Designing a query-efficient attack strategy to generate high-quality adversarial examples under the hard-label black-box setting is a fundamental yet challenging problem, especially in natural language processing (NLP). The process of searching for adversarial examples has many uncertainties (e.g., an unknown impact on the target model's prediction of the added perturbation) when confidence scores cannot be accessed, which must be compensated for with a large number of queries. To address this issue, we propose TextCheater, a decision-based metaheuristic search method that performs a query-efficient textual adversarial attack task by prohibiting invalid searches. The strategies of multiple initialization points and Tabu search are also introduced to keep the search process from falling into a local optimum. We apply our approach to three state-of-the-art language models (i.e., BERT, wordLSTM, and wordCNN) across six benchmark datasets and eight real-world commercial sentiment analysis platforms/models. Furthermore, we evaluate the Robustly optimized BERT pretraining Approach (RoBERTa) and models that enhance their robustness by adversarial training on toxicity detection and text classification tasks. The results demonstrate that our method minimizes the number of queries required for crafting plausible adversarial text while outperforming existing attack methods in the attack success rate, fluency of output sentences, and similarity between the original text and its adversary.

MOTIVATION: Microbiome analyses of clinical samples with low microbial biomass are challenging because of the very small quantities of microbial DNA relative to the human host, ubiquitous contaminating DNA in sequencing experiments and the large and rapidly growing microbial reference databases. RESULTS: We present computational subtraction-based microbiome discovery (CSMD), a bioinformatics pipeline specifically developed to generate accurate species-level microbiome profiles for clinical samples with low microbial loads. CSMD applies strategies for the maximal elimination of host sequences with minimal loss of microbial signal and effectively detects microorganisms present in the sample with minimal false positives using a stepwise convergent solution. CSMD was benchmarked in a comparative evaluation with other classic tools on previously published well-characterized datasets. It showed higher sensitivity and specificity in host sequence removal and higher specificity in microbial identification, which led to more accurate abundance estimation. All these features are integrated into a free and easy-to-use tool. Additionally, CSMD applied to cell-free plasma DNA showed that microbial diversity within these samples is substantially broader than previously believed. AVAILABILITY AND IMPLEMENTATION: CSMD is freely available at https://github.com/liuyu8721/csmd. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.