Hojjat Torabi Goudarzi

Arash Torabi Goodarzi, Roman Kochnev, Waleed Khalid et al.

Neural networks are the backbone of modern artificial intelligence, but designing, evaluating, and comparing them remains labor-intensive. While numerous datasets exist for training, there are few standardized collections of the models themselves. We introduce LEMUR, an open-source dataset and framework that provides a large collection of PyTorch-based neural networks across tasks such as classification, segmentation, detection, and natural language processing. Each model follows a unified template, with configurations and results stored in a structured database to ensure consistency and reproducibility. LEMUR integrates automated hyperparameter optimization via Optuna, includes statistical analysis and visualization tools, and offers an API for seamless access to performance data. The framework is extensible, allowing researchers to add new models, datasets, or metrics without breaking compatibility. By standardizing implementations and unifying evaluation, LEMUR aims to accelerate AutoML research, enable fair benchmarking, and reduce barriers to large-scale neural network experimentation. To support adoption and collaboration, LEMUR and its plugins are released under the MIT license at: https://github.com/ABrain-One/nn-dataset https://github.com/ABrain-One/nn-plots https://github.com/ABrain-One/nn-vr

Hojjat Torabi Goudarzi, Maziyar Baran Pouyan

Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise inherent in scRNA-seq data pose significant analytical challenges. While current embedding methods focus primarily on gene expression levels, they often overlook crucial gene-gene interactions that govern cellular identity and function. To address this limitation, we present a novel embedding approach that integrates both gene expression profiles and data-driven gene-gene interactions. Our method first constructs a Cell-Leaf Graph (CLG) using random forest models to capture regulatory relationships between genes, while simultaneously building a K-Nearest Neighbor Graph (KNNG) to represent expression similarities between cells. These graphs are then combined into an Enriched Cell-Leaf Graph (ECLG), which serves as input for a graph neural network to compute cell embeddings. By incorporating both expression levels and gene-gene interactions, our approach provides a more comprehensive representation of cellular states. Extensive evaluation across multiple datasets demonstrates that our method enhances the detection of rare cell populations and improves downstream analyses such as visualization, clustering, and trajectory inference. This integrated approach represents a significant advance in single-cell data analysis, offering a more complete framework for understanding cellular diversity and dynamics.