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Software

19d4
Name Description
ShenLabGithub Penn Shen Lab Github Repositories
TAP-GPT Interpretable Few-Shot Alzheimer’s Disease Prediction on Multimodal Biomedical Data with Tabular LLMs
FREEFORM FREEFORM | Knowledge-Driven Feature Selection and Engineering with Large Language Models
Watermark-Tradeoff Improve the Trade-off Between Watermark Strength and Speculative Sampling Efficiency for Language Models
BLAE Bi-Lipschitz Autoencoder (BLAE)
GROTIA An Interpretable Graph-Regularized Optimal Transport Framework for Diagonal Single-Cell Integrative Analysis
GoF-for-Watermark-Detection On the Empirical Power of Goodness-of-Fit Tests in Watermark Detection
FR-CCA-ADNI Fair CCA for Fair Representation Learning
IRIS IRIS: Interpretable Risk Clustering Intelligence for Survival Analysis
RestoreLLMCalibration Restoring Calibration for Aligned Large Language Models
AlzSDOH_EHRlit_KGllm Integrating Alz-SDoH info from EHR and literature via KGs and LLMs
MentalChat16K A benchmark dataset designed to support the development and evaluation of large language models (LLMs) for conversational mental health assistance
SDoHenPKG Leveraging Social Determinants of Health in Alzheimer’s Research Using LLM-Augmented Literature Mining and Knowledge Graphs
QOT QOT: Efficient Computation of Sample Level Distance Matrix from Single-Cell Omics Data through Quantized Optimal Transport
AD-SIMLR Clustering Alzheimer’s Disease Subtypes via Similarity Learning and Graph Diffusion
UNITO Automated Cytometric Gating with Human-Level Performance Using Bivariate Segmentation
SDoH-KG Integrating Social Determinants of Health into Knowledge Graphs: Evaluating Prediction Bias and Fairness in Healthcare
PFERM PFERM: A Fair Empirical Risk Minimization Approach with Prior Knowledge
DCSM Deep Clustering Survival Machines (DCSM)
DALK DALK: Dynamic Co-Augmentation of LLMs and KG to answer Alzheimer’s Disease Questions with Scientific Literature
STREAMLINE-CB4AD Streamline code base for Alzheimer’s disease
Homological_Landscape Homological landscape of human brain functional sub-circuits
DWS-Loss DWS-Loss: Distance-Weighted Sinkhorn Loss for Alzheimer’s Disease Classification
GIANT Genetically informed brain atlas (GIANT) for enhancing neuroimaging genetics studies
Fair_CCA Fair Canonical Correlation Analysis
FACIMS Fairness-Aware Class Imbalanced Learning on Multiple Subgroups
CB4AD STREMLINE Code Base for Alzheimer’s Disease
PMSCCA Preference Matrix Guided Sparse Canonical Correlation Analysis
SBFA Structural Bayesian Factor Analysis
AD_Colocalization Brain-wide genome-wide colocalization study 
IGE IGE is a collection of software tools for mining high level imaging genetic associations via enrichment analysis.
RIGEA RIGEA is an R software tool for performing regional imaging genetic enrichment analysis.
NWAS-RP NWAS-RP is an R software tool for network-based GWAS re-prioritization and module identification.
IGEAIGEA is an R software tool for performing two dimensional imaging genetic enrichment analysis.
HDBIG HDBIG is a collection of software tools for high dimensional brain imaging genomics.
HDBIG-SR An HDBIG toolkit for sparse regression with a few regularization terms, including lasso, elastic net, L21 norm, group L21 norm, and network guided L21 norm.
HDBIG-SCCA An HDBIG toolkit for sparse association discovery with a knowledge-guided regularization term.
HDBIG-S2CCA An HDBIG toolkit for structured sparse association discovery with a few Sparse Canonical Correlation Analysis (SCCA) models, including the structure-aware SCCA model (S2CCA), the GraphNet SCCA model (GN-SCCA), the Graph OSCAR SCCA (GOSC-SCCA) model, and the Absolute value based GraphNet SCCA model (AGN-SCCA).
HDBIG-SCCA-NC An HDBIG toolkit for structured sparse association discovery with a generic non-convex penalty.
HDBIG-S2CCA-TLP An HDBIG toolkit for structured sparse association discovery with a truncated l1-norm penalty.
HDBIG-IGEA An HDBIG toolkit for mining high-level imaging genetic associations via applying enrichment analysis to two dimensional imaging genetic modules.
HDBIG-NWAS-RP An HDBIG toolkit for mining high-level imaging genetic associations using tissue-specific functional networks and network GWAS reprioritization strategy.
HDBIG-IGB-W An HDBIG web interface for archiving, visualization and interactive exploration of brain imaging genetics findings.
BECA  BECA is a prototype Brain Explorer for Connectomic Analysis.
SPHARM-MAT SPHARM-MAT is a matlab-based 3D shape modeling and analysis toolkit, and is designed to aid statistical shape analysis for relating morphometric changes in 3D structures of interest to different conditions.