Notice: The reproducibility variables underlying each score are classified using an automated LLM-based pipeline, validated against a manually labeled dataset. LLM-based classification introduces uncertainty and potential bias; scores should be interpreted as estimates. Full accuracy metrics and methodology are described in Coakley et alK. L. Coakley, T. Snelleman, H. Hoos, and O. E. Gundersen, "The embrace of open science: An analysis of a decade of AI research and 56 800 conference papers," Under Review, 2026..
A Heat Diffusion Perspective on Geodesic Preserving Dimensionality Reduction
Authors: Guillaume Huguet, Alexander Tong, Edward De Brouwer, Yanlei Zhang, Guy Wolf, Ian Adelstein, Smita Krishnaswamy
NeurIPS 2023 | Venue PDF | LLM Run Details
| Reproducibility Variable | Result | LLM Response |
|---|---|---|
| Research Type | Experimental | Results show that our method outperforms existing state-of-the-art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. |
| Researcher Affiliation | Academia | Guillaume Huguet1 Alexander Tong1 Edward De Brouwer2 Yanlei Zhang1 Guy Wolf1 Ian Adelstein2 Smita Krishnaswamy2 1Université de Montréal; Mila Quebec AI Institute 2 Yale University |
| Pseudocode | Yes | In Alg. 1, we present the main steps of our algorithm using the heat-geodesic dissimilarity. A detailed version is presented in Appendix A. |
| Open Source Code | Yes | 3https://github.com/KrishnaswamyLab/HeatGeo |
| Open Datasets | Yes | We use the PBMC dataset, the Swiss roll, the Tree dataset, MNIST [8], and COIL-20 [23] dataset. ... and two from the 2022 NeurIPS multimodal single-cell integration challenge4. 4https://www.kaggle.com/competitions/open-problems-multimodal/ |
| Dataset Splits | Yes | For all models, we perform sample splitting with a 50/50 validation-test split. The validation and test sets each consists of 5 repetitions with different random initializations. |
| Hardware Specification | Yes | The experiments were performed on a compute node with 16 Intel Xeon Platinum 8358 Processors and 64GB RAM. |
| Software Dependencies | No | The paper mentions software like 'Pygsp' and 'Scanpy' but does not provide specific version numbers for these or any other key software dependencies. |
| Experiment Setup | Yes | In Table 5, we report the values of hyperparameters used to compute the different embeddings. |