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Every paper Pith has read. Search by title, abstract, or pith.
1822 papers in q-bio · page 7
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Neocortex learns via error-driven prediction in brain circuits
This is how the Neocortex Learns
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Protein folding shifts from static structures to dynamic trajectories
Protein Dynamics Beyond Structure Prediction
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Disentanglement separates cell state from neighbors for tissue counterfactuals
Querying Counterfactuals on Tissue Graphs with Supervised Disentanglement
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Index measures how tightly data pin down each model parameter
Parameter uncertainty in dynamical models: a practical identifiability index
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Triangular matrices enable distance metrics on phylogenetic networks
Matrix representations and distance metrics for unlabeled ranked phylogenetic networks
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Two latent infections at boarding best fit Andes virus cruise outbreak
Cruise Ship-Associated Andes Virus Cluster aboard MV Hondius, 2026: A Stochastic Scenario Analysis
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Open code reproduces Mader model lactate outputs
MetaboliSim: a Python implementation of the Mader model for dynamic and steady-state simulation of muscular energy metabolism
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GNN vaccine ranking cuts epidemic peaks below centrality heuristics
Network-Based Multi-Layer Model Using Machine Learning for Optimal Vaccine Prioritization in Heterogeneous Populations
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Cycle space extracts recurrent patterns from directed interactions
Vector Space of Cycles
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Frequency gating with latent queries improves token aggregation
Frequency-Domain Latent Attention Gating for Cross-Domain Token Aggregation
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Biological reasoning boosts LLM accuracy on regulatory DNA
Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction
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Fork speed variation produces Erlang S-phase times
DNA Replication under Thermal, Chemical, and Genotoxic Stress
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Seagrass meadow collapses to 0.2 ha after 80-year record
Feasibility to detect rapid change and disappearance of seagrass: Lessons from nearly 80 years of vegetation change in the Ako, Seto Inland Sea, Japan
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Constrained projections define potential biodiversity benchmarks
An information-geometric framework for mapping maximum potential biodiversity
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Truck routes connect swine farms 99 percent denser than pig shipments
Multi-network comparison of between-farm contacts for infectious disease surveillance in swine production
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Model forecasts Alzheimer's scores from routine visits with 1.35 error
Reconstructing and forecasting disease trajectories of patients with Alzheimer's disease using routine data in resource-constrained settings
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Explicit memory is required to move LLMs to AGI
Position: Hippocampal Explicit Memory Is the Cornerstone for AGI
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Nine-compartment model fits Italian COVID data at R^2 0.966-0.999
A Nine-Compartment Nonlinear Epidemic Model with Spline-Based Identification of Time-Varying Transmission and Vaccination Dynamics: Application to the COVID-19 Third Wave in Italy
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Heteroclinic orbits expose subnullclines in Hawk-Dove eco-evolution
Nullclines, Subnullclines and the Asymptotic and Transient Attractors in Eco-Evolutionary Dynamics
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Low-rank couplings force global fixed points to combine local ones
Fixed point compositionality via low-rank gluing rules in inhibition-dominated threshold-linear networks
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RdRp structure classifies RNA viruses where sequences fail
Structure-guided taxonomic placement of divergent RNA viruses with ViraClass
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Distance scores predict binding model performance without new labels
CaliPPer: quantifying, predicting and improving AI model performance for binding prediction
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Transformer plus reranker reaches 59.4% top-1 retrosynthesis accuracy
RETROSPECT: RETROsynthesis via Sequential Prediction, and Chemically Transformed-ranking
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GraphPath achieves 0.92 AUROC on prostate targeted therapy
TRAPS: Therapeutic Response Analysis via Pathway-informed Stratification
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Neural networks classify palimpsests from mtGenome data in old parchment
From Genomes to Algorithms: Neural Network Applications for Palimpsest Detection in Medieval Manuscripts
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Diagnostic splits predictability from regulation in DNA models
The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models
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Dataflow optimization parallelizes genome aligners across regions
Dependencies and Dataflow in Seed-Filter-Extend Pipelines
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Deterministic tool lifts AI accuracy on viral data queries to 99.7%
Deterministic access to global viral sequence data enables robust agentic scientific discovery
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Generative models show weaker binding on shallow pockets
ShallowBench: Benchmarking Generative Drug Design Models on Shallow-Pocket Targets
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Adversarial fine-tuning bridges unpaired single-cell modalities
Single-Cell Cross-Modal Transfer by Adversarial Fine-Tuning of Foundation Models
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Subject identity swamps clinical signals in EEG foundation models
The Identity Trap in EEG Foundation Models: A Diagnostic Audit
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Video model spots eight movement disorders after adult-to-child transfer
Simultaneous hyperkinetic movement disorders phenotyping: a cross-cohort pediatric transfer study using routine videos, markerless pose estimation and a tabular foundation model
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Consciousness needs computation selected from internal dynamics
Intrinsic Computational Functionalism: From Observer-Relative Maps to Observer-Independent Structures
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Synthetic fMRI data boosts brain-to-image decoding by 68%
Boosting Brain-to-Image Decoding with TRIBE v2 Data Augmentation
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Early psychosis shifts scaling exponents inside preserved critical regime
Early psychosis shows deviations in scaling behaviour within a critical regime
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AI loop enriches selective triple-drug combos for breast cancer
Iterative AI-guided optimisation of selective triple-drug combinations for breast cancer
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Bi-filtration with p-adic distances lifts genomic accuracy on small datasets
$p$-adic Bi-Filtrations for Topological Machine Learning on Genomic Sequences
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DNAm alone tops median performance in deconvolution benchmark
On the Promises and Limits of Multi-omics Integration for Deconvolution: The HADACA3 Benchmark
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Federated SPARQL annotates variants without copying databases
Federated SPARQL querying for genomic variant functional annotation
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Generative model predicts Alzheimer's thinning from gene data at r=0.94
Cross-scale spatially-aware generative modeling of transcriptomic programs underlying neurodegenerative brain organization
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Three algorithms recover interaction potentials from XL-MS data in three-phase mixtures
Methods for Inferring Interaction Potentials from Cross-Linking Mass Spectrometry Data
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DSU-Net hits 0.9421 Dice on mammogram lesion outlines
DSU-Net: An Attention-Enhanced Dense Skip U-Net for Breast Lesion Segmentation in Mammographic Images
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Learned scorer produces conformation-selective protein binders
AlloGen: Conformation-Selective Binder Generation with Differential State Scoring
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Generalized Allee map has exact tricritical extinction point
Tricriticality and chaos in a generalized Allee-logistic map
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OT potentials make multimarginal flow matching simulation-free
Multimarginal flow matching with optimal transport potentials
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New tests show TCR models fail to generalize to unseen epitopes
New Benchmarking Shows Limited Generalization Power of TCR Antigenic Epitope Prediction Models
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Atomic finding matching scores radiology reports at 97.8% concordance
RadSEM: A Finding-by-Finding Metric for Clinical Consistency in Radiology Reports
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AF_Cache halves AlphaFold2 runtime on 5,000 protein pairs
AF_Cache: Efficient Pipeline for Running AlphaFold for High-Throughput Protein-Protein Interaction Prediction
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Learned boundaries lift histone accuracy 14 points at matched compute
LDARNet: DNA Adaptive Representation Network with Learnable Tokenization for Genomic Modeling
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Recursive algorithm computes tree likelihoods under QBD trait model
Quasi-birth-and-death processes evolving within trees: Applications to comparative phylogenetics