The results of LASSO regression algorithm. by Xue Fu (549661)

Reward function related parameters. by Honglei Pang (22693724)

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Modular architecture design of PyNoetic showing all its constituent functions. by Gursimran Singh (575288)

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Immune infiltration analysis by CIBERSORT algorithm. by Lanying Shen (22755930)

The GOR4 and SOPMA algorithm findings. by Ahmad Abdullah Mahdeen (19704401)

2025-01-14 - PAG Talk - Kmerseek - Olga Botvinnik - Seanome by Olga Botvinnik (20571431)

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Top-ranked hub genes identified by 5 cytoHubba algorithms. by Jun Li (6494)

PATH has state-of-the-art performance versus previous binding affinity prediction algorithms. by Yuxi Long (11024307)

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Two protein-ligand complexes shown with their persistence fingerprint. by Yuxi Long (11024307)

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MEDOC: A Fast, Scalable, and Mathematically Exact Algorithm for the Site-Specific Prediction of the Protonation Degree in Large Disordered Proteins by Martin J. Fossat (3714079)

Subjects: “…mathematically exact algorithm…”

Visualization by PaCMAP [52] shows that persistence fingerprint clusters protein-ligand complexes with similar binding affinity reasonably well, even beyond the training dataset (P... by Yuxi Long (11024307)

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(a-b) The LASSO algorithm was used for hyperparameter tuning and identification of the important predictive features. by Devi Soorya Narayana Sasikumar (22331743)

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Performance of TNet-BP and PATH⁺ on the PDBBind v2020 refined set shows that PATH⁺ achieves similar performance with TNet-BP while having three orders fewer f... by Yuxi Long (11024307)

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PATH (with persistence fingerprint) runs significantly faster than TNet-BP, a representative binding affinity prediction algorithm that uses persistent homology, on larger protein-... by Yuxi Long (11024307)

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Top 15 hub genes in five algorithms. by Tianqi Liu (1625776)

Scatter plots of PATH⁺ and our implementation of TNet-BP’s predictions on a held-out, test subset of PDBBind v2020 refined set for one run (90:10 train:test split ratio,... by Yuxi Long (11024307)

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Python-Based Algorithm for Estimating NRTL Model Parameters with UNIFAC Model Simulation Results by Se-Hee Jo (20554623)

“…This algorithm conducts a series of procedures: (1) fragmentation of the molecules into functional groups from SMILES, (2) calculation of activity coefficients under predetermined temperature and mole fraction conditions by employing universal quasi-chemical functional group activity coefficient (UNIFAC) model, and (3) regression of NRTL model parameters by employing UNIFAC model simulation results in the differential evolution algorithm (DEA) and Nelder–Mead method (NMM). …”

<b>Opti2Phase</b>: Python scripts for two-stage focal reducer by Morgan Najera (21540776)

“…</li></ul><p dir="ltr">The scripts rely on the following Python packages. Where available, repository links are provided:</p><ol><li><b>NumPy</b>, version 1.22.1</li><li><b>SciPy</b>, version 1.7.3</li><li><b>PyGAD</b>, version 3.0.1 — https://pygad.readthedocs.io/en/latest/#</li><li><b>bees-algorithm</b>, version 1.0.2 — https://pypi.org/project/bees-algorithm</li><li><b>KrakenOS</b>, version 1.0.0.19 — https://github.com/Garchupiter/Kraken-Optical-Simulator</li><li><b>matplotlib</b>, version 3.5.2</li></ol><p dir="ltr">All scripts are modular and organized to reflect the design stages described in the manuscript.…”

Identification and functional analysis of hub genes. by Wei Ya Lan (22403712)

“…(E) GO enrichment analysis of shared candidate genes, showing the top three terms for biological process (BP), cellular component (CC), and molecular function (MF).…”

PATH⁺ explains tighter binding of carbonic anhydrase II by brinzolamide. by Yuxi Long (11024307)

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