, 2024 | https://doi.org/10.1371/journal.pcbi.1012468
A computational algorithm for optimal design of a bioartificial organ scaffold architecture
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012079
Molecular dynamics simulations of a multicellular model with cell-cell interactions and Hippo signaling pathway
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012536
Reliability of plastid and mitochondrial localisation prediction declines rapidly with the evolutionary distance to the training set increasing
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012575
Teaching deep networks to see shape: Lessons from a simplified visual world
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012019
A modular protein language modelling approach to immunogenicity prediction
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012511
Deep-learning models reveal how context and listener attention shape electrophysiological correlates of speech-to-language transformation
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012537
Approximate planning in spatial search
PLOS Computational Biology: published November 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012582
Evolutionary history of calcium-sensing receptors unveils hyper/hypocalcemia-causing mutations
PLOS Computational Biology: published November 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012591
An electrodiffusive network model with multicompartmental neurons and synaptic connections
PLOS Computational Biology: published November 12, 2024 | https://doi.org/10.1371/journal.pcbi.1012114
Linear-regression-based algorithms can succeed at identifying microbial functional groups despite the nonlinearity of ecological function
PLOS Computational Biology: published November 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012590
Mechanical stress and anionic lipids synergistically stabilize an atypical structure of the angiotensin II type 1 receptor (AT1)
PLOS Computational Biology: published November 13, 2024 | https://doi.org/10.1371/journal.pcbi.1012559
Human-like dissociations between confidence and accuracy in convolutional neural networks
PLOS Computational Biology: published November 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012578
AI-powered simulation-based inference of a genuinely spatial-stochastic gene regulation model of early mouse embryogenesis
PLOS Computational Biology: published November 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012473
GeM-LR: Discovering predictive biomarkers for small datasets in vaccine studies
PLOS Computational Biology: published November 14, 2024 | https://doi.org/10.1371/journal.pcbi.1012581
A new look at TFPI inhibition of factor X activation
PLOS Computational Biology: published November 15, 2024 | https://doi.org/10.1371/journal.pcbi.1012509
Rapid prediction of key residues for foldability by machine learning model enables the design of highly functional libraries with hyperstable constrained peptide scaffolds
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012609
Integrative pan-cancer analysis reveals a common architecture of dysregulated transcriptional networks characterized by loss of enhancer methylation
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012565
Simplified internal models in human control of complex objects
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012599
Human perception of self-motion and orientation during galvanic vestibular stimulation and physical motion
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012601
A dynamical systems model for the total fission rate in Drp1-dependent mitochondrial fission
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012596
SPARTA: Interpretable functional classification of microbiomes and detection of hidden cumulative effects
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012577
Prediction of virus-host associations using protein language models and multiple instance learning
PLOS Computational Biology: published November 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012597
Efficient modelling of infectious diseases in wildlife: A case study of bovine tuberculosis in wild badgers
PLOS Computational Biology: published November 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012592
Reward Bases: A simple mechanism for adaptive acquisition of multiple reward types
PLOS Computational Biology: published November 19, 2024 | https://doi.org/10.1371/journal.pcbi.1012580
A framework for counterfactual analysis, strategy evaluation, and control of epidemics using reproduction number estimates
PLOS Computational Biology: published November 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012569
Upstream open reading frames may contain hundreds of novel human exons
PLOS Computational Biology: published November 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012543
Co-contraction embodies uncertainty: An optimal feedforward strategy for robust motor control
PLOS Computational Biology: published November 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012598
Learning patterns of HIV-1 resistance to broadly neutralizing antibodies with reduced subtype bias using multi-task learning
PLOS Computational Biology: published November 20, 2024 | https://doi.org/10.1371/journal.pcbi.1012618
An off-lattice discrete model to characterise filamentous yeast colony morphology
PLOS Computational Biology: published November 21, 2024 | https://doi.org/10.1371/journal.pcbi.1012605
Deep neural networks for endemic measles dynamics: Comparative analysis and integration with mechanistic models
PLOS Computational Biology: published November 21, 2024 | https://doi.org/10.1371/journal.pcbi.1012616
Competition for resources can reshape the evolutionary properties of spatial structure
PLOS Computational Biology: published November 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012542
The evolutionary cost of homophily: Social stratification facilitates stable variant coexistence and increased rates of evolution in host-associated pathogens
PLOS Computational Biology: published November 22, 2024 | https://doi.org/10.1371/journal.pcbi.1012619
Socially driven negative feedback regulates activity and energy use in ant colonies
PLOS Computational Biology: published November 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012623
scGRN-Entropy: Inferring cell differentiation trajectories using single-cell data and gene regulation network-based transfer entropy
PLOS Computational Biology: published November 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012638
An inductive bias for slowly changing features in human reinforcement learning
PLOS Computational Biology: published November 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012568
Mathematical modeling suggests heterogeneous replication of Mycobacterium tuberculosis in rabbits
PLOS Computational Biology: published November 25, 2024 | https://doi.org/10.1371/journal.pcbi.1012563
Methods
Structure-aware annotation of leucine-rich repeat domains
PLOS Computational Biology: published November 5, 2024 | https://doi.org/10.1371/journal.pcbi.1012526
EpiFusion: Joint inference of the effective reproduction number by integrating phylodynamic and epidemiological modelling with particle filtering
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012528
Kernel machine tests of association using extrinsic and intrinsic cluster evaluation metrics
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012524
Capturing cell heterogeneity in representations of cell populations for image-based profiling using contrastive learning
PLOS Computational Biology: published November 11, 2024 | https://doi.org/10.1371/journal.pcbi.1012547
MFPSP: Identification of fungal species-specific phosphorylation site using offspring competition-based genetic algorithm
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012607
Storm: Incorporating transient stochastic dynamics to infer the RNA velocity with metabolic labeling information
PLOS Computational Biology: published November 18, 2024 | https://doi.org/10.1371/journal.pcbi.1012606