Han Liu's MAGICS Laboratory @ Northwestern University

The MAGICS Lab Github

Maintainers: current members of the MAGICS lab at Northwestern University.

Repository Description: The MAGICS Lab Github hosts open sourced models and code developed and maintained by the current MAGICS lab members. It includes the source code for DNABERT, DNABERT-2, and DNABERT-S, SparseModernHopfield, and STanHop.

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Highlights

DNABERT, DNABERT-2, DNABERT-S.

Important Features

1 Large language model for genome.

2 More than 2 million times downloads.

3 500+ stars for DNABERT and 150+ for DNABERT-2.

4 Species-aware DNA embedding.

5 Light-weight and high performance.

HUGE: High Dimensional Undirected Graphical Model Estimation

Maintainers: Tuo Zhao and Han Liu.

Software Description: The package "huge" provides a general framework for high-dimensional undirected graph estimation. It integrates data preprocessing, neighborhood screening, graph estimation, and model selection techniques into a pipeline.

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Highlights

Estimating nonparanormal graphical models.

Important Features

1 Instead of using Fortan, it is written in C.

2 Fitting high dimensional Gausian copula models.

3 Graph generation, data generation and visualization.

4 Support lossless and lossy screening rules.

5 Subsampling and Permutation based model selection.

6 Sparse matrix representation for scalability.

fastclime: Parametric Simplex Algorithm for Relaxed LP Problems

Maintainers: Haotian Pang and Han Liu.

Software Description: The package "fastclime" provides a method of recover the precision matrix efficiently by applying parametric simplex method. The computation is based on linear optimization. It also contains a generic LP solver and a parameterized LP solver using parametric simplex method.

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