13 papers · ranked by Valyu relevance
Jacqueline A Jansen, Artür Manukyan, Nour Al Khoury, Altuna Akalin
Data analysis is constrained by a shortage of skilled experts, particularly in biology, where detailed data interpretation is vital for understanding complex biological processes and developing new treatments and diagnostics. To address this, we developed mergen, an R package that leverages Large Language Models (LLMs)…
Huifang Ma, Zhicheng Ji
Large language models have shown remarkable capabilities in algorithm design, but their effectiveness in solving data science challenges remains poorly understood. We conducted a classroom experiment in which graduate students used large language models (LLMs) to solve biomedical data science challenges on Kaggle.…
Robert Haase, Christian Tischer, Jean-Karim Hériché, Nico Scherf
In the computational age, life-scientists often have to write Python code to solve bio-image analysis (BIA) problems. Many of them have not been formally trained in programming though. Code-generation, or coding assistance in general, with Large Language Models (LLMs) can have a clear impact on BIA. To the best of our…
Yi Jiang, Shuang Wang, Shaohong Feng, Cankun Wang + 5 more
Foundation models have transformed AI by leveraging large-scale data to efficiently perform diverse tasks, and their applications in bioinformatics are primarily focused on data-centric tasks like cell type annotation and gene expression analysis. However, their potential extends beyond data analysis, offering…
Balaji Kumar, Supreet Saini
Many theories have been proposed attempting to explain the origin of the genetic code. While strong reasons remain to believe that the genetic code evolved as a frozen accident, at least for the first few amino acids, other theories remain viable. In this work, we test the optimality of the standard genetic code…
Ihsan Tolga Medeni, Metehan Ünal, Roberto Galizi, Bryan Bartley + 4 more
Large language models have transformed software engineering practices. However, generated artefacts are not always developer-friendly and may partially meet complex requirements. As the need to standardise, integrate, and develop tools in engineering biology increases, novel approaches are needed to create and maintain…
Jiayi Li, Litian Liang, Shiyi Du, Shijie Tang + 2 more
Codon sequence design is crucial for generating mRNA sequences with desired functional properties for tasks such as creating novel mRNA vaccines or gene editing therapies. Yet existing methods lack flexibility and controllability to adapt to various design objectives. We propose a novel framework, ARCADE, that enables…
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…
Ali Madani, Bryan McCann, Nikhil Naik, Nitish Shirish Keskar + 4 more
Generative modeling for protein engineering is key to solving fundamental problems in synthetic biology, medicine, and material science. We pose protein engineering as an unsupervised sequence generation problem in order to leverage the exponentially growing set of proteins that lack costly, structural annotations. We…
W. B. Langdon
Grow and graft genetic programming (GGGP) can automatically evolve an existing state-of-the art program to give more accurate predictions of the secondary structures adapted by RNA molecules using their base sequence alone. That is, genetic improvement (GI) can make functional as well as non-functional source code…
Ali Madani, Ben Krause, Eric R. Greene, Subu Subramanian + 8 more
Bypassing nature’s evolutionary trajectory, de novo protein generation—defined as creating artificial protein sequences from scratch—could enable breakthrough solutions for biomedical and environmental challenges. Viewing amino acid sequences as a language, we demonstrate that a deep learning-based language model can…
Antony M Jose
Our tremendous progress in understanding living things can mask our ignorance of the information needed to perpetuate life. As the basic unit of life, cells hold information in two distinct forms: in the stable DNA sequence that is faithfully replicated during cell divisions, and in the changing arrangement of…
Aaron Pfennig, Alexandre Lomsadze, Mark Borodovsky
Some of recently discovered in human gut microbiome highly divergent crAssphages were reported to use multiple genetic codes. Opal or amber stop codon reassignments were present in parts of the genomes, while the standard genetic code was used in the remaining genome sections. Essentially, the phage genomes were…