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Every paper Pith has read. Search by title, abstract, or pith.
1822 papers in q-bio · page 5
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Tinnitus arises as side effect when brain boosts weak signal detection
Ten Years of the Stochastic Resonance Model of Tinnitus: From Phantom Perception to Adaptive Sensory Optimization
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Transformer directly forecasts multi-step molecular dynamics
ASTEROID: A Spatiotemporal Information Transformer for Forecasting Multi-Step Time Series of Molecular Dynamics
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Aggregation shortens extinction time in fear-Allee models
Aggregation as a Double-Edged Sword: Fear, Allee Effects, and Finite-Time Collapse
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Compact model matches large AI on Bangladeshi fish ID
Protein-Based Fish Species Identification: Dataset, Models, and Insights from Native Bangladeshi Fish
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Aging blurs SR-mitochondria contacts in muscle
Aging induced structural alterations in SR-Mitochondria interaction in skeletal muscle: Emerging insights
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Virtual infant model matches real rolling development
Embodiment Shapes Rolling Behavior in a Multimodal Infant Model
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Reweighted bridge matching aligns tau PET across sites
Feynman Kac Reweighted Schr\"odinger Bridge Matching for Surface-Based Tau PET Harmonization
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Knotting creates distinct scores in persistent homology cycles
A Persistent Homology Signature of Knotting
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Thermodynamic hardware solves codon optimization at 10^6 lower energy
Energy-efficient codon optimization on thermodynamic hardware
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Unsupervised archetypes flag high N2O emissions in sludge
Archetypal Microbiome Profiles as Indicators of Nitrous Oxide Emission States in Activated Sludge
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Dual-discriminator GAN generates lab-validated modified antimicrobial peptides
Agentic Discovery of Non-Canonical Antimicrobial Peptides with AMPGAN v3
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Hybrid SIT strategy cuts sterile males for Anopheles elimination by 5%
Tipping the Balance: Allee Thresholds, Saddle-Node Bifurcations, and Optimal Sterile-Male Release Strategies for Anopheles Mosquitoes
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Division redirects identical cells to opposite fates
Cell Division Changes Fate Decisions in a Genetic Toggle Switch
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Infant movement noise improves deep RL exploration
Infant Spontaneous Movement Noise Improves Exploration in Deep RL
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Stage composition beats extra supervision for biology reasoning models
How Post-Training Shapes Biological Reasoning Models
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FM representations hold up on shifted cancer data
Probing, Fusion, and Trustworthiness: A Systematic Evaluation of Foundation Model Representations for Multimodal Cancer Analysis
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Entropy cost per heartbeat stays constant across body sizes
Biological proper time and entropy-cost invariance in cardiac and respiratory lifespan scaling
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Self-organizing networks develop path integration without pre-wiring
Prospective Coding and Path Integration Emerge as Equilibrium Solutions of Self-Organizing Neural Networks with Firing-Rate Adaptation
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Latent diffusion generates macrocyclic peptides with ring closures
PepALD: Macrocyclic Peptide Generation via Autoregressive Latent Diffusion
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Local observation plus global reputation stabilizes cooperation
A model of local and global reciprocity
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Three labels balance cost and power in lipid metabolism models
Balancing label resolution and computational cost in dynamical models of lipid metabolism
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Genomic profile sets Bayesian prior to separate nature from nurture
Is It You or Your Environment? A Bayesian Inference Framework for Genomically-Anchored Personalized Physiological Interpretation
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Framework recovers both growth laws and noise from data
A likelihood-based framework for simultaneously learning both noise and growth dynamics using biologically-informed neural networks
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Langurs show intentionality hallmarks when begging from humans
Begging with a Purpose? Testing Behavioural Hallmarks of First-Order Intentionality in Free-ranging Hanuman Langurs
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Model ties HDV drop to fourfold HBV DNA production rise
Mathematical Modeling of HDV RNA, HBV DNA, and HBsAg Dynamics during Lonafarnib-Based Therapy: Insights from the LOWR HDV-1 Study
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Contrastive learning extracts equations from noisy latent dynamics
Extracting Governing Equations from Latent Dynamics via Multi-View Contrastive Learning
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Policy compression now adds cost for action uncertainty
Including the Cost of Irreducible Uncertainty in the Policy Compression Framework
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Irregular focal-adhesion curvature keeps Piezo1 active in cancer cells under ultrasound
Irregular curvature at focal adhesions modulates Piezo1 activity and low frequency ultrasound induced apoptosis in cancer cells
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EEG criticality features classify deep sleep at 87% accuracy
Deep Sleep Classification via EEG Signal Criticality: A Passive BCI Approach for Sleep-Improvement Neurofeedback
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Small LLMs surpass GPT-4o on biomedical claims at low cost
Small LLMs for Biomedical Claim Verification: Cost-Effective Fine-Tuning, Structural Dataset Shortcuts, and Cross-Domain Generalization
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Vanilla Transformer reaches SOTA on cell perturbation prediction
OCOO-T : A Simple and Scalable Virtual Cell Model for Transcriptional Perturbation Response Prediction
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Feature library recovers parameters from time series data
Interpretable model-free inference of parametric variation across time-series data through large-scale feature extraction
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Gradient descent on distograms designs epitope-specific nanobody CDRs
EasyNano: rapid epitope-targeted nanobody CDR design via differentiable distogram optimization with ESMFold2
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Drosophila NMJ release probabilities do not maximize information
Predictions for and lack of maximal information transmission in the neuromuscular junction
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High acetylcholine splits networks into stable neuron clusters
Phase model analysis of the effect of M-current on neural synchrony in hippocampal networks
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PINNs show Michaelis-Menten PK model needs tissue data
Physics-Informed Neural Networks for Chemotherapy Pharmacokinetics: Benchmarking the Clinical Estimator and Exposing Parameter Identifiability
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Physics losses raise OOD AUC of synthesizability GNN
Physics-Aware Auxiliary Losses Improve Out-of-Distribution Generalization of a GNN Synthesizability Filter
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Metric choice reverses winner in drug-response models
The Metric Picks the Winner: Evaluation Choice Flips Model Rankings for Drug-Response Prediction in Unseen Chemistry
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Viral proteins expose nativeness axis in protein model embeddings
Viral Proteins Reveal Geometry of Protein Language Models
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Brain-heart signals show anti-correlation at life's end
Multifractal human signals at the edge of life reveal a heart-brain anti-correlation
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EvAMs gain do-operator interventions for target ranking
A structural causal framework for interventions on evolutionary accumulation models
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EvAMs predict intervention effects via do-operator on parameters
A structural causal framework for interventions on evolutionary accumulation models
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Reaction networks implement linear regression at steady state
Implementation of Linear Regression and Linear Interpolation using Reaction Networks
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School model shows teen substance use can lock into high or low states
SCAR dynamics of adolescent substance use: peer influence, dropout, and bifurcation structure in a school-based model
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m6A-FORM predicts m6A sites at PR-AUC 0.635
m6A-FORM: A Foundation Model for Decoding N6-methyladenosine Biology
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ESMC autoencoder features predict enzyme functions at 79% accuracy
Interpretable enzyme function prediction via sparse autoencoder features of ESMC across the microbial protein universe
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Brain signals boost LLM reasoning accuracy by up to 13 percent
Beyond representational alignment with brain-guided language models for robust reasoning
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Span doubles early ctDNA warnings for indolent breast cancer progression
Seeing Below the Limit of Detection: A Censored-Poisson Bayesian Latent-Growth Change-Point Detector (the Span Detector) for Serial ctDNA in HR+/HER2- Metastatic Breast Cancer
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Memory bank restores spectrum use in peptide sequencing
MemNovo: Look Back at the Spectrum for Balanced De Novo Peptide Sequencing from Mass Spectrometry
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Model generates fMRI for unseen tasks from language
Flow Matching with In-Context Priors for Out-of-Distribution Brain Dynamics