Motivation: PCR is more economical and quicker than Next Generation Sequencing for detecting target organisms, with primer design being a critical step. In epidemiology with rapidly mutating viruses, designing effective primers is challenging. Traditional methods require substantial manual intervention and struggle to ensure effective primer design across different strains. For organisms with large, similar genomes like Escherichia coli and Shigella flexneri, differentiating between species is also difficult but crucial. Results: We developed Primer C-VAE, a model based on a Variational Auto-Encoder framework with Convolutional Neural Networks to identify variants and generate specific primers. Using SARS-CoV-2, our model classified variants (alpha, beta, gamma, delta, omicron) with 98% accuracy and generated variant-specific primers. These primers appeared with >95% frequency in target variants and <5% in others, showing good performance in in-silico PCR tests. For Alpha, Delta, and Omicron, our primer pairs produced fragments <200 bp, suitable for qPCR detection. The model also generated effective primers for organisms with longer gene sequences like E. coli and S. flexneri. Conclusion: Primer C-VAE is an interpretable deep learning approach for developing specific primer pairs for target organisms. This flexible, semi-automated and reliable tool works regardless of sequence completeness and length, allowing for qPCR applications and can be applied to organisms with large and highly similar genomes.

Classifying genome sequences based on metadata has been an active area of research in comparative genomics for decades with many important applications across the life sciences. Established methods for classifying genomes can be broadly grouped into sequence alignment-based and alignment-free models. Conventional alignment-based models rely on genome similarity measures calculated based on local sequence alignments or consistent ordering among sequences. However, such methods are computationally expensive when dealing with large ensembles of even moderately sized genomes. In contrast, alignment-free (AF) approaches measure genome similarity based on summary statistics in an unsupervised setting and are efficient enough to analyze large datasets. However, both alignment-based and AF methods typically assume fixed scoring rubrics that lack the flexibility to assign varying importance to different parts of the sequences based on prior knowledge. In this study, we integrate AI and network science approaches to develop a comparative genomic analysis framework that addresses these limitations. Our approach, termed the Genome Misclassification Network Analysis (GMNA), simultaneously leverages misclassified instances, a learned scoring rubric, and label information to classify genomes based on associated metadata and better understand potential drivers of misclassification. We evaluate the utility of the GMNA using Naive Bayes and convolutional neural network models, supplemented by additional experiments with transformer-based models, to construct SARS-CoV-2 sampling location classifiers using over 500,000 viral genome sequences and study the resulting network of misclassifications. We demonstrate the global health potential of the GMNA by leveraging the SARS-CoV-2 genome misclassification networks to investigate the role human mobility played in structuring geographic clustering of SARS-CoV-2.

G-Quadruplexes are the four-stranded non-canonical nucleic acid secondary structures, formed by the stacking arrangement of the guanine tetramers. They are involved in a wide range of biological roles because of their exceptionally unique and distinct structural characteristics. After the completion of the human genome sequencing project, a lot of bioinformatic algorithms were introduced to predict the active G4s regions \textit{in vitro} based on the canonical G4 sequence elements, G-\textit{richness}, and G-\textit{skewness}, as well as the non-canonical sequence features. Recently, sequencing techniques like G4-seq and G4-ChIP-seq were developed to map the G4s \textit{in vitro}, and \textit{in vivo} respectively at a few hundred base resolution. Subsequently, several machine learning approaches were developed for predicting the G4 regions using the existing databases. However, their prediction models were simplistic, and the prediction accuracy was notably poor. In response, here, we propose a novel convolutional neural network with Bi-LSTM and attention layers, named G4-attention, to predict the G4 forming sequences with improved accuracy. G4-attention achieves high accuracy and attains state-of-the-art results in the G4 prediction task. Our model also predicts the G4 regions accurately in the highly class-imbalanced datasets. In addition, the developed model trained on the human genome dataset can be applied to any non-human genome DNA sequences to predict the G4 formation propensities.

A species' genetic code or genome encodes valuable evolutionary, biological, and phylogenetic information that aids in species recognition, taxonomic classification, and understanding genetic predispositions like drug resistance and virulence. However, the vast number of potential species poses significant challenges in developing a general-purpose whole genome classification tool. Traditional bioinformatics tools have made notable progress but lack scalability and are computationally expensive. Machine learning-based frameworks show promise but must address the issue of large classification vocabularies with long-tail distributions. In this study, we propose addressing this problem through zero-shot learning using TEPI, Taxonomy-aware Embedding and Pseudo-Imaging. We represent each genome as pseudo-images and map them to a taxonomy-aware embedding space for reasoning and classification. This embedding space captures compositional and phylogenetic relationships of species, enabling predictions in extensive search spaces. We evaluate TEPI using two rigorous zero-shot settings and demonstrate its generalization capabilities qualitatively on curated, large-scale, publicly sourced data.

Decoding the linguistic intricacies of the genome is a crucial problem in biology, and pre-trained foundational models such as DNABERT and Nucleotide Transformer have made significant strides in this area. Existing works have largely hinged on k-mer, fixed-length permutations of A, T, C, and G, as the token of the genome language due to its simplicity. However, we argue that the computation and sample inefficiencies introduced by k-mer tokenization are primary obstacles in developing large genome foundational models. We provide conceptual and empirical insights into genome tokenization, building on which we propose to replace k-mer tokenization with Byte Pair Encoding (BPE), a statistics-based data compression algorithm that constructs tokens by iteratively merging the most frequent co-occurring genome segment in the corpus. We demonstrate that BPE not only overcomes the limitations of k-mer tokenization but also benefits from the computational efficiency of non-overlapping tokenization. Based on these insights, we introduce DNABERT-2, a refined genome foundation model that adapts an efficient tokenizer and employs multiple strategies to overcome input length constraints, reduce time and memory expenditure, and enhance model capability. Furthermore, we identify the absence of a comprehensive and standardized benchmark for genome understanding as another significant impediment to fair comparative analysis. In response, we propose the Genome Understanding Evaluation (GUE), a comprehensive multi-species genome classification dataset that amalgamates $28$ distinct datasets across $7$ tasks, with input lengths ranging from $70$ to $1000$. Through comprehensive experiments on the GUE benchmark, we demonstrate that DNABERT-2 achieves comparable performance to the state-of-the-art model with $21 \times$ fewer parameters and approximately $56 \times$ less GPU time in pre-training.

Due to the high mutation rate of the virus, the COVID-19 pandemic evolved rapidly. Certain variants of the virus, such as Delta and Omicron, emerged with altered viral properties leading to severe transmission and death rates. These variants burdened the medical systems worldwide with a major impact to travel, productivity, and the world economy. Unsupervised machine learning methods have the ability to compress, characterize, and visualize unlabelled data. This paper presents a framework that utilizes unsupervised machine learning methods to discriminate and visualize the associations between major COVID-19 variants based on their genome sequences. These methods comprise a combination of selected dimensionality reduction and clustering techniques. The framework processes the RNA sequences by performing a k-mer analysis on the data and further visualises and compares the results using selected dimensionality reduction methods that include principal component analysis (PCA), t-distributed stochastic neighbour embedding (t-SNE), and uniform manifold approximation projection (UMAP). Our framework also employs agglomerative hierarchical clustering to visualize the mutational differences among major variants of concern and country-wise mutational differences for selected variants (Delta and Omicron) using dendrograms. We also provide country-wise mutational differences for selected variants via dendrograms. We find that the proposed framework can effectively distinguish between the major variants and has the potential to identify emerging variants in the future.

Next-generation sequencing technologies have enhanced the scope of Internet-of-Things (IoT) to include genomics for personalized medicine through the increased availability of an abundance of genome data collected from heterogeneous sources at a reduced cost. Given the sheer magnitude of the collected data and the significant challenges offered by the presence of highly similar genomic structure across species, there is a need for robust, scalable analysis platforms to extract actionable knowledge such as the presence of potentially zoonotic pathogens. The emergence of zoonotic diseases from novel pathogens, such as the influenza virus in 1918 and SARS-CoV-2 in 2019 that can jump species barriers and lead to pandemic underscores the need for scalable metagenome analysis. In this work, we propose MG2Vec, a deep learning-based solution that uses the transformer network as its backbone, to learn robust features from raw metagenome sequences for downstream biomedical tasks such as targeted and generalized pathogen detection. Extensive experiments on four increasingly challenging, yet realistic diagnostic settings, show that the proposed approach can help detect pathogens from uncurated, real-world clinical samples with minimal human supervision in the form of labels. Further, we demonstrate that the learned representations can generalize to completely unrelated pathogens across diseases and species for large-scale metagenome analysis. We provide a comprehensive evaluation of a novel representation learning framework for metagenome-based disease diagnostics with deep learning and provide a way forward for extracting and using robust vector representations from low-cost next generation sequencing to develop generalizable diagnostic tools.

Surges that have been observed at different periods in the number of COVID-19 cases are associated with the emergence of multiple SARS-CoV-2 (Severe Acute Respiratory Virus) variants. The design of methods to support laboratory detection are crucial in the monitoring of these variants. Hence, in this paper, we develop a semi-automated method to design both forward and reverse primer sets to detect SARS-CoV-2 variants. To proceed, we train deep Convolution Neural Networks (CNNs) to classify labelled SARS-CoV-2 variants and identify partial genomic features needed for the forward and reverse Polymerase Chain Reaction (PCR) primer design. Our proposed approach supplements existing ones while promoting the emerging concept of neural network assisted primer design for PCR. Our CNN model was trained using a database of SARS-CoV-2 full-length genomes from GISAID and tested on a separate dataset from NCBI, with 98\% accuracy for the classification of variants. This result is based on the development of three different methods of feature extraction, and the selected primer sequences for each SARS-CoV-2 variant detection (except Omicron) were present in more than 95 \% of sequences in an independent set of 5000 same variant sequences, and below 5 \% in other independent datasets with 5000 sequences of each variant. In total, we obtain 22 forward and reverse primer pairs with flexible length sizes (18-25 base pairs) with an expected amplicon length ranging between 42 and 3322 nucleotides. Besides the feature appearance, in-silico primer checks confirmed that the identified primer pairs are suitable for accurate SARS-CoV-2 variant detection by means of PCR tests.

The major problem of fitting a higher order Markov model is the exponentially growing number of parameters. The most popular approach is to use a Variable Length Markov Chain (VLMC), which determines relevant contexts (recent pasts) of variable orders and form a context tree. A more general approach is called Sparse Markov Model (SMM), where all possible histories of order $m$ form a partition so that the transition probability vectors are identical for the histories belonging to a particular group. We develop an elegant method of fitting SMM using convex clustering, which involves regularization. The regularization parameter is selected using BIC criterion. Theoretical results demonstrate the model selection consistency of our method for large sample size. Extensive simulation studies under different set-up have been presented to measure the performance of our method. We apply this method to classify genome sequences, obtained from individuals affected by different viruses.

Maria Bartiromo investigates the future of the artificial intelligence industry and its impact on business. Artificial intelligence (AI) could be key in helping scientists identify the next animal virus that is capable of infecting humans, according to researchers. In a Tuesday study published in the journal PLoS Biology, the Glasgow-based team said it had devised a genomic model that could "retrospectively or prospectively predict the probability that viruses will be able to infect humans." The group developed machine learning models to single out candidate zoonotic viruses using signatures of host range encoded in viral genomes. With a dataset of 861 viral species with known zoonotic status, the researchers collected a single representative genome sequence from the hundreds of RNA and DNA virus species, spanning 36 viral families.