Denario Example Papers

This repository includes different AI-generated research papers with Denario. Please refer to that repository for the source code used to generate these examples.

Papers

Below we show a list of papers generated by Denario across scientific disciplines. We note that we have not tried to filter the papers. For that reason, beyond the papers shown in the Denario presentation paper, we also include papers that can be good or bad. We do this to illustrate that Denario can generate both innovative papers but also bad ones, so human expertise is currently needed to evaluate the paper.

We note that the papers below were generated across several months while developing and improving the software. For that reason, the quality, quantity, style, and even author may change from one paper to another. On top of that, some modules have been added later than others, so there may be papers with some folders, containing the output of a module, missing.

Cosmology & Astrophysics

• Predicting the Direction of Dark Matter Halo Concentration Evolution with Graph Neural Networks and Contrastive Learning ⇒ pdf | files

• Predicting Halo Mass Function Proxies from Merger Tree Distributions using a Hybrid GNN and Gaussian Mixture Model ⇒ pdf | files

• Predicting Halo Assembly Bias from Merger Trees using Graph Neural Networks with Formation Time Regularization ⇒ pdf | files

• Hierarchical Contrastive Graph Representation Learning for Cosmological Merger Trees and Parameter Inference ⇒ pdf | files

• Contrastive Learning of Merger Tree Embeddings for Likelihood-Free Cosmological Inference ⇒ pdf | files

• Quantifying and Attributing Waveform Model-Dependent Systematics in GW231123: A Multi-Scale Posterior Analysis ⇒ pdf | files

• Attributing Waveform Model Discrepancies in GW231123: A Feature-Based Diagnostic and Robust Astrophysical Inference ⇒ pdf | files

• Dissecting Multi-Model Posterior Landscapes of GW231123: Unveiling Intrinsic Degeneracies via Mode-Finding and Shared Manifold Analysis ⇒ pdf | files

• Unveiling Structural Discrepancies: A Manifold and Information-Theoretic Comparison of Gravitational Waveform Posteriors for GW231123 ⇒ pdf | files

• Physics-Informed Discrepancy Decomposition and Robust Astrophysical Inference for GW231123 ⇒ pdf | files

• Spatio-Topological and Multi-Physics Analysis of Instantaneous Mass Ejection and its Statistical Properties in a Red Supergiant Binary ⇒ pdf | files

• Unveiling the Inhomogeneous 3D Mass Transfer Stream in a Red Supergiant Binary: From Convective Driving to Clumpy Outflows ⇒ pdf | files

• Convection, Radiation, and the Instantaneous Mass Transfer in Red Supergiant Binaries: A 3D Simulation Analysis ⇒ pdf | files

• The Turbulent Architecture and Convective Drivers of Mass Transfer in a Red Supergiant Binary ⇒ pdf | files

• The Instantaneous Convective-Radiative Fingerprint on Mass Ejection in a Red Supergiant Binary: A 3D Morphological and Statistical Analysis ⇒ pdf | files

• Mapping the Diversity of the Black Hole-Stellar Mass Relation Across Cosmological and Feedback Parameter Space ⇒ pdf | files

• Regime-Specific Performance of 1D CNN and FCNN Architectures for Non-linear Matter Power Spectrum Emulation in ΛCDM Cosmology ⇒ pdf | files

Biology

• Comparative Single-Cell Transcriptomics Reveals Divergent Stage Transition Dynamics and Regulatory Strategies in Lab-Adapted and Field Isolates of Plasmodium falciparum ⇒ pdf | files

• Divergent Transcriptional Programs and Regulatory Networks Govern Plasmodium falciparum Development in Laboratory-Adapted Strains and Field Isolates ⇒ pdf | files

• Single-cell Transcriptomics Reveals Patient-Specific Heterogeneity in Transiently Expressed Regulators of Plasmodium falciparum Gametocytogenesis in Field Isolates ⇒ pdf | files

• Single-Cell Analysis Reveals Profound Divergence in Transcriptional Regulatory Programs Between Laboratory and Field Isolates of Plasmodium falciparum ⇒ pdf | files

Biophysics

• Comprehensive Kinetic and Free Energy Analysis of NTL9 Folding via Systematic Collective Variable Selection and Markov State Models ⇒ pdf | files

Biomedical informatics

• Challenges in Learning Universal Gait Fingerprints: Evaluating Adversarial Invariance and Demographic Bias for Wearable Step Counting ⇒ pdf | files

• Quantifying the Robustness of Accelerometer-Derived Gait Features for Step Counting Across Sensor Locations and Sampling Frequencies ⇒ pdf | files

• An Investigation into Deep Generative Reconstruction for Low-Frequency Step Counting: Unveiling Data Integrity and Workflow Challenges ⇒ pdf | files

• Quantifying and Characterizing Step Counting Uncertainty in Wearable Accelerometer Data ⇒ pdf | files

• Self-Supervised Feature Learning for Robust and Interpretable Step Event Detection in Multi-Fidelity Wearable Data ⇒ pdf | files

• Cross-Configuration Transfer Learning Framework for Robust Step Counting in Free-Living Conditions ⇒ pdf | files

• Wearable Step Counting: A Comparative Analysis of Deep Learning and Traditional Methods Highlighting Data Imbalance Challenges ⇒ pdf | files

Chemistry

• Dynamic Multiscale Graph Analysis Reveals Structural Signatures of Peptide Aggregate Stability and Splitting ⇒ pdf | files

• Dynamic Weighted Peptide Network Analysis for Characterizing and Predicting Aggregate Stability ⇒ pdf | files

• Dynamic, Weighted, Hierarchical Graph Analysis for Predicting Peptide Aggregate Instability and Identifying Molecular Determinants ⇒ pdf | files

• Linking Residue-Level Network Dynamics to Peptide Aggregate Stability: A Hierarchical Spectral Graph Analysis of KYFIL Self-Assembly ⇒ pdf | files

Neuroscience

• Epigenetic Aging, Regional Brain Morphology, and the Spectrum of Cognitive Decline in Long-Lived Egyptian Fruit Bats ⇒ pdf | files

• Unraveling Brain Structural Correlates of Cognitive Aging and Resilience in Long-Lived Bats: An Integrated Study of Epigenetic Age and Spatial Memory ⇒ pdf | files

• Investigating Cognitive Resilience in Long-Lived Bats: Challenges in Integrating Epigenetic Age, Spatial Memory, and Brain Structure ⇒ pdf | files

• Brain Structural Preservation in Long-Lived Bats: An Epigenetic Investigation of Rousettus aegyptiacus ⇒ pdf | files

• Critical Assessment of a Multimodal Pipeline for Studying Cognitive Resilience in Aging Bats: Insights from Data Integration Failures ⇒ pdf | files

• Microstructural Brain Signatures of Adaptive Cognitive Strategies in Long-Lived Bats: An ROI-based DTI and Behavioral Resilience Analysis ⇒ pdf | files

• Aging and Cognition in Long-Lived Egyptian Fruit Bats: Behavioral Performance and the Unmet Promise of Microstructural Biomarkers ⇒ pdf | files

• Cognitive-Structural Decoupling in Long-Lived Bats: Quantifying Resilience Beyond Age and Global Brain Structure ⇒ pdf | files

• Regional Brain Morphometry and Adaptive Foraging Reveal Age-Related Cognitive Flexibility and Resilience Trends in Egyptian Fruit Bats ⇒ pdf | files

• Exploratory Multi-Modal Investigation of Brain Microstructure and Epigenetic Aging in Egyptian Fruit Bats: Identifying Phenotypes of Resilience and Vulnerability ⇒ pdf | files

• Cognitive Resilience and the Neuroepigenetic Landscape of Spatial Memory in Aging Egyptian Fruit Bats ⇒ pdf | files

• Unveiling Predictive Neural Signatures of Cognitive Adaptability in Aging Bats: A Multi-Region DTI and Machine Learning Approach ⇒ pdf | files

• Neuro-Cognitive Resilience in Long-Lived Bats: An Epigenetic Age-Adjusted Analysis of Spatial Memory and Brain Microstructure ⇒ pdf | files

• A Neuro-Cognitive Decoupling Framework for Investigating Resilience and Vulnerability in Aging Egyptian Fruit Bats ⇒ pdf | files

• Brain Microstructural Pattern Age Acceleration (BMPAA) in Long-Lived Bats: Disentangling Age-Related, Sex-Related, and Origin-Specific Signatures ⇒ pdf | files

Medicine

• Analysis of Principal Diagnosis Present on Admission Status and Resource Utilization in Texas Inpatient Data ⇒ pdf | files

• Evaluating Attention-Based Learning of Patient Diagnosis Representations with Present On Admission Status for In-Hospital Mortality and Prolonged Length of Stay Prediction ⇒ pdf | files

• Modeling Inpatient Morbidity Dynamics Using Present on Admission Data: Predicting Emergent Conditions and Analyzing Resource Utilization in Texas Hospitals ⇒ pdf | files

• Efficiency Analysis of US ART Clinics: A Data Envelopment Analysis Approach (2020-2022) ⇒ pdf | files

• Characterizing the Variability and Correlates of U.S. ART Clinic Performance During the COVID-19 Pandemic (2020-2022) ⇒ pdf | files

Planetary science

• Constraining Asteroid Thermal Properties Through Analysis of Spin-Orbital Correlations Within Families ⇒ pdf | files

• Statistical Evidence for Coupled Spin-Orbit Evolution in Asteroid Families ⇒ pdf | files

• Unveiling the Intrinsic Structure of the Asteroid Belt: Correcting for Observational Selection Bias in Physical and Compositional Properties ⇒ pdf | files

• The Limited Predictability of Asteroid Spin Obliquity from Age, Size, Type, and Family: A Gaussian Process Regression Study ⇒ pdf | files

• Identifying Anomalous Asteroids via Predictive Modeling of Physical and Spin Properties based on Orbit and Age ⇒ pdf | files

• The Spatial Architecture of the Main Asteroid Belt: Size, Composition, and Dynamical Gradients ⇒ pdf | files

• Mapping Thermophysical Diversity in Asteroid Families via Spin-Orbit V-Shape Morphology ⇒ pdf | files

• Quantifying Yarkovsky-Driven Orbital Dispersion Gradients and Proxy Efficacy in Asteroid Families ⇒ pdf | files

• Spin-Orbit V-Shapes in Asteroid Families: Empirical Constraints for Yarkovsky-YORP Evolution ⇒ pdf | files

• Quantifying Spin-Dependent Yarkovsky Drift: Empirical Evidence from Asteroid Family V-Shapes ⇒ pdf | files

• Unraveling Asteroid Family Evolution: Deconstructing Yarkovsky V-Shapes through Comparative Analysis with YORP-Evolved Distributions ⇒ pdf | files

• Unveiling the Yarkovsky Effect: Enhanced V-Shape Clarity in Asteroid Families via a Spin-Diameter Metric ⇒ pdf | files

• Quantitative Morphological Fingerprints of Yarkovsky-YORP Co-evolution in Asteroid Families ⇒ pdf | files

• Yarkovsky Drift Fidelity: Unveiling Dynamical Boundaries in Asteroid Family Dispersal and Implications for Spin Evolution ⇒ pdf | files

Physics

• Mathematical Interpretation of PINN Latent Space for Burger’s Equation: Learned Dynamics and Geometric Structure ⇒ pdf | files

• Characterizing the Multi-Scale and Geometric Structure of PINN Latent Space via Wavelets and Ricci Scalar ⇒ pdf | files

• Analyzing the Local Intrinsic Dimension of Physics-Informed Neural Network Latent Spaces for Burger’s Equation ⇒ pdf | files

• Geometric Structure of PINN Latent Space for Burger’s Equation: Low-Dimensional Manifolds and Initial Condition Encoding ⇒ pdf | files

• Viscosity-Dependent Latent Space Structure in a PINN for Burger’s Equation: Analysis via PCA and Fractal Dimension with a Renormalization Group Analogy ⇒ pdf | files

• Intrinsic Dimensionality of PINN Latent Spaces for Burger’s Equation: Evidence for a Renormalization Group-like Flow ⇒ pdf | files

• Quantifying the Evolution of Learned Feature Structure in PINN Latent Space for 2D Burger’s Equation via Principal Component Analysis ⇒ pdf | files

• Renormalization Group Analysis of PINN Latent Space Structure for the 2D Burger’s Equation ⇒ pdf | files

Quantum physics + Cosmology

• QITT-Enhanced Multi-Scale Substructure Analysis with Learned Topological Embeddings for Cosmological Parameter Estimation ⇒ pdf | files

• Parameterized Manifold Learning and Sparse Tensor Train Regression for Cosmological Parameter Inference from Merger Trees ⇒ pdf | files

• Cosmological Parameter Inference from Merger Trees Using Hierarchical Quantum Tensor Networks ⇒ pdf | files

• QTT-Based Compression of Merger Tree Trajectories for Assembly Bias Studies: A Proof-of-Concept with Dummy Implementation ⇒ pdf | files

• Cosmological Parameter Inference from Filtered Merger Tree Motifs via Quantum Tensor Train Decomposition ⇒ pdf | files

• QTT-Informed Subgraph Feature Engineering for Merger Tree Regression: A Proof-of-Concept ⇒ pdf | files

Material science

• Mapping Interfacial Water States on Functionalized Graphene: A Machine Learning-Augmented Approach to Uncover Design Principles for Tunable Water ⇒ pdf | files

Downloading

To download the material associated with a paper you can use, e.g.,:

wget -r -np -e robots=off --reject “index.html*” https://users.flatironinstitute.org/~fvillaescusa/Denario/Quantum+Cosmology/Project1/

Contributing

If you generate an interesting article with Denario please feel free to open a pull request with the full project files (including code and latex files).