Antibiotics are often grouped by their mechanisms of action, such as blocking protein synthesis, disrupting folate biosynthesis, changing cell wall construction, compromising the cell membrane integrity and affecting DNA replication [93, 25]. These antibiotics, whether created in labs or found in nature, serve as the primary defence against bacterial infections. However, bacteria employ a series of strategies in response to resist these antibiotics, including inactivating antibiotics through enzymatic degradation, altering the antibiotic target, modifying cell membrane permeability, and using efflux pumps to maintain intracellular antibiotic concentrations of antibiotics below inhibitory levels [25]. Moreover, the gene transfer of antibiotic-resistant bacteria (ARB) further aggravates this challenge [92].

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

As the world continues to grapple with the Covid-19 pandemic, another health crisis is looming: antibiotic resistance. Bacterial resistance is something that occurs naturally, but widespread antibiotic misuse has propelled antimicrobial resistance (AMR) to major global health threat status; at least 700,000 people are killed by drug-resistant superbugs every year – and by 2050, this number could reach 10 million. A report by the World Health Organization, published earlier this year, also found that none of the 43 antibiotics currently under development "sufficiently address the problem of drug resistance" in the bacteria considered most dangerous to public health. The situation, as it stands, looks bleak – but there is hope. Advances in technology are vastly improving the way researchers discover and develop drugs, and antibiotics are no exception.

The advent of high-throughput genomic technologies has resulted in the accumulation of massive amounts of genomic information. However, biologists are challenged with how to effectively analyze these data. Machine learning can provide tools for better and more efficient data analysis. Unfortunately, because many plant biologists are unfamiliar with machine learning, its application in plant molecular studies has been restricted to a few species and a limited set of algorithms. Thus, in this study, we provide the basic steps for developing machine learning frameworks and present a comprehensive overview of machine learning algorithms and various evaluation metrics. Furthermore, we introduce sources of important curated plant genomic data and R packages to enable plant biologists to easily and quickly apply appropriate machine learning algorithms in their research. Finally, we discuss current applications of machine learning algorithms for identifying various genes related to resistance to biotic and abiotic stress. Broad application of machine learning and the accumulation of plant sequencing data will advance plant molecular studies. The advent of high-throughput sequencing technologies has produced several large-scale data sets. This enormous amount of information enables biologists to explore topics that were once difficult or impossible to investigate, such as associations between microRNA and certain diseases, the causes of vascular inflammation and atherosclerosis in humans [1–3] and stress breeding in plants [4]. However, many challenges have also emerged. For example, the European Bioinformatics Institute now stores 273 petabytes of raw molecular data on humans, plants and animals (https://www.ebi.ac.uk/).