MOTIVATION: Taxonomic classification of short reads and taxonomic profiling of metagenomic samples are well-studied yet challenging problems. The presence of species belonging to groups without close representation in a reference dataset is particularly challenging. While k-mer-based methods have performed well in terms of running time and accuracy, they tend to have reduced accuracy for such novel species. Thus, there is a growing need for methods that combine the scalability of k-mers with increased sensitivity. RESULTS: Here, we show that using locality-sensitive hashing (LSH) can increase the sensitivity of the k-mer-based search. Our method, which combines LSH with several heuristics techniques including soft lowest common ancestor labeling and voting, is more accurate than alternatives in both taxonomic classification of individual reads and abundance profiling. AVAILABILITY AND IMPLEMENTATION: CONSULT-II is implemented in C++, and the software, together with reference libraries, is publicly available on GitHub https://github.com/bo1929/CONSULT-II.

Abstract Named entity recognition (NER) aims to identify mentions of named entities in an unstructured text and classify them into predefined named entity classes. While deep learning-based pre-trained language models help to achieve good predictive performances in NER, many domain-specific NER applications still call for a substantial amount of labeled data. Active learning (AL), a general framework for the label acquisition problem, has been used for NER tasks to minimize the annotation cost without sacrificing model performance. However, the heavily imbalanced class distribution of tokens introduces challenges in designing effective AL querying methods for NER. We propose several AL sentence query evaluation functions that pay more attention to potential positive tokens and evaluate these proposed functions with both sentence-based and token-based cost evaluation strategies. We also propose a better data-driven normalization approach to penalize sentences that are too long or too short. Our experiments on three datasets from different domains reveal that the proposed approach reduces the number of annotated tokens while achieving better or comparable prediction performance with conventional methods.

MOTIVATION: With the wide availability of single-cell RNA-seq (scRNA-seq) technology, population-scale scRNA-seq datasets across multiple individuals and time points are emerging. While the initial investigations of these datasets tend to focus on standard analysis of clustering and differential expression, leveraging the power of scRNA-seq data at the personalized dynamic gene co-expression network level has the potential to unlock subject and/or time-specific network-level variation, which is critical for understanding phenotypic differences. Community detection from co-expression networks of multiple time points or conditions has been well-studied; however, none of the existing settings included networks from multiple subjects and multiple time points simultaneously. To address this, we develop Multi-subject Dynamic Community Detection (MuDCoD) for multi-subject community detection in personalized dynamic gene networks from scRNA-seq. MuDCoD builds on the spectral clustering framework and promotes information sharing among the networks of the subjects as well as networks at different time points. It clusters genes in the personalized dynamic gene networks and reveals gene communities that are variable or shared not only across time but also among subjects. RESULTS: Evaluation and benchmarking of MuDCoD against existing approaches reveal that MuDCoD effectively leverages apparent shared signals among networks of the subjects at individual time points, and performs robustly when there is no or little information sharing among the networks. Applications to population-scale scRNA-seq datasets of human-induced pluripotent stem cells during dopaminergic neuron differentiation and CD4+ T cell activation indicate that MuDCoD enables robust inference for identifying time-varying personalized gene modules. Our results illustrate how personalized dynamic community detection can aid in the exploration of subject-specific biological processes that vary across time. AVAILABILITY AND IMPLEMENTATION: MuDCoD is publicly available at https://github.com/bo1929/MuDCoD as a Python package. Implementation includes simulation and real-data experiments together with extensive documentation.