| 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. |
| IGEA |
IGEA 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. |
