Fungi-Kcr: a language model for predicting lysine crotonylation in pathogenic fungal proteins by Yong-Zi Chen, Yong-Zi Chen, Xiaofeng Wang, Zhuo-Zhi Wang, Haixin Li, Haixin Li

“…DiscussionThe proposed model provides a valuable computational tool for the large-scale identification of Kcr sites, contributing to a deeper understanding of fungal pathogenesis and potential therapeutic targets. The source code and dataset for Fungi-Kcr are available at https://github.com/zayra77/Fungi-Kcr.…”
Get full text

geeSSEBI: Evaluating Actual Evapotranspiration Estimated with a Google Earth Engine Implementation of S-SEBI by Jerzy Piotr Kabala, Jose Antonio Sobrino, Virginia Crisafulli, Dražen Skoković, Giovanna Battipaglia

“…This paper introduces geeSSEBI, a Google Earth Engine implementation of the S-SEBI (Simplified Surface Energy Balance Index) model, for deriving ET from Landsat data and ERA5-land radiation. The source code and a graphical user interface implemented as a Google Earth Engine application are provided. …”
Get full text

Bayesian Neural Networks With Robust Feature Interpretation for Enhanced Compressive Strength Prediction of Ultra‐High‐Performance Concrete by Tao Zhang, Ji Hao, Jie Zhang, Lina Du, Yunhao Zhang, Wenbin Jiao

“…The complete implementation and source code are openly available at https://github.com/sean‐jiao/UHPC‐prediction.…”
Get full text

Prevalence of non-alcoholic fatty liver disease and its association with cardiovascular risk factors (data from Russian epidemiological studies) by O. M. Drapkina, S. E. Evstifeeva, S. A. Shalnova, V. A. Kutsenko, Yu. A. Balanova, A. E. Imaeva, A. V. Kapustina, M. B. Kotova, S. A. Maksimov, G. A. Muromtseva, O. A. Litinskaya, M. S. Pokrovskaya, E. M. Filichkina, A. G. Soplenkova, L. I. Gomanova, Yu. V. Doludin, I. A. Efimova, A. L. Borisova, N. S. Karamnova, O. B. Shvabskaya, I. A. Viktorova, N. N. Prishchepa, A. N. Redko, S. S. Yakushin, T. V. Repkina, T. O. Gonoshilova, A. V. Kudryavtsev, N. I. Belova, L. L. Shagrov, M. A. Samotrueva, A. L. Yasenyavskaya, E. N. Chernysheva, S. V. Glukhovskaya, I. A. Levina, E. A. Shirshova, E. B. Dorzhieva, E. Z. Urbanova, N. Yu. Borovkova, V. K. Kurashin, A. S. Tokareva, Yu. I. Ragino, G. I. Simonova, A. D. Khudyakova, V. N. Nikulin, O. R. Aslyamov, G. V Khokhlova, A. V. Solovyova, A. A. Rodionov, O. V. Kryachkova, Yu. Yu. Shamurova, I. V. Tantsyreva, I. N. Baryshnikova, M. G. Ataev, M. O. Radzhabov, M. M. Isakhanova, M. A. Umetov, L. V. Elgarova, I. A. Khakuasheva, E. I. Yamashkina, M. V. Esina, T. A. Kunyaeva, A. M. Nikitina, Yu. E. Spiridonova, N. V. Savvina, E. A. Naumova, V. S. Yudin, A. A. Keskinov, D. A. Kashtanova, S. M. Yudin, A. B. Kontsevaya

“…Statistical analysis was performed using the statistical programming language and the R environment (version 3.6.1) with open-source code. The significance level for all tested hypotheses was p≤0,05.Results. …”
Get full text

IGN: Invariable gene set-based normalization for chromatin accessibility profile data analysis by Shengen Shawn Hu, Hai-Hui Xue, Chongzhi Zang

“…As the first chromatin accessibility normalization method that accounts for global differences, IGN can be widely applied to differential ATAC-seq and DNase-seq analysis. The package and source code are available on GitHub at https://github.com/zang-lab/IGN.…”
Get full text

An approach of method‐level bug localization by Zhen Ni, Lili Bo, Bin Li, Tianhao Chen, Xiaobing Sun, Xiaoxue Wu

“…In this way, the comments of the source code are ignored or treated as plain text, which will lose some semantic information. …”
Get full text

Comprehensive Micromagnetic Modeling: Practical Techniques, Applications, and Emerging Challenges by Ahmet Bahadir Trabzon, Taichi Goto, Mehmet Cengiz Onbasli

“…Accompanying Jupyter notebook provide the source code for the examples. Finally, the tutorial addresses micromagnetic modeling limitations in capturing quantum effects, multi-domain couplings, and temperature-dependent phenomena. …”
Get full text

Food Waste Detection in Canteen Plates Using YOLOv11 by João Ferreira, Paulino Cerqueira, Jorge Ribeiro

“…Given these promising results and the provision of open-source code on a GitHub repository, the platform can be readily utilized by the research community and educational institutions to monitor FW in student meals and proactively implement reduction strategies.…”
Get full text

Comparing 545 Million Years of Sea-Level Change: New Insights from the TopoChronia QGIS Plugin by F. Franziskakis, C. Vérard, S. Castelltort, G. Giuliani

“…To address this, we have entirely rewritten and enhanced the source code into a QGIS plugin named <code>TopoChronia</code>. …”
Get full text

A Deep Variational Approach to Multiterminal Joint Source-Channel Coding Based on Information Bottleneck Principle by Shayan Hassanpour, Matthias Hummert, Dirk Wubben, Armin Dekorsy

“…To that end, tractable objective functions are developed, together with the pertinent learning architectures, generalizing the concepts of Variational Auto-Encoders and (Distributed) Deep Variational Information Bottleneck for (remote) source coding to the context of distributed joint source-channel coding. …”
Get full text

CSMA: A Standalone and ImageJ-Compatible Tool for Enhanced Wound Healing Assay Analysis by Tri Thanh Pham, Amina Sagymbayeva, Timur Elebessov, Zhadyra Onzhanova, Ferdinand Molnar

“…CSMA is available as a standalone and ImageJ-compatible tool with its source code at <uri>https://github.com/AminaSagymbayeva/CSMA_WoundHealing</uri>…”
Get full text

Noisy Token Removal for Bug Localization: The Impact of Semantically Confusing Misguiding Terms by Youngkyoung Kim, Misoo Kim, Eunseok Lee

“…A bug report is a technical document describing bugs that have occurred in the software. Finding the source code files to resolve a reported bug is a laborious task. …”
Get full text

A wavelet CNN with appropriate feed-allocation and PSO optimized activations for diabetic retinopathy grading by Chandrasekaran Raja, Santhosh Krishna B V, Balaji Loganathan, Sanjay Kumar Suman, L. Bhagyalakshmi, Mubarak Alrashoud, Jayant Giri, T. Sathish

“…The entire implementation of the wavelet CNN is made available under source code.…”
Get full text

A code for the 2D simulation of the steady-state fluid flow in porous blocks containing transmissive fractures by Fidelibus Corrado, Xu Chaoshui, Wang Zhihe, Dowd Peter

“…The proposed method has the additional benefit of reducing computational costs, which is particularly useful for cases with large-scale fracture networks embedded in a conductive rock matrix. The source code is available for downloading at the link: https://github.com/cx-adelaide/BEMFEM_FlowSim.…”
Get full text

DAI-TIRS: An AI-Powered Threat Intelligence and Response System for Securing the Metaverse by Mohini Sharma, Raghav Sandhane, Jaydeep Rajeshkumar Katariya

“…This research establishes DAI-TIRS as an advanced cybersecurity framework that has demonstrated its adaptability and effectiveness in countering AI-driven threats across multiple sectors. The source code for DAI-TIRS is available on GitHub: [https://github.com/sharmamohini762/DAI-TIRS-Code]…”
Get full text

Strategic priorities and challenges in research software funding: Results from an international survey [version 2; peer review: 2 approved, 1 approved with reservations, 1 not appr... by Daniel S. Katz, Eric A. Jensen

“…It spans a broad spectrum, including source code files, algorithms, scripts, computational workflows, and executables, all created for or during research. …”
Get full text

BUSClean: Open-source software for breast ultrasound image pre-processing and knowledge extraction for medical AI. by Arianna Bunnell, Kailee Hung, John A Shepherd, Peter Sadowski

“…Adaptation of the lesion caliper detection method to account for a type of caliper specific to the case study demonstrates the intended use of BUSClean in new data distributions and improved performance in lesion caliper detection from 43.3% and 93.3% out-of-the-box to 92.1% and 92.3% sensitivity and specificity, respectively. Source code, example notebooks, and sample data are available at https://github.com/hawaii-ai/bus-cleaning.…”
Get full text

Fluid-Structure Interaction Analysis of Carotid Artery Blood Flow with Machine Learning Algorithm and OpenFOAM by Banu Körbahti, Murad Kucur

“…Here, the machine learning algorithm was created by the help of an open source code Phyton. Then, using trained values of machine learning, and the known systole and diastole blood pressures for a specific chosen patient, the patient-specific pulsatile velocity cycle was estimated. …”
Get full text

AAGP integrates physicochemical and compositional features for machine learning-based prediction of anti-aging peptides by Saptashwa Datta, Jen-Chieh Yu, Yi-Hsiang Lin, Yun-Chen Cheng, Ching-Tai Chen

“…Our feature importance analysis shows that physicochemical features are more crucial for the first dataset, whereas compositional features hold greater importance for the second. The source code of AAGP is available at https://github.com/saptawtf/AAGP .…”
Get full text

Three Machine Learning Techniques for Melanoma Cancer Detection by Hadi Naghavipour, GholamReza Zandi, Abdulaziz Al-Nahari

“…In order to mitigate the biases in existing studies, the source code of this research is available at hadi-naghavipour.com/ml to serve aspiring researchers for improvement, correction and learning and provide a guideline for technology manager practitioners.…”
Get full text