Execution time comparisons between AntEpiSeeker(A), DECMDR(D), HS-MMGKG(G), SEE(S), SHEIB-AGM(B), SNPHarvester(H), SNPRuler(R) and Epi-SSA(P) on the DNME 100 dataset. حسب Liyan Sun (760586)

الموضوعات:

Execution time comparisons between AntEpiSeeker(A), DECMDR(D), HS-MMGKG(G), SEE(S), SHEIB-AGM(B), SNPHarvester(H), SNPRuler(R) and Epi-SSA(P) on the DNME 1000 dataset. حسب Liyan Sun (760586)

الموضوعات:

The penetrance tables for the 8 DME models. حسب Liyan Sun (760586)

الموضوعات:

F-measure comparisons between DECMDR(D), HS-MMGKG(G), SEE(S), SHEIB-AGM(B) and Epi-SSA(P) on the DNME3 100 dataset. حسب Liyan Sun (760586)

الموضوعات:

The penetrance tables for the 6 DNME3 models. حسب Liyan Sun (760586)

الموضوعات:

Power comparisons between AntEpiSeeker(A), DECMDR(D), HS-MMGKG(G), SEE(S), SHEIB-AGM(B), SNPHarvester(H), SNPRuler(R) and Epi-SSA(P) on the DNME 100 dataset. حسب Liyan Sun (760586)

الموضوعات:

F-measure comparisons between AntEpiSeeker(A), DECMDR(D), HS-MMGKG(G), SEE(S), SHEIB-AGM(B), SNPHarvester(H), SNPRuler(R) and Epi-SSA(P) on the DNME 100 dataset. حسب Liyan Sun (760586)

الموضوعات:

Part of epistatic interactions found by Epi-SSA (n = 600 maxG = 800000). حسب Liyan Sun (760586)

الموضوعات:

Benchmark data and code for evaluating and enhancing spatial cognition abilities of large language models (LLMs) حسب Yang (16534473)

(A) Illustration of grouping and segmentation based on the global similarity structure when the number of elements is small. A, B, C, and D represent stimulus elements at different... حسب Yen-Ju Chen (354876)

Replication package for Exploring the relation between source code commit information and SonarQube issues حسب Liviu Marian Berciu (17797934)

Mixed Quantum/Classical Theory Approach to Rotationally Inelastic Molecular Collisions Implemented on a Quantum Computer حسب Jonathan Andrade-Plascencia (21546959)

الموضوعات:

Table 1_Comprehensive analysis of multi-omics vaccine response data using MOFA and Stabl algorithms.xlsx حسب Aanya Gupta (22611515)

"…In this project, we used the MOFA and Stabl algorithms to analyze FluPRINT, estimate the population structure from the data, and identify the most important features for predicting response to the vaccine.…"

S1 Data - A GNSS receiver positioning algorithm based on weighting the statistical properties of discontinuous signals at lower rotation speeds حسب Jiahui Gan (22793753)

"…Weighted Kalman Filter Algorithm in C Code. S3 File. NavSolveKalman.h. Weighted Kalman Filter Algorithm in C Code. …"

Schematic diagram of chromosome coding. حسب Meilin Zhu (688698)

Data and codes for the paper "Machine-Learning-Enabled Spatial Pattern Mining: Evaluating the Impact of Imperfect Inputs". حسب Zhili Li (18836803)

DNW-VCD_Code.zip حسب Bo Xiong (115379)

"…The code and demo data of DNW-VCD algorithm…"

Source_Code_With_Help.rar حسب Zisong Wang (19838553)

TRENDY method code files حسب Yue Wang (20581715)

"…<p dir="ltr">code files for TRENDY method, used for inferring gene regulatory networks (GRN) from single-cell gene expression data</p><p dir="ltr">TRENDY algorithm itself uses the following packages: numpy=1.24.3, scipy=1.13.1, sklearn=1.4.2, torch=2.2.2,</p><p dir="ltr">other algorithms and comparison files need extra packages: pingouin=0.5.3, pandas=2.2.2, xgboost=2.0.3</p><p dir="ltr">warning: the NonlinearODEs algorithm (xgbgrn.py) runs well on Windows, but might crash on MacOS</p><p dir="ltr">manuscript for TRENDY method: GRN_transformer.pdf</p><p dir="ltr">major code files:</p><p dir="ltr">TRENDY_tutorial.py: a tutorial for using TRENDY method. to apply the TRENDY method, it also needs the following files: models.py, wendy_solver.py in previous_methods folder, trendy_1.pth and trendy_2.pth in weights folder</p><p dir="ltr">models.py: contains all three versions of the TE(k) model</p><p dir="ltr">train_trendy_first_half.py: train the TE(k=1) model for the first half of TRENDY method. the trained weights trendy_1.pth is in the folder weights</p><p dir="ltr">train_trendy_second_half.py: train the TE(k=3) model for the second half of TRENDY method. the trained weights trendy_2.pth is in the folder weights</p><p dir="ltr">code files for training other models:</p><p dir="ltr">train_GENIE3_rev.py: train the GENIE3_rev method. the trained weights genie_rev.pth is in the folder weights</p><p dir="ltr">train_NonlinearODEs_rev.py: train the NonlinearODEs_rev method. the trained weights nlode_rev.pth is in the folder weights</p><p dir="ltr">train_SINCERITIES_rev.py: train the SINCERITIES_rev method. the trained weights sinc_rev.pth is in the folder weights</p><p dir="ltr">code files for comparing different methods:</p><p dir="ltr">test_SINC_new.py: used to compare different methods on SINC data</p><p dir="ltr">test_DREAM4_new.py: used to compare different methods on DREAM4 data</p><p dir="ltr">test_THP1_new.py: used to compare different methods on THP-1 data</p><p dir="ltr">test_hESC_new.py: used to compare different methods on hESC data</p><p dir="ltr">code for previously known methods, all in the folder previous_methods:</p><p dir="ltr">sincerities.py: code for SINCERITIES method</p><p dir="ltr">xgbgrn.py: code for NonlinearODEs method</p><p dir="ltr">GENIE3.py: code for GENIE3 method</p><p dir="ltr">wendy_solver.py: code for WENDY method</p><p dir="ltr">auxiliary code files:</p><p dir="ltr">methods.py: contains functions for different methods</p><p dir="ltr">evaluation.py: compare the inferred GRN with the ground truth GRN and calculate AUROC and AUPRC</p><p dir="ltr">plots_new.py: draw plots</p><p dir="ltr">nd_alg.py: code for network deconvolution method for enhancing inferred GRNs</p><p dir="ltr">brane_alg.py: code for BRANE Cut method for enhancing inferred GRNs</p><p dir="ltr">generate training data, all in the folder Data_generation:</p><p dir="ltr">A_data_generation.py generates a random GRN, generate.py generates all files in the following folder total_data_10, the other four files are previously known methods</p><p dir="ltr">data sets:</p><p dir="ltr">folder total_data_10 (<a href="https://zenodo.org/records/13929908" rel="nofollow" target="_blank">https://zenodo.org/records/13929908</a>, not uploaded here): saves the generated data for training and validation. for different endings: A is the ground truth GRN, cov is the covariance matrix, data is the original data, genie is the inferred GRN by GENIE3, nlode is the inferred GRN by NonlinearODEs, revcov is the Ktstar matrix, sinc is the inferred GRN by SINCERITIES, wendy is the inferred GRN by WENDY. these data files are generated by the files in folder Data_generation. here we only upload the files for testing. for full files of this folder, see <a href="https://zenodo.org/records/13929908" rel="nofollow" target="_blank">https://zenodo.org/records/13929908</a></p><p dir="ltr">folder rev_wendy_all_10 (not uploaded here. see <a href="https://zenodo.org/records/13929908" rel="nofollow" target="_blank">https://zenodo.org/records/13929908</a>): saves the inferred Kt' matrix (xxx_ktstar files) and A_1 matrix (xxx_revwendy files) in TRENDY</p><p dir="ltr">folder SINC: ground truth GRNs and inferred GRNs in SINC data set. …"

Mandelbrot set source codes. حسب Khairul Habib Alam (20521419)