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Every paper Pith has read. Search by title, abstract, or pith.
1822 papers in q-bio · page 1
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Pipeline annotates mechanisms for 19,293 human genes from papers
Affinage: genome-scale mechanistic gene annotation from the published literature
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Graph-structured kernels improve omics classification
Structured Gaussian Processes for Uncertainty-Aware Classification of High-Dimensional, Small-Sampled Omics Data
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Positive cues raise dog approaches to humans
Operant Conditioning in Indian Free-Ranging Dogs: Effects of Positive and Threatening Cues on Sociability
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MolSight adds bond adjacency to vision tokens for molecular images
MolSight: A Graph-Aware Vision-Language Model for Unified Chemical Image Understanding
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3D models cut plant reconstruction time from 6.5 minutes to 1.6 seconds
The Turning Point of 3D Plant Phenotyping: 3D Foundation Models Enable Minute-to-Second Cross-Crop Reconstruction and Beyond
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Point source restores identifiability of spatial dynamics from snapshots
Identifiability Limits of Physics-Informed Inference for Spatial Stochastic Dynamics from Static Snapshots
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Framework forecasts glycosylation under ammonia stress
GlycoMAC: A Multiscale Metabolic-Glycosylation Framework for Predicting Glycosylation Across Conditions in Mammalian Cell Cultures
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Brain model signals show no link to YouTube replays
A global predicted-fMRI drive signal from TRIBE does not predict YouTube replay heatmaps
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NNPs reach near-chemical accuracy on 545-atom enzyme clusters with under 1,000 points
Enerzyme: A Framework for Efficient Training of Reactive Neural Network Potentials for Enzyme Catalysis with Application to Methyltransferases
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New model raises CNS tumor classification accuracy from 82% to 86%
A Novel Machine Learning Approach for Central Nervous System Tumor Classification from DNA Methylation
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Factor-two peak approximation holds under Erlang scaling in multistage SIR
Approximating Peak Prevalence in Multistage SIR Epidemics
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Immune history stabilizes recurrent variant epidemics
Immune history shapes recurrent epidemics of antigenically related variants
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Algebraic descriptors raise B-factor accuracy 34.5% over GNM
Commutative Algebra Learning for Protein Flexibility Analysis
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Toolkit unifies neuron selectivity with population manifold analysis
DRIADA: A Python Toolkit for Cross-Scale Analysis of Single-Neuron Selectivity and Population Dynamics
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Birth-regulated species fixate more often despite neutral mean growth
Effective population sizes for asymmetrically regulated birth-death processes
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Pontryagin principle yields optimal control for heterogeneous SI epidemics
Optimal control on a heterogeneous SI epidemic model
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Land cover beats single metrics as bird diversity predictor
How Environment and Urbanization Shape Bird Diversity in Sri Lanka
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Active-GRPO raises average SRxSim to 0.1773 by updating references
Active-GRPO: Adaptive Imitation and Self-Improving Reasoning for Molecular Optimization
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LLM features form stable cognitive parcels conserved across models
NeuroCogMap Reveals Cognitive Organization of Large Language Models
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One image yields pairwise fitness flows in expanding colonies
Radial Interaction Tomography: Recognizing Non-Transitive Evolutionary Games from One Range-Expansion Image
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Senescence mortality matches multi-level selection patterns
Demographic senescence as multi-level selection in miniature
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Frustration patterns lift alternative conformation recovery over AF-Cluster
SF-Cluster: Frustration-Guided MSA Subsampling for Alternative Protein Conformation Recovery
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Closed equation derived for covariance spectra in discrete non-normal dynamics
Stationary covariance spectra of discrete-time non-normal random recurrent dynamics
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Size-dependent dispersal creates four invasion growth regimes
Invasion with size-dependent dispersion range
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Full ITN use by one host can raise disease in another
Nonlinear Feedbacks Between Host Behavior and Vector Adaptation in a Multi-Host Vector-Borne Disease Model
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Extrinsic dynamics cap cooperation
The Cooperation Ceiling: Extrinsic Population Dynamics and the Intrinsic Escape
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Transposable elements link development to ageing
A conceptual model for the evo-devo role of transposable elements and its implications for the ageing phenomenon
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SAEs restore geometry in neuron image representations for RNA alignment
Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images
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SAEs restore geometry in neuron image models for scRNA-seq alignment
Resolving superposition in AI for interpretability and cross-modal alignment in patient-neuronal images
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Mutation induces effective mortality threshold for population persistence
Persistence, Thresholds, and Trait Composition in a Regulated Mutation-Selection Model
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Tabular in-context learners match on protein fitness with fixed reps
Can Tabular In-Context Learners Generalize to Biomolecular Property Prediction?
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Soccer headers carry under 20% concussion risk
Head Kinematics and Brain Tissue Deformation from Soccer Heading: A Review of Implications for Brain Injury Risk
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TCR model shows generated structures yield weaker contact maps
Structure-Regularized Interpretable TCR-Epitope Prediction
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Locked prior lifts Andes virus source ranking from 13.8% to 37.9% top-1
A Transferable Learned Temporal Prior for Transmission Reconstruction and Decision-Relevant Uncertainty in Real Outbreak Labels
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Adaptation tunes chaotic networks through four oscillatory regimes
Mean-field theory of rich oscillatory dynamics in low-rank recurrent networks with activity-dependent adaptation
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Brain models personalize in seconds without sharing patient data
Cohort-amortized personalization: navigating the privacy-utility frontier for virtual brain twins
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Phosphorylation model admits regime with two stable equilibria
Thermodynamic Limits of Stochastic Chemical Reaction Networks with Phosphorylation
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Clathrin coats develop stiffness and memory from growth conditions
Pathway variability, coat stiffening and mechanical adaptation during clathrin-mediated endocytosis
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Pretraining may not pay off for DNA transformers
DNA Language Models: An Assessment of Pre-Training for Fine-Tuning Tasks
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Lightweight module turns H&E slides into molecular pathway predictors
Data-Efficient Multimodal Alignment for Histopathology-based Molecular Prediction
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LLM reasoning graphs match within and between case clusters
Clinical Reasoning Graphs: Structured Evaluation of LLM Diagnostic Reasoning Reveals Competence Without Consistency
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Meditation raises brain signal-to-noise ratio
Clear Mind: Meditation and the Brain's Signal-to-Noise Ratio
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Closed-loop cell-cycle head improves drug perturbation forecasts
Modeling Cell-Cycle-Aware Single-Cell Drug Perturbation Responses
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Geometric stability of neural codes tracks behavior apart from drift
Geometric Stability of Neural Population Codes: Regional Variation, Behavioral Relevance, and Circuit Dependence
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Hybrid system turns spatial transcriptomics into reproducible SLURM bundles
DiSTILL: A Hybrid Cloud-HPC Workflow System for Reproducible Spatial Transcriptomics Analysis
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Manganese-GelMA hydrogels enable MRI-guided cancer immunotheranostics
Manganese-Functionalized GelMA Hydrogels for MRI-Guided Immunotheranostics in Precision Oncology
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Generative models couple protein sequences to evolutionary dynamics
Modeling Protein Evolution with Generative Models: from Extant Sequence Data to Evolutionary Dynamics
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Alzheimer's model reaches one equilibrium when new plaque formation stops
Global stability analysis of a mathematical model from Alzheimer's disease
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Single-pass graph model lifts mass-spectrum retrieval accuracy
GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem
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Relaxed noise assumptions yield directed brain connectivity estimates
Connectivity Estimation using Stochastic Graph Heat Modelling