chore: import upstream snapshot with attribution

examples/finetune/embedder/example_data/clustering-no_in_batch_neg/arXiv_title.jsonl

@@ -0,0 +1,10 @@
+{"query": "Rational Solutions of the Painlev\\'e-II Equation Revisited", "pos": ["A Generalised Sextic Freud Weight"], "neg": ["Formal groups and quantum cohomology", "Hypergeometric heritage of W.N. Bailey. With an appendix: Bailey's\n  letters to F. Dyson", "Scaling-violation phenomena and fractality in the human posture control\n  systems", "Glucodensities: a new representation of glucose profiles using\n  distributional data analysis", "Minimum Description Length codes are critical", "Universal Axial Algebras and a Theorem of Sakuma", "Prediction and description of a chiral pseudogap phase", "Bifurcation analysis of a normal form for excitable media: Are stable\n  dynamical alternans on a ring possible?", "One-dimensional foliations on topological manifolds", "Multiclass Diffuse Interface Models for Semi-Supervised Learning on\n  Graphs", "Synchronization patterns in LIF Neural Networks: Merging Nonlocal and\n  Diagonal Connectivity", "Longitudinal b-operators, Blups and Index theorems", "A two-scale model for sheared fault gouge: Competition between\n  macroscopic disorder and local viscoplasticity", "Online monitoring for safe pedestrian-vehicle interactions", "Accelerating Laue Depth Reconstruction Algorithm with CUDA", "An Algebraic Programming Style for Numerical Software and its\n  Optimization", "Compressible Baker Maps and Their Inverses. A Memoir for Francis Hayin\n  Ree [ 1936-2020 ]", "Multi-task Neural Networks for Personalized Pain Recognition from\n  Physiological Signals", "The Speed of Gravity in General Relativity and Theoretical\n  Interpretation of the Jovian Deflection Experiment"], "category": "nlin.SI math-ph math.CA math.MP", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Linear perturbations in a universe with a cosmological constant", "pos": ["On the Shape of the First Collapsed Objects"], "neg": ["The Revival of White Holes as Small Bangs", "Plasmon-Exciton Coupling Effect on Plasmon Damping", "How Users Explore Ontologies on the Web: A Study of NCBO's BioPortal\n  Usage Logs", "The covariance matrix of the potts model: A random cluster analysis", "Configurable Per-Query Data Minimization for Privacy-Compliant Web APIs", "Bilinear expansions of lattices of KP $\\tau$-functions in BKP\n  $\\tau$-functions: a fermionic approach", "The Universal Generating Function of Analytical Poisson Structures", "Applications of quantum Monte Carlo methods in condensed systems", "Study of the Kramers-Fokker-Planck quadratic operator with a constant\n  magnetic field", "xTras: a field-theory inspired xAct package for Mathematica", "Intersection of almost complex submanifolds", "Annealing schedule from population dynamics", "An Analytic Grothendieck Riemann Roch Theorem", "Complexity and cohomology of cohomological Mackey functors", "A Semi-Analytical Method for Calculating Revisit Time for Satellite\n  Constellations with Discontinuous Coverage", "Spectral Theory of Unsigned and Signed Graphs. Applications to Graph\n  Clustering: a Survey"], "category": "astro-ph gr-qc", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Hadron production in pA collisions at the LHC from the Color Glass\n  Condensate", "pos": ["Searching for Lepton Flavour (Universality) Violation and Collider\n  Signals from a Singly-Charged Scalar Singlet"], "neg": ["Anomaly detection in reconstructed quantum states using a\n  machine-learning technique", "Evidence for Non-Random Hydrophobicity Structures in Protein Chains", "A Borsuk-Ulam theorem for digital images", "Learning the ground state of a non-stoquastic quantum Hamiltonian in a\n  rugged neural network landscape", "A Random Matrix Approach to Differential Privacy and Structure Preserved\n  Social Network Graph Publishing", "AGNet: Weighing Black Holes with Deep Learning", "Towards automated patient data cleaning using deep learning: A\n  feasibility study on the standardization of organ labeling", "Intrinsically-limited timing jitter in molybdenum silicide\n  superconducting nanowire single-photon detectors", "Ionization of atoms by slow heavy particles, including dark matter", "Maxwell's equations in media as a contact Hamiltonian vector field and\n  its information geometry -- An approach with a bundle whose fiber is a\n  contact manifold", "Estimating country-specific space heating threshold temperatures from\n  national consumption data", "Agafonov's Proof of Agafonov's Theorem: A Modern Account and New\n  Insights", "Monotonicity of a relative R\\'enyi entropy", "Definable (co)homology, pro-torus rigidity, and (co)homological\n  classification", "Dynamical and Hamiltonian formulation of General Relativity", "Differential Expression Analysis of Dynamical Sequencing Count Data with\n  a Gamma Markov Chain", "Constraints on long range force from perihelion precession of planets in\n  a gauged $L_e-L_{\\mu,\\tau}$ scenario", "Deep image prior for 3D magnetic particle imaging: A quantitative\n  comparison of regularization techniques on Open MPI dataset", "Deep Learning for the Benes Filter", "Assessing the Causal Impact of COVID-19 Related Policies on Outbreak\n  Dynamics: A Case Study in the US"], "category": "hep-ph hep-ex nucl-ex nucl-th", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Topology of (some) tiling spaces without finite local complexity", "pos": ["A KAM theorem for generalized Hamiltonian systems without action-angle\n  variables"], "neg": ["Yet another proof of the Morse index theorem", "Convergence to the boundary for random walks on discrete quantum groups\n  and monoidal categories", "Computation with competing patterns in Life-like automaton", "Josephson-junction infrared single-photon detector", "Spectral Cross-Cumulants for Multicolor Super-resolved SOFI Imaging", "Modeling a Slicer Mirror Using Zemax User-Defined Surface", "The Universal Aspect Ratio of Vortices in Rotating Stratifi?ed Flows:\n  Experiments and Observations", "The Schottky Conjecture and beyond", "Noisy time series generation by feed-forward networks", "Return migration of German-affiliated researchers: Analyzing departure\n  and return by gender, cohort, and discipline using Scopus bibliometric data\n  1996-2020", "Quantum Spin probabilities at positive temperature are H\\\"older Gibbs\n  probabilities", "Computing zeta functions of large polynomial systems over finite fields", "Exact solutions of the (2+1) Dimensional Dirac equation in a constant\n  magnetic field in the presence of a minimal length", "SL(3|N) Wigner quantum oscillators: examples of ferromagnetic-like\n  oscillators with noncommutative, square-commutative geometry", "Exact Results for the Kuramoto Model with a Bimodal Frequency\n  Distribution", "Functional Control of Oscillator Networks", "Modeling the Adoption of Good Tech: Extending TAM3 to Incorporate the\n  Phenomenon of Warm-Glow"], "category": "math.DS math-ph math.MP", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Some remarks on twin groups", "pos": ["On metric relative hyperbolicity"], "neg": ["Electrostatic T-matrix for a torus on bases of toroidal and spherical\n  harmonics", "Classical Anthropic Everett model: indeterminacy in a preordained\n  multiverse", "Emergence and Synchronization in Chaotic Oscillators and in the Human\n  Cortical Network", "Modeling Cascading Failures in the North American Power Grid", "Phase transitions in anisotropic superconducting and magnetic systems\n  with vector order parameters: Three-loop renormalization-group analysis", "Nina Nikolaevna Uraltseva", "Broadband model-based inversion enables optoacoustic microscopy beyond\n  the acoustic diffraction limit", "Distinguishing resonance symmetries with energy-resolved photoion\n  angular distributions from ion-pair formation in O$_2$ following two-photon\n  absorption of a 9.3 eV femtosecond pulse", "Large-scale multilingual audio visual dubbing", "Liquid Cloud Storage", "Unsupervised seismic facies classification using deep convolutional\n  autoencoder", "Detecting Fast solvability of equations via small powerful Galois groups", "Approximating Holant problems by winding", "Information-theoretic thresholds from the cavity method", "Wound Healing Modeling Using Partial Differential Equation and Deep\n  Learning", "The Einstein-Jordan conundrum and its relation to ongoing foundational\n  research in local quantum physics", "Solution of the classical Yang--Baxter equation with an exotic symmetry,\n  and integrability of a multi-species boson tunneling model", "On the State of Computing in Statistics Education: Tools for Learning\n  and for Doing", "Hierarchical Graph Convolutional Networks for Semi-supervised Node\n  Classification", "Agile, Antifragile, Artificial-Intelligence-Enabled, Command and Control", "Universal patterns in sound amplitudes of songs and music genres", "Compound-tunable embedding potential method and its application to\n  fersmite crystal", "Asymptotic Normality of Scrambled Geometric Net Quadrature"], "category": "math.GR math.GT", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Non-adiabatic coupling and adiabatic population transfer in quantum\n  molecular systems", "pos": ["Total angular momentum representation for state-to-state quantum\n  scattering of cold molecules in a magnetic field"], "neg": ["Symplectic fermions and a quasi-Hopf algebra structure on $\\bar{U}_i\n  sl(2)$", "Loewner's Differential Equation and Spidernets", "Cosmology with a decaying vacuum", "Aggregation of Sub-mm Particles in Strong Electric Fields under\n  Microgravity Conditions", "Comparative analysis of the structures and outcomes of geophysical flow\n  models and modeling assumptions using uncertainty quantification", "DOLPHIn - Dictionary Learning for Phase Retrieval", "Applications of Finite Fields to Dynamical Systems and Reverse\n  Engineering Problems", "Analytic self-similar solutions of the Kardar-Parisi-Zhang interface\n  growing equation with various noise term", "Proximity-Aware Balanced Allocations in Cache Networks", "Local Moduli of Semisimple Frobenius Coalescent Structures", "Cavity ring-down spectroscopy of CO$_2$ near $\\lambda$ = 2.06 $\\mu$m:\n  Accurate transition intensities for the Orbiting Carbon Observatory-2 (OCO-2)\n  \"strong band\"", "A Nonlinear Evolution Equation in an Ordered Banach Space, Reconsidered", "Intrinsic scales for high-dimensional LEVY-driven models with\n  non-Markovian synchronizing updates", "SpaceHub: A high-performance gravity integration toolkit for few-body\n  problems in astrophysics", "How to choose which explanation to use with students? Discussing the\n  tensiometer with beginning teachers", "Graph Product Multilayer Networks: Spectral Properties and Applications", "Optimization with learning-informed differential equation constraints\n  and its applications", "Total nonnegativity of GCD matrices and kernels", "SN1987A: Revisiting the Data and the Correlation between Neutrino and\n  Gravitational Detectors", "Hecke operators and analytic Langlands correspondence for curves over\n  local fields", "Green Application Placement in the Cloud-IoT Continuum", "Structured Filtering"], "category": "physics.chem-ph physics.atom-ph", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Emergence of Haldane pseudo-potentials in systems with short-range\n  interactions", "pos": ["A Hamiltonian Approach for Obtaining Irreducible Projective\n  Representations and the $k\\cdot p$ Perturbation for Anti-unitary Symmetry\n  Groups"], "neg": ["How Likely Are Large Elections Tied?", "Collisional cooling of light ions by co-trapped heavy atoms", "jVMC: Versatile and performant variational Monte Carlo leveraging\n  automated differentiation and GPU acceleration", "Contrast Enhancement of Binary Star System Using an Optical Vortex\n  Coronagraph", "Cover Story Management", "Primitive point packing", "Matrix Tile Analysis", "Berry Phase in Neutrino Oscillations", "Tunable quantum logic gate on photonic qubits with a ladder emitter", "Inherent Stochastic Linearization of Random Laser Modes", "Exact scaling in the expansion-modification system", "Poincare isomorphism in K-theory on manifolds with edges", "Improved test of Lorentz Invariance in Electrodynamics using Rotating\n  Cryogenic Sapphire Oscillators", "Large Batch Simulation for Deep Reinforcement Learning", "Solving Polynomial Systems by Penetrating Gradient Algorithm Applying\n  Deepest Descent Strategy", "MARS: Middleware for Adaptive Reflective Computer Systems", "Matching with Text Data: An Experimental Evaluation of Methods for\n  Matching Documents and of Measuring Match Quality", "Phase retrieval for wide-band signals", "Sparsity Preserving Algorithms for Octagons", "On unique continuation for solutions of the Schr{\\\"o}dinger equation on\n  trees", "Robust Binary Neural Network Operation from 233 K to 398 K via Gate\n  Stack and Bias Optimization of Ferroelectric FinFET Synapses"], "category": "math-ph cond-mat.str-el math.MP", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Noncommutative generalizations of theorems of Cohen and Kaplansky", "pos": ["Prime Principal Right Ideal Rings"], "neg": ["A small-world of weak ties provides optimal global integration of\n  self-similar modules in functional brain networks", "Solving the radial Dirac equations: a numerical odyssey", "Social cohesion V.S. task cohesion: An evolutionary game theory study", "Learning to Locomote with Deep Neural-Network and CPG-based Control in a\n  Soft Snake Robot", "Inverse Design and Experimental Verification of a Bianisotropic\n  Metasurface Using Optimization and Machine Learning", "Self-Supervised Graph Representation Learning via Topology\n  Transformations", "Fast and Scalable Image Search For Histology", "Rips complexes as nerves and a Functorial Dowker-Nerve Diagram", "Application of gradient descent algorithms based on geodesic distances", "How Developers Iterate on Machine Learning Workflows -- A Survey of the\n  Applied Machine Learning Literature", "Social Information Processing in Social News Aggregation", "Algebraic structures connected with pairs of compatible associative\n  algebras", "Solving 1ODEs with functions", "The dynamics of the HIV infection: a time-delay differential equation\n  approach", "Besov spaces in multifractal environment and the Frisch-Parisi\n  conjecture", "Logic Learning in Hopfield Networks", "Exact model comparisons in the plausibility framework", "A Multiscale Kinetic-Fluid Solver with Dynamic Localization of Kinetic\n  Effects", "Quantum dynamics of the avian compass"], "category": "math.RA math.AC", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Interplay between Kondo physics and spin-orbit coupling in carbon\n  nanotube quantum dots", "pos": ["Dirac's method for constraints - an application to quantum wires,the 0.7\n  conductance anomaly"], "neg": ["\"Building\" exact confidence nets", "HMC, an Algorithms in Data Mining, the Functional Analysis approach", "Ansatz for the Jahn-Teller triplet instability", "Distributed Submodular Maximization", "PhasePack User Guide", "Position sensitive resonant Schottky cavities for heavy ion storage\n  rings", "Higher-order effects in the dynamics of hierarchical triple systems.\n  Quadrupole-squared terms", "Stochastic Minority on Graphs", "Active learning using weakly supervised signals for quality inspection", "On zeros of self-reciprocal polynomials", "Infinite Dimensional Multipliers and Pontryagin Principles for\n  Discrete-Time Problems", "Is the atomic metal vapor a dielectric state?", "Control of chaotic systems by Deep Reinforcement Learning", "The symmetry structure of the heavenly equation", "Tensor computations in computer algebra systems", "Asynchronous Decentralized Federated Learning for Collaborative Fault\n  Diagnosis of PV Stations", "On the Critical Coupling of the Finite Kuramoto Model on Dense Networks", "PageRank for evolving link structures", "Conley-Morse-Forman theory for generalized combinatorial multivector\n  fields on finite topological spaces"], "category": "cond-mat.str-el cond-mat.mes-hall", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Quantum Inverse Scattering Method and (Super)Conformal Field Theory", "pos": ["Rigidity and defect actions in Landau-Ginzburg models"], "neg": ["Generalized elimination of the global translation from explicitly\n  correlated Gaussian functions", "Sparse Recovery With Non-Linear Fourier Features", "Pricing in Social Networks with Negative Externalities", "Inferring the size of the causal universe: features and fusion of causal\n  attribution networks", "Tracking Attosecond Electronic Coherences Using Phase-Manipulated\n  Extreme Ultraviolet Pulses", "Building fast Bayesian computing machines out of intentionally\n  stochastic, digital parts", "The Gerrymandering Jumble: Map Projections Permute Districts'\n  Compactness Scores", "Embedding Symbolic Knowledge into Deep Networks", "Solar and planetary oscillation control on climate change: hind-cast,\n  forecast and a comparison with the CMIP5 GCMs", "Lagrangian shadows of ample algebraic divisors", "Surgery on Lagrangian and Legendrian Singularities", "Distributed Processing for Encoding and Decoding of Binary LDPC codes\n  using MPI", "Satisfiability Modulo ODEs", "Categorial Minimalist Grammar", "Three-Dimensional Lattice Boltzmann Model for High-Speed Compressible\n  Flows", "QNLP in Practice: Running Compositional Models of Meaning on a Quantum\n  Computer", "The word problem for free adequate semigroups", "Bose-Einstein condensation of magnons in spin pumping systems", "Regularity Normalization: Neuroscience-Inspired Unsupervised Attention\n  across Neural Network Layers", "Gluon Transport Equations with Condensate in the Small Angle\n  Approximation", "The evolution of Jordan curves on $\\mathbb{S}^2$ by curve shortening\n  flow"], "category": "hep-th math-ph math.MP math.QA", "prompt": "Identify the main and secondary category of Arxiv papers based on the titles.", "type": "symmetric_clustering"}

examples/finetune/embedder/example_data/clustering-no_in_batch_neg/bioRXiv_title.jsonl

@@ -0,0 +1,10 @@
+{"query": "Information processing dynamics in neural networks of macaque cerebral cortex reflect cognitive state and behavior.", "pos": ["Here's the twist: How the brain updates the representations of naturalistic events as our understanding of the past changes"], "neg": ["A network approach to genetic circuit designs", "Citation needed? Wikipedia and the COVID-19 pandemic", "Fishing for biodiversity by balanced harvesting", "XRN2-mediated regulation of let-7 microRNAs is of critical pathophysiological significance in Humans", "Active enhancers strengthen insulation by RNA-mediated CTCF binding at TAD boundaries", "Tardigrade CAHS Proteins Act as Molecular Swiss Army Knives to Mediate Desiccation Tolerance Through Multiple Mechanisms", "Protein-protein interactions on membrane surfaces analysed using pull-downs with supported bilayers on silica beads", "RapidoPGS: A rapid polygenic score calculator for summary GWAS data without a test dataset", "Antennapedia and optix regulate metallic silver wing scale development and cell shape in Bicyclus anynana butterflies", "Conformist social learning leads to self-organised prevention against adverse bias in risky decision making", "Microorganisms Characterization in Anaerobic Solventogenic Processing of Volatile Fatty Acids", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Maternal Western-Style Diet Impairs Bone Marrow Development and Drives a Hyperinflammatory Phenotype in Hematopoietic Stem and Progenitor Cells in Fetal Rhesus Macaques", "A novel two-generation approach to the population dynamics of gregarious parasitoids", "Plant inositol-phosphate-glycans and a fucosylated xyloglucan oligosaccharide are accumulated upon Arabidopsis thaliana/ Botrytis cinerea infection", "Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic andtargetable tissue states", "Localization of signaling receptors maximizes cellular informationacquisition in spatially-structured natural environments", "Evolution of phenotypic variance during adaptation to high temperature in Drosophila", "Virus-host interactions and genetic diversity of Antarctic sea ice bacteriophages", "INPP4B drives lysosome biogenesis to restrict leukemic stem cell differentiation and promote leukemogenesis", "Structural effects driven by rare point mutations in amylin hormone, the type II diabetes-associated peptide", "Adipose triglyceride lipase promotes prostaglandin-dependent actin remodeling by regulating substrate release from lipid droplets", "Leaf Aqueous Extract of Manilkara hexandra influenced Glucose Metabolism in fish: An observation with Labeo rohita Fingerlings as model organism", "Neuronal Activation of the Gastrointestinal Tract Shapes the Gut Environment in Mice"], "category": "neuroscience", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM", "pos": ["Morphogenesis and cell ordering in confined bacterial biofilms"], "neg": ["Estrogen-related receptor alpha and Rplp1-dependent translation coordinately regulate starvation response and decrease NASH progression", "Bayesian Additive Regression Trees for Genotype by Environment Interaction Models", "Identifying critical transcriptional targets of the MYC oncogene using a novel competitive precision genome editing (CGE) assay", "Ecological correlates of gene family size in a pine-feeding sawfly genome and across Hymenoptera", "Structure-Functional-Selectivity Relationship Studies on A-86929 Analogs and Small biaryl Fragments toward Discovery of biased D1 agonists", "Common variants in breast cancer risk loci predispose to distinct tumor subtypes", "mTORC2 contributes to murine systemic autoimmunity", "EEG and behavioral correlates of attentional processing while walking and navigating naturalistic environments", "Frequency modulated timer regulates mammalian hibernation", "Small extracellular vesicles from young mice prevent frailty, improve healthspan and decrease epigenetic age in old mice.", "A chemical screen based on an interruption of zebrafish gastrulation identifies the HTR2C inhibitor Pizotifen as a suppressor of EMT-mediated metastasis", "Cytokinin oxidase/dehydrogenase family genes exhibit functional divergence and overlap in rice growth and development", "The extracellular matrix controls stem cell specification and crypt morphology in the developing and adult gut", "Evaluation of US state pollinator plans using 3 evidence-based policymaking frameworks", "Quantifying the Morphology and Mechanisms of Cancer Progression in 3D in-vitro environments: Integrating Experiments and Multiscale Models", "Development of an exosomal gene signature to detect residual disease in dogs with osteosarcoma using a novel xenograft platform and machine learning", "A Novel Paradigm for Deep Reinforcement Learning of Biomimetic Systems", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "TeamTree analysis: a new approach to evaluate scientific production", "Neuroinvasion and neurotropism by SARS-CoV-2 variants in the K18-hACE2 mouse", "Single molecule tracking the uncoupling of assembly and membrane insertion in Perfringolysin O", "Bulk-assembly of monodisperse coacervates and giant unilamellar vesicles with programmable hierarchical complexity", "Effects of a 33-ion sequential beam galactic cosmic ray analog on male mouse behavior and evaluation of CDDO-EA as a radiation countermeasure", "Cell Intrinsic Control of Death and Proliferation of Lymphocytes in Immune Response and Tumor Cells by pH"], "category": "microbiology", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Thalamic control of sensory enhancement and sleep spindle properties in a biophysical model of thalamoreticular microcircuitry", "pos": ["Face dissimilarity judgements are predicted by representational distance in 3D-morphable and image-computable models"], "neg": ["DeepMAPS: Single-cell biological network inference using heterogeneous graph transformer", "Nanoscale ligand density modulates gap junction intercellular communication of cell condensates during chondrogenesis", "Microbiota-instructed regulatory T cell differentiation is mediated by a distinct ROR\u03b3t+ antigen presenting cell subset", "ALLOPURINOL BLOCKS THE AORTIC ANEURYSM IN A MOUSE MODEL OF MARFAN SYNDROME VIA REDUCING AORTIC OXIDATIVE STRESS", "Super-enhancer signature reveals key mechanisms associated with resistance to non-alcoholicsteatohepatitis in humans with obesity", "Modular Dynamic Biomolecular Modelling with Bond Graphs: The Unification of Stoichiometry, Thermodynamics, Kinetics and Data.", "Conformist social learning leads to self-organised prevention against adverse bias in risky decision making", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Utility of SARS-CoV-2 infection models using in vitro and in vivo ACE2-lentivirus transduction", "ZIKV disrupts placental ultrastructure and drug transporter expression in mice", "Synthetic periphyton as a model system to understand species dynamics in complex microbial freshwater communities", "Strain and rupture of HIV-1 capsids during uncoating", "First evidence of in vitro cytotoxic effects of marine microlitter on Merluccius merluccius and Mullus barbatus, two Mediterranean commercial fish species", "Identifying and testing marker-trait associations for growth and phenology in three pine species: implications for genomic prediction", "Imbalanced segregation of recombinant haplotypes in hybrid populations reveals inter- and intrachromosomal Dobzhansky-Muller incompatibilities", "AFFORDABLE, REPLICABLE ROBOTIC MINIRHIZOTRON SAMPLING FOR ROOT DYNAMICS STUDIES", "Propionate ameliorates diabetes-induced neurological dysfunction through regulating the PI3K/Akt/eNOS signaling pathway", "The Tabula Sapiens: a multiple organ single cell transcriptomic atlas of humans", "Serological fingerprints link antiviral activity of therapeutic antibodies to affinity and concentration", "Mapping the genetic and environmental aetiology of autistic traits in Sweden and the United Kingdom", "Analysis of science journalism reveals gender and regional disparities in coverage", "Single-nucleus RNA Sequencing and Spatial Transcriptomics Reveal the Immunological Microenvironment of Cervical Squamous Cell Carcinoma", "Tetraspanin Cd9b and Cxcl12a/Cxcr4b have a synergistic effect on the control of collective cell migration", "Non-targeted multimodal metabolomics and lipidomics data from ovine rumen fluid fractions"], "category": "neuroscience", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Emerging experience-dependent dynamics in primary somatosensory cortex reflect behavioral adaptation", "pos": ["The organizational principles of de-differentiated topographic maps in somatosensory cortex"], "neg": ["An hidden Markov model to estimate homozygous-by-descent probabilities associated with nested layers of ancestors", "Actin isovariant ACT7 controls root meristem development in Arabidopsis through modulating auxin and ethylene responses", "Tackling polypharmacology of kinase inhibitors and selecting chemical kinase probes by transcription factor activity profiling.", "Multi-layered regulation of neuroectoderm differentiation by retinoic acid in a primitive streak-like context", "kmtricks: Efficient and flexible construction of Bloom filters for large sequencing data collections", "A Hierarchy of Biomolecular Proportional-Integral-Derivative Feedback Controllers for Robust Perfect Adaptation and Dynamic Performance", "Alkaline phosphatase activity of serum affects osteogenic differentiation cultures", "CRISPR-based kinome-screening revealed MINK1 as a druggable player to rewire 5FU-resistance in OSCC through AKT/MDM2/p53 axis", "Hierarchical clustering optimizes the tradeoff between compositionality and expressivity of task structures for flexible reinforcement learning", "Erythropoietin supplementation ameliorates the immunological and hematological deficiencies of lysinuric protein intolerance in mice", "Designer Scaffolds for Interfacial Bioengineering", "Microbial populations are shaped by dispersal and recombination in a low biomass subseafloor habitat", "Tree encroachment threatens the conservation potential and sustainability of U.S. rangelands", "Genome editing excisase origins illuminated by somatic genome of Blepharisma", "Re-convolving the compositional landscape of primary and recurrent glioblastoma reveals prognostic andtargetable tissue states", "Improved radiation expression profiling in blood by sequential application of sensitive and specific gene signatures", "Naming of human diseases on the wrong side of history", "An Extended Motif in the SARS-CoV-2 Spike Modulates Binding and Release of Host Coatomer in Retrograde Trafficking", "Resolving when (and where) the Thylacine went extinct", "Reduced glutathione decreases cell adhesion and increases cell volume.", "An estimate of the deepest branches of the tree of life from ancient vertically-evolving genes", "A TIR-1/SARM1 phase transition underlies p38 immune pathway activation in the C. elegans intestine", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Effect of a low concentration in chloride, sodium and potassium on oocyte maturation, oocyte hydration, ovulation and egg quality in rainbow trout."], "category": "neuroscience", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Dissociating the Neural Correlates of Planning and Executing Tasks with Nested Task Sets", "pos": ["Performance of three freely available methods for extracting white matter hyperintensities: FreeSurfer, UBO Detector and BIANCA"], "neg": ["Limited selection towards lighter seeds in Danish grasslands over an eight-year period", "The origins and drivers of Neotropical diversity", "Elucidation of SARS-CoV-2 budding mechanisms through molecular dynamics simulations of M and E protein complexes", "The unfolded protein response triggers the immune deficiency pathway in ticks", "Co-infection of Candidatus Piscichlamydia trichopodus (order Chlamydiales) and Henneguya sp (Myxosporea, Myxobolidae) in snakeskin gourami Trichopodus pectoralis (Regan 1910)", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Small extracellular vesicles from young mice prevent frailty, improve healthspan and decrease epigenetic age in old mice.", "Distinct mutations and lineages of SARS-CoV-2 virus in the early phase of COVID-19 pandemic and subsequent one-year global expansion", "The Mitochondrial RNA Granule Modulates Manganese-Dependent Cell Toxicity", "Groping in the fog: soaring migrants exhibit wider scatter in flight directions and respond differently to wind under low visibility conditions", "A cell cycle-dependent GARP-like transcriptional repressor regulates the initiation of differentiation in Giardia lamblia", "Structural basis for cell-type specific evolution of viral fitness by SARS-CoV-2", "Integrative Modelling of Signalling Network Dynamics Identifies Cell Type-selective Therapeutic Strategies for FGFR4-driven Cancers", "Faster short-read mapping with strobemer seeds constructed from syncmers", "Reconstitution of minimal motility system based on Spiroplasma swimming by expressing two bacterial actins in synthetic minimal bacterium", "TeamTree analysis: a new approach to evaluate scientific production", "Enhancers regulate 3' end processing activityto control expression of alternative 3'UTR isoforms", "F1F0 ATP Hydrolysis is a Determinant of Metabolic Rate, a Correlate of Lifespan, and a Weakness of Cancer", "The perceptual relevance of the speech envelope-following response in normal hearing and age-related hearing impaired listeners", "Poly(rC)-binding protein 1 limits hepatitis C virus assembly and secretion", "An epigenetic memory of inflammation controls context-dependent lineage plasticity in the pancreas", "PIN-FORMED1 polarity in the shoot is insensitive to the polarity of neighbouring cells", "Effects of Ancestry and Hypopigmentation Alleles on Skin Color in a Caribbean Native American Population", "First evidence of in vitro cytotoxic effects of marine microlitter on Merluccius merluccius and Mullus barbatus, two Mediterranean commercial fish species"], "category": "neuroscience", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Migrators Within Migrators: Exploring Transposable Element Landscapes, Activity, and Host Gene Associations in the Monarch Butterfly, Danaus plexippus", "pos": ["H2A.B is a cancer/testis factor involved in activation of ribosome biogenesis in Hodgkin Lymphoma"], "neg": ["Analysis of science journalism reveals gender and regional disparities in coverage", "Royal knifefish generate powerful suction feeding through large neurocranial elevation and high epaxial muscle power", "Cascade screening following a polygenic risk score test: what is the risk of a relative conditional on a high score of a proband?", "Using networks to analyze and visualize the distribution of overlapping reading frames in virus genomes", "Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces", "Differential fate of acellular vascular scaffolds in vivo involves macrophages and T-cell subsets", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Titers of antibodies the receptor-binding domain (RBD) of ancestral SARS-CoV-2 are predictive for levels of neutralizing antibodies to multiple variants", "Cell Cycle Delay, Pro-metaphase Arrest and C-metaphase Inducing Effects of Petroleum Ether Fraction of Leaf Aqueous Extract of Clerodendrum viscosum Vent.", "The evolution of stomatal traits along the trajectory towards C4 photosynthesis", "Limitations of composability of cis-regulatory elements in messenger RNA", "Integrated analysis of cervical squamous cell carcinoma cohorts from three continents reveals conserved subtypes of prognostic significance.", "The initial response of females towards congeneric males matches the propensity to hybridise in Ophthalmotilapia.", "Enhancing Sampling of Water Rehydration on Ligand Binding: A Comparison of Techniques", "A chemical screen based on an interruption of zebrafish gastrulation identifies the HTR2C inhibitor Pizotifen as a suppressor of EMT-mediated metastasis", "Only 2 of 12 now-deleted genes of 19 identified and predicted Myb family DNA binding proteins are directly involved in rice Magnaporthe oryzae pathogenicity", "Stress-dependent cell stiffening by tardigrade tolerance proteins through reversible formation of cytoskeleton-like filamentous network and gel-transition", "Analysis of the leaf metabolome in Arabidopsis thaliana mutation accumulation lines reveals association of pleiotropy and fitness consequences", "Genome editing in the unicellular holozoan Capsaspora owczarzaki suggests a premetazoan role for the Hippo pathway in multicellular morphogenesis", "Expression and subcellular localization of USH1C/harmonin in the human retina provides insights into pathophysiology and therapy of Usher syndrome", "Hotspots of pest-induced US urban tree death, 2020-2050", "A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike", "Eye movements reveal spatiotemporal dynamics of visually-informed planning in navigation", "Rho Kinase regulates neutrophil NET formation that is involved in UVB-induced skin inflammation"], "category": "genomics", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "PRDM9 losses in vertebrates are coupled to those of paralogs ZCWPW1 and ZCWPW2", "pos": ["Recurring adaptive introgression of a supergene variant that determines social organization"], "neg": ["ZAF -- The First Open Source Fully Automated Feeder for Aquatic Facilities", "The pH Dependence of Niclosamide Solubility, Dissolution, and Morphology Motivates Potentially Universal Mucin-Penetrating Nasal and Throat Sprays for COVID19, its Contagious Variants, and Other Respiratory Viral Infections", "Suppression of sost/sclerostin and dickkopf-1 promote intervertebral disc structure in mice", "Raman Signal Denoising using Fully Convolutional Encoder Decoder Network", "A temporal parcellation of the sensory-evoked responses during the rubber hand illusion reveals manipulation- and illusion-specific correlates", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Oxytocin promotes social grooming in bonobos", "The unfolded protein response triggers the immune deficiency pathway in ticks", "LPS-TLR4 pathway exaggerates alcohol-induced acute-on-chronic liver failure via provoking NETs formation", "Monitoring fish communities through environmental DNA metabarcoding in the fish pass system of the second largest hydropower plant in the world", "Fungicide resistance characterised across seven modes of action in a Botrytis cinerea isolated from Australian vineyards", "Thirteen independent genetic loci associated with preserved processing speed in a study of cognitive resilience in 330,097 individuals in the UK Biobank", "Deep Transfer Learning of Drug Responses by Integrating Bulk and Single-cell RNA-seq data", "The obstacles and potential clues of prime editing applications in tomato, a dicot plant", "Genetic interactions drive heterogeneity in causal variant effect sizes for gene expression and complex traits", "3D Reconstructions of Mouse Skeletal Muscle Reveal a Decrease in the MICOS Complex and Altered Mitochondrial Networks", "Obesity affects mitochondrial metabolism and proliferative potential of equine endometrial progenitor cells.", "Engineered disulfide reveals structural dynamics of locked SARS-CoV-2 spike", "Synergy of chemotherapy and macrophage depletion leads to B cell-mediated T cell memory activation and durable triple negative breast cancer regression", "\"Adopt a Microorganism\" methodology enhances the discourse richness of high school students in both hybrid learning and remote education", "A flux-based machine learning model to simulate the impact of pathogen metabolic heterogeneity on drug interactions", "Mouse lemur, a new animal model to investigate cardiac pacemaker activity in primates.", "Identifying and testing marker-trait associations for growth and phenology in three pine species: implications for genomic prediction", "Conserved organ-specific microbial assemblages in different populations of a terrestrial crab"], "category": "evolutionary biology", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Distinct corticostriatal compartments drive competition between adaptive and automatized behavior", "pos": ["Behavioral distractibility in preschoolers from different socio-economic backgrounds"], "neg": ["The number of cytokinesis nodes in mitotic fission yeast scales with cell size", "A Wnt/\u03b2-catenin signaling driven adipocyte population required for beiging and glucose homeostasis", "Co-infection of Candidatus Piscichlamydia trichopodus (order Chlamydiales) and Henneguya sp (Myxosporea, Myxobolidae) in snakeskin gourami Trichopodus pectoralis (Regan 1910)", "\"Adopt a Microorganism\" methodology enhances the discourse richness of high school students in both hybrid learning and remote education", "The Ensemble of Gene Regulatory Networks at Mutation-Selection Balance", "Active feature selection discovers minimal gene sets for classifying cell types and disease states with single-cell mRNA-seq data", "In vitro pectate lyase activity and carbon uptake assays and whole genome sequencing of Bacillus amyloliquefaciens subsp. plantarum strains for a pectin defective pathway", "Phenotypic heterogeneity driven by plasticity of the intermediate EMT state governs disease progression and metastasis in breast cancer", "Host factors drive the within-host competition between highly and low pathogenic H5N8 avian influenza viruses", "Induction of exaggerated cytokine production in human peripheral blood mononuclear cells by a recombinant SARS-CoV-2 spike glycoprotein S1 and its inhibition by dexamethasone", "Exploring functional protein covariation across single cells using nPOP", "Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes", "A humanized nanobody phage display library yields potent binders of SARS CoV-2 spike", "Diversity of SARS-CoV-2 genome among various strains identified in Lucknow, Uttar Pradesh", "Nascent alt-protein chemoproteomics reveals a repressor of ribosome biogenesis", "Targeting SARS-CoV-2 infection through CAR-T like bispecific T cell engagers incorporating ACE2", "A novel two-generation approach to the population dynamics of gregarious parasitoids", "A rat model of pregnancy in the male parabiont", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Force-correction Analysis Method for Derivation of Multidimensional Free Energy Landscapes from Adaptively Biased Replica Simulations", "A Physiometric Investigation of Inflammatory Composites: Comparison of A Priori Aggregates, Empirically-identified Factors, and Individual Proteins", "A multivariate view of cognitive performance reveals positive correlation in the Trinidadian Guppy (Poecilia reticulata)", "Challenges in modelling the sediment retention ecosystem service for an ecosystem account, with examples from the Mitchell catchment", "Clonal evolution in serially passaged Cryptococcus neoformans x deneoformans hybrids reveals a heterogenous landscape of genomic change"], "category": "neuroscience", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Identification of two cancer stem cell-like populations in triple-negative breast cancer xenografts", "pos": ["Striatin 3 and MAP4K4 cooperate towards oncogenic growth and tissue invasion in medulloblastoma"], "neg": ["A novel two-generation approach to the population dynamics of gregarious parasitoids", "ConVarT: a search engine for orthologous variants and functional inference of human genetic variants", "Naming of human diseases on the wrong side of history", "Tunable Cellular Localization and Extensive Cytoskeleton-Interplay of Reflectins", "Embracing curiosity eliminates the exploration-exploitation dilemma", "Admp regulates tail bending by controlling ventral epidermal cell polarity via phosphorylated myosin translocation.", "ALLOPURINOL BLOCKS THE AORTIC ANEURYSM IN A MOUSE MODEL OF MARFAN SYNDROME VIA REDUCING AORTIC OXIDATIVE STRESS", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Atrazine induced In vivo immunotoxicity in Bivalves", "A novel, computationally tractable algorithm flags in big matrices every column associated in any way with others or a dependent variable, with much higher power when columns are linked like mutations in chromosomes", "Omicron-specific mRNA vaccination alone and as a heterologous booster against SARS-CoV-2", "T606-phosphorylation deprives the function of Kaiso as a transcription factor and cancer repressor", "Outer hair cell electro-mechanical power conversion", "Computation of the mitochondrial age distribution along the axon length", "The physics of liquid-to-solid transitions in multi-domain protein condensates", "A bacterial effector counteracts host autophagy by promoting degradation of an autophagy component", "Evolution of phenotypic variance during adaptation to high temperature in Drosophila", "Structural predictions of the SNX-RGS proteins suggest they belong to a new class of lipid transfer proteins", "Fine-scale adaptations to environmental variation and growth strategies drive phyllosphere Methylobacterium diversity.", "De novo identification of maximally deregulated subnetworks based on multi-omics data with DeRegNet", "In Vivo Multi-Day Calcium Imaging of CA1 Hippocampus in Freely Moving Rats Reveals a High Preponderance of Place Cells with Consistent Place Fields", "Reconstitution of minimal motility system based on Spiroplasma swimming by expressing two bacterial actins in synthetic minimal bacterium", "Hot and cold spots of pest-induced US urban tree death, 2020-2050", "Genome-wide mechanisms of rediploidization in paleopolyploid teleosts revealed by a high-resolution comparative atlas across 74 fishes"], "category": "cancer biology", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}
+{"query": "Motor attention to the tactile modality induces sensory attenuation for sounds", "pos": ["Serotonin signals through postsynaptic G\u03b1q, Trio RhoGEF, and diacylglycerol to promote C. elegans egg-laying circuit activity and behavior"], "neg": ["ALLOPURINOL BLOCKS THE AORTIC ANEURYSM IN A MOUSE MODEL OF MARFAN SYNDROME VIA REDUCING AORTIC OXIDATIVE STRESS", "Reduced glutathione decreases cell adhesion and increases cell volume.", "Transcriptional condensates formed by phase-separated ALOG family proteins control shoot meristem maturation for flowering", "A terrain treadmill to study animal locomotion through large obstacles", "Structural basis for the inhibition of the Bacillus subtilis c-di-AMP cyclase CdaA by the phosphoglucomutase GlmM", "Similarities Between Bacterial GAD and Human GAD65: Implications in Gut Mediated Autoimmune Type 1 Diabetes", "A novel two-generation approach to the population dynamics of gregarious parasitoids", "The role of Kabuki Syndrome genes KMT2D and KDM6A in development: Analysis in Human sequencing data and compared to mice and zebrafish", "Fusobacterium nucleatum induces pancreatic cancer cell proliferation and migration by regulating host autocrine and paracrine signaling", "Structural Analysis of Spike Protein Mutations in the SARS-CoV-2 P.3 Variant", "Diverse stem-chondrichthyan oral structures and evidence for an independently acquired acanthodid dentition", "Changes to the mtDNA copy number during yeast culture growth", "Differential fate of acellular vascular scaffolds in vivo involves macrophages and T-cell subsets", "C. elegans PEZO-1 is a Mechanosensitive Ion Channel Involved in Food Sensation", "Omicron BA.2 specifically evades broad sarbecovirus neutralizing antibodies", "Centimeter-scale quorum sensing dictates collective survival of differentiating embryonic stem cells", "Cell-specific Bioorthogonal Tagging of Glycoproteins", "Missing the sweet spot: one of the two N-glycans on human Gb3/CD77 synthase is expendable", "Impaired activation of Transposable Elements in SARS-CoV-2 infection", "Host phenology can drive the evolution of intermediate virulence strategies in some parasites", "Identification and characterization of the WYL BrxR protein and its gene asseparable regulatory elements of a BREX phage restriction system", "Naming of human diseases on the wrong side of history", "Mapping the planet's critical natural assets", "Cellular feedback to organotelluranes displays modulation of antioxidant proteins gene expression"], "category": "neuroscience", "prompt": "Identify the main category of Biorxiv papers based on the titles.", "type": "symmetric_clustering"}