archive
Every paper Pith has read. Search by title, abstract, or pith.
1822 papers in q-bio · page 3
-
Binary absent-word matrix yields ML trees with branch support
ML-MAWS: Alignment-Free Maximum Likelihood Phylogeny Estimation Using Minimal Absent Words
-
Algae phototaxis modeled as information-seeking via chemical networks
Implementation of reinforcement learning in chemical reaction networks: application to phototaxis as curiosity-driven exploration
-
Two-step test validates stochastic reconstructions without thresholds
Data-Based Dynamical Systems Reconstruction: An Adequacy/Reliability Test
-
Agentic workflow hits 66% top-1 recall on birth defect variants
DeepBD: A Grounded Agentic Workflow for Variant Prioritization and Diagnosis of Genetic Birth Defects
-
Key taxa preservation fails to stabilize tabular models on microbiome shifts
Are Tabular Foundation Models Robust to Realistic Query Distribution Shifts in Microbiome Data?
-
Light therapy to prefrontal cortex eases insomnia in students
A pilot study examining transcranial photobiomodulation therapy intervention in college students with insomnia
-
Neural net recovers phase-field energy terms from snapshots
Extended pseudo-spectral physics-informed neural networks for phase-field models
-
Parameterized H_alpha indices extend B2 balance to phylogenetic networks
A parameterized family of balance indices for phylogenetic networks
-
Command-line tool runs protein flexibility and docking simulations
CABS-flex standalone 3: an open command-line platform for protein flexibility simulation, peptide structure modeling, and protein-peptide docking
-
cuSBF hits 9x throughput on genomic Bloom filters
cuSBF: A Minimizer-Aware Bloom Filter for Genomic Sequence Data on Modern GPUs
-
Phylogenetic networks from triples built in polynomial time
Novel Triple-Based Problems for the Construction of Phylogenetic Networks via Least Common Ancestors
-
Heterogeneous rates speed minimum first passage times by 10x
The impact of population heterogeneity on the redundancy principle
-
Different chants produce distinct EEG power and connectivity patterns
EEG Interpretation Across Chant Listening: A Single-Subject Pilot Investigation Using Spectral and Functional Connectivity Analysis
-
No single pipeline wins for EEG motor imagery across subjects
Average Rankings Mask Per-Subject Optimality: A Friedman-Nemenyi Benchmark of EEG Motor-Imagery BCI Decoders
-
ML models predict Alzheimer's inhibitors at AUC-ROC above 0.9
Machine learning-based modeling to predict inhibitors for targets of Alzheimer's Disease
-
Clustering assigns new cytokine profiles to inflammatory groups in cNORSE
Graph-based analysis of inflammatory profiles in New Onset Refractory Status Epilepticus (NORSE)
-
Orchard networks enumerated by product of matching polynomials
Exact Enumeration of Phylogenetic Networks: The Tree-Child, Reticulation-Visible and Orchard Hierarchy
-
Orchard networks enumerated exactly by product of matching polynomials
Exact Enumeration of Phylogenetic Networks: The Tree-Child, Reticulation-Visible and Orchard Hierarchy
-
Scale-splitting extracts dominant pathways and analytical formulas from reaction networks
Hierarchical models for large chemical reaction networks
-
Zero-code platform runs multiplayer experiments on cooperation
The Morality Game: An online multiplayer platform to standardize, expedite, and expand research on cooperation
-
3D masked autoencoders beat 2D versions on cell microscopy tasks
3D Masked Autoencoders are Robust Learners of Volumetric and Multimodal Cellular Representations for Microscopy
-
Attention-free memory cuts Koopman rollout errors over 1000 steps
Learning the Koopman Operator using Attention Free Transformers
-
Rare migration reduces deme evolution to low-dimensional chain
Mutant Fixation for a Stochastic Evolutionary Model in Fragmented Populations
-
Biological context maps unseen genes into response basis
Stable-Shift: Biologically Structured Prediction of Transcriptional Responses to Unseen Gene Perturbations
-
Local 2- and 3-cycles boost RNN computation on Boolean tasks
Identifying structural design principles shaping the computational abilities of recurrent neural networks
-
Federated models match centralized survival prediction on breast cancer data
Federated Survival Analysis in Healthcare: A Multi-Model Evaluation on Cross-Institutional Heterogeneous Breast Cancer Data
-
Federated SVD merge recovers immune programs across institutions
Privacy-preserving federated tensor decomposition of single-cell immune data: recovering multicellular programs across institutions
-
DNA hairpin sensor separates intercalators from groove binders
Electrochemical DNA Hairpin Sensors for Differentiating Small Molecule Intercalation from Minor Groove Binding
-
Lab bee survival data scaled to landscape model yields negligible population effects
From Lab to Landscape: Assessing the Impact of Pesticides on Pollinator Populations Based on Laboratory Data by Combining ALMaSS and BufferGUTS
-
Optimal evidence choice produces confirmation bias for minimal memory
The adaptive nature of confirmation bias
-
Eight-class alphabet turns cyclic peptide design into QUBO
Reduced-Alphabet QUBO/Ising Formulation for Constraint-Driven Cyclic Peptide Sequence Design
-
Crab cues raise limpet host attachment and survival on mobile hosts
Predator-associated cues promote host riding, and coupling to mobile hosts improves survival in an epizoic limpet
-
Movement restrictions alone leave Salmonella Dublin endemic on Öland
Bayesian modelling of herd-level infection dynamics in cattle: Local spread as the primary driver of Salmonella Dublin persistence on \"Oland
-
Distinct timescales turn closed organizations into agents
A Matter of Time: Towards a General Theory of Agency
-
Output networks buffer core clock period variability
Circadian output network can buffer period variability
-
Three methods estimate common synaptic input from motor unit spike trains
Estimating common synaptic inputs to spinal motor neurons from motor unit spike trains using openhdemg
-
Abundance correlations reveal no niche overlap in standard models
When do correlations reflect biological similarity in ecological dynamics?
-
Retrieval of similar enzymes lifts low-homology ESI accuracy
Retrieval-Augmented Multimodal Learning for Enzyme-Substrate Interaction Prediction Under Low-Homology Shift
-
SPIDER recovers directed brain flow from unaligned multi-lab recordings
SPIDER -- Stitched Power-spectra for Inferring Directed information flow from incomplete and asynchronous Experimental Recordings
-
Computer systems must be redesigned for biological data analysis
Architecture for Health Initiative (Arch4Health): Computational Challenges in Health-Related Applications and the Role of Computer Architecture in Addressing Them
-
Model turns ligand 3D shapes into ready-to-make DNA libraries
JEDEL: Zero-Shot DNA-Encoded Library Design for Early-Stage Drug Discovery
-
Transformers edge CNNs in colorectal histology classification
Performance and Interpretability of Convolutional, Transformer, and Hybrid Deep Learning Models in Colorectal Histology Classification
-
Optimal network degree maximizes upstream reciprocity
Upstream reciprocity versus downstream reciprocity: Catalyzing cooperation
-
Three LLM agents create evolving culture in decaying store
Emergent Culture in Minimal LLM Systems
-
R package detects introgression from gene tree discordance
quaint: An R Package for detecting introgression across a phylogeny using discordant gene tree topologies
-
Iterative method computes T7 polymerase speed and accuracy million times faster
Kinetics of multistate DNA polymerases
-
Matrix iterations solve multistate copolymerization kinetics exactly
Kinetics of template-directed multistate copolymerization
-
Method extracts geometric phase from noisy sperm and nematode data
Data-driven geometric phase in biological locomotion
-
Randomized test isolates which prompt parts drive clinical AI accuracy
PROMPT: A Pre-registered Randomized Protocol for Component-Level Evaluation of Clinical AI Prompts
-
Glass stretching creates physical model for tissue deformation
Glass-based physical models for tissue mechanics