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 | Conference PDF | Archive PDF | Plain Text | 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. |