13 papers · ranked by Valyu relevance
Muhammad Hammad, Önder Babur, Hamid Abdul Basit, Mark van den Brand + 1 more
'Yilun Shang'] Software developers frequently reuse source code from repositories as it saves development time and effort. Code clones (similar code fragments) accumulated in these repositories represent often repeated functionalities and are candidates for reuse in an exploratory or rapid development. To facilitate…
Andrea Gurioli, Maurizio Gabbrielli, Stefano Zacchiroli, Stefan Wagner
'Stefan Wagner'] Code stylometry is the application of stylometry techniques to determine the authorship of software source code snippets. It is used in the industry to address use cases like plagiarism detection, code audits, and code review assignments. Most works in the code stylometry literature use machine…
Qihong Song, Haize Hu, Tebo Dai
Code search aims to search for code snippets from large codebase that are semantically related to natural query statements. Deep learning is a valuable method for solving code search tasks in which the quality of training data directly impacts the performance of deep-learning models. However, most existing…
Binita Rajbanshi, Anuj Guruacharya
Emerging generative models for biology focus on DNA, non-coding RNA, or proteins, ignoring information hidden in mRNA. Additionally, in protein engineering and mRNA therapeutics the design of mRNA sequences is still a challenge, lacking a clear framework. Here, we introduce and rigorously evaluate two novel methods: a…
Marc Joiret, Marine Leclercq, Gaspard Lambrechts, Francesca Rapino + 3 more
'Pierre Close' 'Gilles Louppe' 'Liesbet Geris'] The genetic code is textbook scientific knowledge that was soundly established without resorting to Artificial Intelligence (AI). The goal of our study was to check whether a neural network could re-discover, on its own, the mapping links between codons and amino acids…
Valeriy Berezovskiy, Anastasia Gorodilova, Ekaterina Trofimova, Andrey Ustyuzhanin + 1 more
'Andrey Ustyuzhanin' 'Syed Hassan Shah'] Program code has recently become a valuable active data source for training various data science models, from code classification to controlled code synthesis. Annotating code snippets play an essential role in such tasks. This article presents a novel approach that leverages…
Logan Hallee, Nikolaos Rafailidis, Jason P. Gleghorn
Recent advancements in Protein Language Models (pLMs) have enabled high-throughput analysis of proteins through primary sequence alone. At the same time, newfound evidence illustrates that codon usage bias is remarkably predictive and can even change the final structure of a protein. Here, we explore these findings by…
Kristína Machová, Marián Mach, Michal Porezaný, Seongsoo Cho
This article focuses on the problem of detecting disinformation about COVID-19 in online discussions. As the Internet expands, so does the amount of content on it. In addition to content based on facts, a large amount of content is being manipulated, which negatively affects the whole society. This effect is currently…
Zhangyang Gao, Cheng Tan, Stan Z. Li
Protein structure tokenization has attracted increasing attention in both protein representation learning and generation. While recent work, like FoldToken2 and ESM3, has achieved good reconstruction performance, the compressoin ratio is still limited. In this work, we propose FoldToken3, a novel protein structure…
Jianhui Zeng, Zhiheng Qu, Bo Cai, Boris Ryabko
Source code summarization focuses on generating qualified natural language descriptions of a code snippet (e.g., functionality, usage and version). In an actual development environment, descriptions of the code are missing or not consistent with the code due to human factors, which makes it difficult for developers to…
Yanshuo Chen, Yuming Zhang, Joshua Li, Boxue Tian + 1 more
Codon optimization involves selecting synonymous codons to match host-specific preferences. It is critical for heterologous expression but remains challenging due to the combinatorial design space. Under long-term evolutionary selection, natural coding sequences are near-optimal compromises between translational…
Melissa Sanabria, Jonas Hirsch, Anna R. Poetsch
Large Language Models (LLMs) on natural language have achieved a level of performance that allows the generation of coherent and syntactically correct text. DNA sequence of genomes follows rules similar to natural language, but a distinguishing factor is the absence of a concept analogous to words. We established…
Jiayi Li, Hong-Sheng Lai, Litian Liang, Shiyi Du + 2 more
Codon sequence design is crucial for generating mRNA sequences with desired functional properties for tasks such as developing mRNA vaccines or gene editing therapies. Yet existing methods lack flexibility and controllability to adapt to various design objectives. We propose a novel machine learning-based framework…