<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.…”

NRPStransformer, an Accurate Adenylation Domain Specificity Prediction Algorithm for Genome Mining of Nonribosomal Peptides by Zhihan Zhang (1403308)

“…Leveraging the sequences within the flavodoxin-like subdomain, we developed a substrate specificity prediction algorithm using a protein language model, achieving 92% overall prediction accuracy for 43 frequently observed amino acids, significantly improving the prediction reliability. …”

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). …”

Core genes were selected through PPI analysis based on three algorithms. by Dong-Hee Han (140305)

“…<p>Among 46 DEGs whose expression significantly changed in A549 and BEAS-2B cell lines, the core genes were selected using three algorithms: MCC, MNC, and DEGREE. <b>(A)</b> The top 10 genes were prioritized using MCC analysis, which identifies the largest clique within the PPI network and selects the central proteins within the clique. …”

Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes by Vijay Subramanian (20718933)

“…<p dir="ltr">Supplementary material for Morpheus: A fragment-based algorithm to predict metamorphic behaviour in proteins across proteomes.…”

Protein-Protein Interaction (PPI) and ceRNA Regulatory Network Analysis. by Jie Chu (293795)

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

“…(C, D) Top 10 hub genes identified using the Maximal Clique Centrality (MCC) algorithm; darker colors indicate higher centrality within the PPI network. …”

Pipeline of the interactor algorithm. by Jose Cleydson F. Silva (8685594)

Reward function related parameters. by Honglei Pang (22693724)

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EFGs: A Complete and Accurate Implementation of Ertl’s Functional Group Detection Algorithm in RDKit by Gonzalo Colmenarejo (650249)

“…In this paper, a new RDKit/Python implementation of the algorithm is described, that is both accurate and complete. …”

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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Activation functions: Sigmoid function and ReLU function. by Wan-Hua Zhang (21601139)

FAR-1: A Fast Integer Reduction Algorithm Compared to Collatz and Half-Collatz by Faizan Ali (21689861)

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Alphaviruses nsP4 protein alignment. by Marie-France Martin (12118879)

Examples of between- and within-community Beta distributions. by Alexandria M. Jensen (6494957)

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Distribution of cross correlations in functional connectivity in ABIDE sample. by Alexandria M. Jensen (6494957)

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The algorithm is designed to identify patterns in the treatment dataset. by Belén Otero-Carrasco (21262360)

A) Ranking of models trained on different feature sets across all tested algorithms, sorted by their F1-score. by Jose Cleydson F. Silva (8685594)

Overview of the wavess algorithm and R package. by Narmada Sambaturu (4989539)

Isologs, function and residue information of 12 key proteins in MPV replication. by Huaichuan Duan (6458477)