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Every paper Pith has read. Search by title, abstract, or pith.
508 papers in q-bio · page 2
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Condensation transition emerges below critical entropy in probability simplex
Condensation Transition in Entropy-Constrained Probability Spaces
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BP180 homotrimer model stays folded in simulations
A putative, computationally stable structure of homotrimeric BP180/collagen XVII
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Expert fusion model lifts microbial operon accuracy
MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning
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Graph pooling extracts functional protein substructures from ESM-2 features
Structural Interpretations of Protein Language Model Representations via Differentiable Graph Partitioning
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Normalized optical density aligns myelin slides with 7T MRI
Automated Optical Density Normalization for Myelin Quantification: Cross-Modal Validation with 7T Ex Vivo MRI
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SGRPO widens biomolecular utility-diversity frontier
Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization
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Geometry-aware flow matching uncovers latent regimes in unpaired snapshots
FLUX: Geometry-Aware Longitudinal Flow Matching with Mixture of Experts
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Statin eligibility drops 3M or rises 21M under 2026 guidelines
Statin Recommendations among US Adults with the 2026 Dyslipidemia Guidelines
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No LLM masters all three protein design stages
VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design
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Pretrained model restores 3D microscopy images from sparse scans
MicroDiffuse3D: A Foundation Model for 3D Microscopy Imaging Restoration
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R package MeTime stores all metabolomics steps in one container
MeTime: An R package for reproducible longitudinal metabolomics data analysis
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Unified benchmark shows foundation models only marginally beat task-specific ones
NeuralBench: A Unifying Framework to Benchmark NeuroAI Models
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Grid cells optimize radial basis kernels
Neurally-plausible radial basis kernels using distributed Fourier embeddings
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Bursting gene networks reach unique equilibria with explicit rates
Quantitative ergodicity for gene regulatory networks with transcriptional bursting
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Frontier reasoning models align with human game learning and brain scans
Reason to Play: Behavioral and Brain Alignment Between Frontier LRMs and Human Game Learners
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Multi-timescale inhibition widens theta oscillator locking range
Dynamical mechanisms of flexible phase-locking in cortical theta oscillators
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Graph model connects protein networks to cancer pathways at 90% accuracy
PPI-Net connects molecular protein interactions to functional processes in disease
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Flow matching on raw counts beats baselines with fewer parameters
Flow Matching for Count Data
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Switching control makes gene densities forget their initial state
Predictive-Switching Control of Stochastic Gene Regulatory Networks: A Contractive PIDE Framework
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Models trained on real folds design RNA under mixed constraints
GoForth: Language Models for RNA Design under Structure, Sequence, and Coding Constraints
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Masked-position latent prediction beats MLM on protein tasks
ProteinJEPA: Latent prediction complements protein language models
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Model estimates R0 of 2.76 for cruise ship hantavirus
Modeling the Impact of Exposed Cases in a Hantavirus Outbreak on a Cruise Ship
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Benchmark trains models on noisy DEL screens and tests them on real Ki affinities
CA-DEL: An Open Multi-Target, Multi-Modal Benchmark for Learning from DNA-Encoded Library Screens
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Weighted MaxSMT finds biological models despite conflicting observations
Inference of Qualitative Models from Steady-State Data via Weighted MaxSMT
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Rhythms bias binary sequences to form catalytic and information systems
Genetic Information as a "Chord" of Chemical Oscillations: Emergence of Catalyst-RNA Systems Driven by Superposed Rhythms
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Papal names follow random copying rule across 2000 years
Quo nomine vis vocari? A random-copying model explains the temporal sequence of papal names
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Disentangled multi-atlas model aligns brain disorder representations
Learning Cross-Atlas Consistent Brain Disorder Representations via Disentangled Multi-Atlas Functional Connectivity Learning
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Extrinsic noise required to explain E
Essential Role of Extrinsic Noise in Models of E. coli Division Control
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Shared neural co-variability peaks in V1 and falls higher up
Partitioning Neural Co-Variability
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Mutation modeling improves protein function prediction
Better Protein Function Prediction by Modeling Survivorship Bias
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Hybrid model lowers error in grapevine trait prediction across years
A Linear-Transformer Hybrid for SNP-Based Genotype-to-Phenotype Prediction in Grapevine
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Slowing cyclin B synthesis lengthens early fly cell cycles
Mathematical Modeling of Early Embryonic Cell Cycles of Drosophila melanogaster
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Logistic regression outperforms complex models on rare breast cancer subtypes
Feature Dimensionality Outweighs Model Complexity in Breast Cancer Subtype Classification Using TCGA-BRCA Gene Expression Data
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Burst timing shapes vesicle signaling activation
Activation in Vesicle-Mediated Signaling Shaped by Batch Arrival Statistics
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Brains and DNNs align on preserved stimulus transformations
Beyond Object-Level Alignment: Do Brains and DNNs Preserve the Same Transformations?
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Neural geometry stretches informative directions and shrinks the rest
A multi-scale information geometry reveals the structure of mutual information in neural populations
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Pairwise models can mask higher-order interactions in ecology
Higher-order interactions in ecology can be hidden in plain sight
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New edge-based μ-representation yields distance for orchard networks
A $\mu$-distance for semidirected orchard phylogenetic networks
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AI agent outperforms physicians on rare disease diagnosis
A Versatile AI Agent for Rare Disease Diagnosis and Risk Gene Prioritization
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AI agent outperforms physicians on rare disease diagnosis
A Versatile AI Agent for Rare Disease Diagnosis and Risk Gene Prioritization
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Multimodal LLM reasons with omics numbers and language together
OmicsLM: A Multimodal Large Language Model for Multi-Sample Omics Reasoning
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Scenario-guided multi-agents lead on biomedical discovery benchmarks
BioResearcher: Scenario-Guided Multi-Agent for Translational Medicine
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Positive feedbacks create multiple stable states in ecosystems
Towards a unified framework for multiple stable states in ecological systems
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Decoding alignment can arise from small neuron subsets
Decoding Alignment without Encoding Alignment: A critique of similarity analysis in neuroscience
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Four dietary patterns emerge from UK survey via K-means
An Explainable Unsupervised-to-Supervised Machine Learning Framework for Dietary Pattern Discovery Using UK National Dietary Survey Data
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Tree search guides diffusion to balance multiple protein design goals
MP2D: Constrained Monte Carlo Tree-Guided Diffusion for Multi-Objective Protein Sequence Design
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Boundary registration plus quasi-conformal fill quantifies planar shape variation
Planar morphometry via functional shape data analysis and quasi-conformal mappings
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Stochastic matching resolves bias-precision paradox in medical AI
Resolving the bias-precision paradox with stochastic causal representation learning for personalized medicine
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Origin of life requires evolution before LUCA
The Origin of Life in the Light of Evolution
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LUCA was already complex and adapted long before modern life
The Origin of Life in the Light of Evolution