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Every paper Pith has read. Search by title, abstract, or pith.
504 papers in q-bio · page 1
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3D model checks if cell division rules build plant symmetry
3D mechano-geometric multicellular model of apical stem cell-driven plant morphogenesis
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Time discard rule orders population behavior for free
Conditioning as a route to stereotyped behavior in growing populations
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Mamba forecaster decodes mouse choice from spikes at 76 percent
Implicit Behavioral Decoding from Next-Step Spike Forecasts at Population Scale
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Spike forecasting ranks brain regions consistently across models
SpikeProphecy: A Large-Scale Benchmark for Autoregressive Neural Population Forecasting
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Language descriptions capture monkey neuron selectivity
Letting the neural code speak: Automated characterization of monkey visual neurons through human language
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Conductance synapses and correlations yield realistic variability
Empirical scaling laws in balanced networks with conductance-based synapses
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Genome embeddings predict microbiome abundances for novel species
Set-Aggregated Genome Embeddings for Microbiome Abundance Prediction
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Lab variance sets PROTAC prediction ceiling at 0.67 AUROC
Decomposing the Generalization Gap in PROTAC Activity Prediction: Variance Attribution and the Inter-Laboratory Ceiling
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Contrastive video training yields MT-like direction maps
Self-organized MT Direction Maps Emerge from Spatiotemporal Contrastive Optimization
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Missed events correction clarifies IP3R Park and Drive modes
Accounting for Missed Events in the Bayesian Modeling of IP3R Multimodal Gating
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NORI resolves ambiguous biology mappings orders of magnitude faster
NORI: Fast probabilistic inference for ambiguous observation-entity mappings
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Benchmark with 40 epidemic datasets enables fair model comparisons
EpiCastBench: Datasets and Benchmarks for Multivariate Epidemic Forecasting
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Vertex measures match VR in spotting cancer genes
Scalable vertex guided filtrations identify structurally relevant genes in cancer networks
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One futile cycle network combines bistability with fixed final product
Bistability, Absolute Concentration Robustness, and Hysteresis in Dual-Site Futile Cycles with Bifunctional Enzymes
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Local discrete programs re-rank DNA edits for higher rewards
LPDP: Inference-Time Reward Control for Variable-Length DNA Generation with Edit Flows
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Analogical reasoning lifts LLM diversity in science by 90-173%
Unlocking LLM Creativity in Science through Analogical Reasoning
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Seven papers let LLM workflow expand TPD databases by 81-92%
Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows
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Regression to the Mean and Dilution Share One Root Cause
The Same Problem by Different Names: Unifying Regression Dilution and Regression to the Mean
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Deep learning with protein hierarchy predicts complexes better
Deep Learning for Protein Complex Prediction and Design
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Generalist LLMs beat specialists on 1,920 CRISPR screens
AssayBench: An Assay-Level Virtual Cell Benchmark for LLMs and Agents
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Five-phase curriculum stabilizes JEPA rollouts on ICU trajectories
Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories
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Five-phase curriculum stabilizes EHR trajectory rollouts
Clin-JEPA: A Multi-Phase Co-Training Framework for Joint-Embedding Predictive Pretraining on EHR Patient Trajectories
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Fourier embeddings turn angles into periodic high-dimensional vectors
On periodic distributed representations using Fourier embeddings
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Periodic signals encoded as controllable high-dimensional vectors
On periodic distributed representations using Fourier embeddings
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Mitigation inverts epidemic trend on scale-free networks
Susceptible-Infected-Susceptible Model with Mitigation on Scale-Free Networks
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Log scaling turns sweeps into tents or houses
Logarithmic scaling of selective sweep curves: from tents to houses
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Persistence speeds one bacterial invasion wave but not the reverse
Travelling waves of invasion in microbial communities with phenotypic switching
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Cerebellar module speeds RNN learning on temporal tasks
Cortico-cerebellar modularity as an architectural inductive bias for efficient temporal learning
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AI Alignment Must Promote Human Flourishing
Positive Alignment: Artificial Intelligence for Human Flourishing
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Sparse coding and timing preserve knowledge across context switches
Joint sparse coding and temporal dynamics support context reconfiguration
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Compact tokenizer generates plausible proteins from scratch with 10x fewer parameters
Yeti: A compact protein structure tokenizer for reconstruction and multi-modal generation
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L3 paths added to any PPI predictor via graph prompts
Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach
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Virtual L3 paths raise protein interaction prediction accuracy
Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach
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New diffusion model generates directional agonists and antagonists
TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation
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Spike encoders recast as causal wavelets with error bounds
Encoding and Decoding Temporal Signals with Spiking Bandpass Wavelets
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Kurdistan study finds seven hawthorn taxa with major fruit variation
Morpho-Physiological and Genetic Diversity of Crataegus Taxa (Rosaceae) in Selected Locations of Iraqi Kurdistan-Region
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Mobile nuclei shuttle signals like pigeon post in slime mold
Coexistence of trapped and flow-transported nuclei enables fast pigeon post communication across multinucleated cell
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Protein embeddings classify bacterial operons at 0.71 ROC-AUC
SCOPE: Siamese Contrastive Operon Pair Embeddings for Functional Sequence Representation and Classification
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MiRA app enables interactive visualization of biological multilayer networks
Interactively visualizing biological multilayer networks using MiRA
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Random forest surrogate cuts likelihood evaluations in phylogenetic SMC
Accelerating Bayesian Phylogenetic Inference via Delayed Acceptance Sequential Monte Carlo with Random Forest Surrogates
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Prediction signals match group brain patterns in language learning
Predictive and feedback signals differently shape the formation of group-level and individualized language representations
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2B model surpasses larger ones on medical VQA with reasoning transfer
LiteMedCoT-VL: Parameter-Efficient Adaptation for Medical Visual Question Answering
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Two fear channels trigger state switches in stochastic Allee populations
Dual Fear Mechanisms Shaping Stochastic Population Dynamics under the Allee Effect
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Brain data trades for task samples at alignment-dependent rates
How Much is Brain Data Worth for Machine Learning?
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Quad-modal AI reads cat intent from video
Meow-Omni 1: A Multimodal Large Language Model for Feline Ethology
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Internal errors trigger sparse neural net updates
Internally triggered retrospective learning in neural networks
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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