Document Classifier

Place a document in the atlas

See its field, frameworks, inherited assumptions, and concept origins.

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Examples

Benchmark documents and classifier results

These samples come from the taxonomy ablation set used to evaluate the live classifier.

Paper

Quantum journal note on Hamiltonian phase flow

Although the venue is a quantum foundations workshop, the argument treats a pendulum as a conservative classical system in canonical coordinates. It derives trajectories from a Hamiltonian, compares the result with Euler-Lagrange equations, and uses Poisson brackets to explain conserved quantities.

Natural SciencesPhysicsClassical Mechanics95%

The document applies Hamiltonian mechanics to a classical pendulum, deriving trajectories from a Hamiltonian and using Poisson brackets to analyze conserved quantities, while comparing the result with the Euler-Lagrange equations from Lagrangian mechanics. Despite its title and workshop venue suggesting a quantum focus, the content is entirely classical.

Result details

Frameworks

  • Hamiltonian Mechanicsuses / 95%
  • Lagrangian Mechanicscompares / 90%

Inherited Assumptions

  • Time is a continuous and reversible parameter.
  • The system is conservative (total energy constant).

Concepts

  • Hamiltonian Functioncentral
  • Phase Spacebackground
  • Canonical Equationscentral
  • Poisson Bracketcentral

Map Gaps

  • Euler-Lagrange Equations
  • Generalized Coordinates
Paper

Entropy production in heat engines

The paper studies a finite heat engine connected to hot and cold reservoirs. It estimates work extraction, irreversible entropy production, thermal efficiency, and the limits imposed by the first and second laws without deriving ensemble probabilities from microstates.

Natural SciencesPhysicsThermodynamics95%

This document analyzes a finite heat engine operating between two reservoirs, focusing on work extraction, irreversible entropy production, and thermal efficiency as constrained by the first and second laws of thermodynamics. Its intellectual home is thermodynamics within physics, with a specific emphasis on finite-time effects rather than statistical microstate derivations.

Result details

Frameworks

  • Classical Thermodynamicsuses / 90%
  • Finite-Time Thermodynamicsuses / 70%

Inherited Assumptions

  • The first law of thermodynamics applies to the heat engine cycle.
  • The second law of thermodynamics imposes an upper bound on efficiency via entropy production.

Concepts

  • Entropymissing
  • Thermal efficiencymissing
  • Irreversible processmissing

Map Gaps

  • Entropy
  • Thermal efficiency
  • Irreversible process
Article

Protein folding as an ensemble problem

The biological example is protein folding, but the analysis centers on canonical ensembles, partition functions, free energy landscapes, Boltzmann weights, and fluctuations around equilibrium. The proteins are used as a case where statistical mechanics links microstates to macroscopic observables.

Natural SciencesPhysicsStatistical Mechanics95%

The document uses protein folding as a case study to explore equilibrium statistical mechanics, focusing on canonical ensembles, partition functions, free energy landscapes, and Boltzmann weights. Its primary intellectual home is physics, specifically statistical mechanics, with no active engagement with biological mechanisms or experimental data.

Result details

Frameworks

  • Boltzmann Statistical Mechanicsuses / 90%
  • Gibbsian Ensemble Theoryuses / 80%

Inherited Assumptions

  • The system is at or near equilibrium, allowing the use of canonical ensembles and Boltzmann weights.
  • Time averages equal ensemble averages, justifying ensemble theory for protein conformational states.

Concepts

  • Free energy landscapemissing
  • Partition functionmissing
  • Canonical ensemblemissing
  • Boltzmann weightmissing

Map Gaps

  • Free energy landscape
  • Partition function
  • Canonical ensemble
Paper

SN1 and SN2 rate evidence

The article uses rate laws and activation barriers, but its main object is the choice between substitution pathways in alkyl halides. It reasons through leaving groups, nucleophile strength, carbocation stability, stereochemical inversion, and electron-pushing mechanisms.

Natural SciencesChemistryOrganic Chemistry95%

The document investigates the evidence for SN1 versus SN2 substitution mechanisms in alkyl halides by analyzing rate laws, activation barriers, leaving group ability, nucleophile strength, carbocation stability, and stereochemical inversion. Its intellectual home is organic chemistry, specifically the methodological school of physical organic chemistry.

Result details

Frameworks

  • Physical Organic Chemistryuses / 90%
  • Stereochemistryuses / 85%
  • Electronic Theory of Organic Chemistryuses / 80%

Inherited Assumptions

  • Reaction rates can be analyzed in terms of elementary steps and concentration-dependent rate laws.
  • Transition state structure and stability determine reaction barriers.

Concepts

  • Rate lawscentral
  • Reaction mechanismscentral
  • Kinetic studiesbackground
  • Solvent effectbackground

Map Gaps

  • Carbocation stability
  • Leaving group ability
  • Nucleophile strength
Paper

Transcriptional regulation of inherited variants

The study mentions inheritance and genotypes, but it investigates how promoter architecture, transcription factors, mRNA abundance, translation, and protein expression mediate the effect of variants. The central vocabulary is gene expression rather than pedigree ratios.

Natural SciencesBiologyMolecular Biology90%

The document investigates how inherited genetic variants influence molecular phenotypes by tracing effects through promoter architecture, transcription factors, mRNA abundance, translation, and protein expression. Its intellectual home is molecular biology, specifically the intersection of the Central Dogma and systems-level quantification of gene expression.

Result details

Frameworks

  • Central Dogmauses / 90%
  • Gene-Centered Frameworkuses / 80%
  • Eukaryotic Cis-Regulatory Element Paradigmuses / 80%

Inherited Assumptions

  • Information flows from DNA to RNA to protein, and variant effects can be traced along this path.
  • The gene is the primary unit of inheritance and analysis.

Concepts

  • variant effectmissing
  • promoter architecturemissing
  • transcription factormissing
  • mRNA abundancemissing

Map Gaps

  • variant effect
  • promoter architecture
  • transcription factor
Paper

Predator-prey resilience after disturbance

The document studies food webs, trophic cascades, carrying capacity, population dynamics, and ecosystem resilience after a fire. It briefly notes economic costs of conservation, but the explanatory model is ecological rather than valuation-based.

Natural SciencesBiologyEcology95%

The document is an ecological study examining predator-prey dynamics, food webs, trophic cascades, and ecosystem resilience following a fire disturbance. Its intellectual home is in disturbance and non-equilibrium ecology, with strong roots in population and ecosystem ecology frameworks.

Result details

Frameworks

  • Lotka-Volterra Population Ecologyuses / 90%
  • Non-Equilibrium and Disturbance Ecologyuses / 90%
  • Tansley-Odum Ecosystem Ecologyuses / 80%

Inherited Assumptions

  • Predator-prey interactions can be modeled using differential equations.
  • Disturbances are discrete events that alter successional trajectories.

Concepts

  • Resiliencemissing
  • Trophic cascademissing
  • Disturbancemissing
  • Carrying capacitymissing

Map Gaps

  • Resilience
  • Trophic cascade
  • Disturbance
Paper

Elastic response of DNA under force

The text uses polymer physics to explain force-extension curves for DNA molecules. It treats thermal fluctuations, persistence length, entropic elasticity, and molecular motors as physical models of biological macromolecules.

Natural SciencesPhysicsBiophysics90%

This document applies polymer physics to explain the force-extension curves of DNA, treating thermal fluctuations, persistence length, and entropic elasticity as core concepts. It is primarily situated in biophysics, with strong roots in scaling concepts from polymer physics and single-molecule biophysics.

Result details

Frameworks

  • Scaling Concepts in Polymer Physicsuses / 90%
  • Single-Molecule Biophysicsuses / 80%
  • Active Matter Frameworkuses / 70%

Inherited Assumptions

  • DNA can be modeled as a continuous elastic rod with a persistence length.
  • Thermal fluctuations dominate the mechanical response at small forces.

Concepts

  • Persistence lengthmissing
  • Entropic elasticitymissing
  • Force-extension curvemissing
  • Thermal fluctuationsmissing

Map Gaps

  • Persistence length
  • Entropic elasticity
  • Force-extension curve
Paper

Generalization in deployed classifiers

The paper studies training and test distributions, overfitting, regularization, cross-validation, empirical risk minimization, and model capacity for predictive systems. It cites statistical learning theory, but the operational concern is machine-learning generalization in deployed models.

Computer ScienceArtificial IntelligenceMachine Learning95%

The document is a machine-learning paper focused on the practical challenge of generalization in deployed predictive systems. It discusses training and test distributions, overfitting, regularization, cross-validation, empirical risk minimization, and model capacity, drawing on statistical learning theory as a conceptual foundation.

Result details

Frameworks

  • Statistical Learninguses / 90%

Inherited Assumptions

  • Generalization error can be decomposed into bias and variance components.
  • Empirical risk minimization is a valid principle for learning, tempered by regularization.

Concepts

  • Generalization Errorcentral
  • Overfittingcentral
  • Regularizationcentral
  • Bias-Variance Tradeoffbackground

Map Gaps

  • Empirical Risk Minimization
  • Cross-Validation
  • Model Capacity
Paper

Transformer scaling laws without language tasks

The paper mentions language models in the introduction, but its experiments compare transformer depth, width, representation learning, optimization stability, and scaling behavior across synthetic modalities. Token semantics are not the main object.

Computer ScienceArtificial IntelligenceDeep Learning90%

This paper empirically studies the scaling behavior of transformers on synthetic modalities, stripping away language-specific semantics to examine how depth, width, representation learning, and optimization stability affect performance. Its intellectual home is the intersection of Transformer Architecture and Representation Learning.

Result details

Frameworks

  • Transformer Architectureuses / 90%
  • Representation Learninguses / 70%

Inherited Assumptions

  • Transformers benefit from scaling depth and width in a predictable manner, independent of data modality.
  • Representation quality can be evaluated through optimization stability and scaling behavior.

Concepts

  • Self-Attentioncentral
  • Layer Normalizationbackground
  • Residual Connectionsbackground
  • Scaling Lawsmissing

Map Gaps

  • Scaling Laws
  • Synthetic Modalities
  • Optimization Stability
Paper

Actor-critic learning for resource allocation

A control problem supplies the example, but the method is reinforcement learning: an agent optimizes policy gradients with value-function baselines, temporal-difference targets, exploration, and discounted returns in a Markov decision process.

Computer ScienceArtificial IntelligenceReinforcement Learning95%

This document's main intellectual home is reinforcement learning, specifically actor-critic methods applied to resource allocation. It introduces a control problem framed as a Markov decision process, where an agent optimizes policy gradients with value-function baselines and temporal-difference targets.

Result details

Frameworks

  • Actor-Critic Methodsuses / 95%
  • Policy Gradient Methodsuses / 90%
  • Temporal-Difference Learninguses / 85%

Inherited Assumptions

  • The environment can be modeled as a Markov decision process with stationary dynamics.
  • Policy optimization is based on stochastic gradient ascent of expected cumulative discounted reward.

Concepts

  • Policy gradientmissing
  • Temporal-difference learningmissing
  • Value function baselinemissing
  • Credit assignment problemmissing

Map Gaps

  • Policy gradient
  • Temporal-difference learning
  • Value function baseline