Large Language Model (LLM) techniques play an increasingly important role in Natural Language to SQL (NL2SQL) translation. LLMs trained by extensive corpora have strong natural language understanding and basic SQL generation abilities without additional tuning specific to NL2SQL tasks. Existing LLMs-based NL2SQL approaches try to improve the translation by enhancing the LLMs with an emphasis on user intention understanding. However, LLMs sometimes fail to generate appropriate SQL due to their lack of knowledge in organizing complex logical operator composition. A promising method is to input the LLMs with demonstrations, which include known NL2SQL translations from various databases. LLMs can learn to organize operator compositions from the input demonstrations for the given task. In this paper, we propose PURPLE (Pre-trained models Utilized to Retrieve Prompts for Logical Enhancement), which improves accuracy by retrieving demonstrations containing the requisite logical operator composition for the NL2SQL task on hand, thereby guiding LLMs to produce better SQL translation. PURPLE achieves a new state-of-the-art performance of 80.5% exact-set match accuracy and 87.8% execution match accuracy on the validation set of the popular NL2SQL benchmark Spider. PURPLE maintains high accuracy across diverse benchmarks, budgetary constraints, and various LLMs, showing robustness and cost-effectiveness.

DNA methylation plays a crucial role in transcriptional regulation. Reduced representation bisulfite sequencing (RRBS) is a technique of increasing use for analyzing genome-wide methylation profiles. Many computational tools such as Metilene, MethylKit, BiSeq and DMRfinder have been developed to use RRBS data for the detection of the differentially methylated regions (DMRs) potentially involved in epigenetic regulations of gene expression. For DMR detection tools, as for countless other medical applications, P-values and their adjustments are among the most standard reporting statistics used to assess the statistical significance of biological findings. However, P-values are coming under increasing criticism relating to their questionable accuracy and relatively high levels of false positive or negative indications. Here, we propose a method to calculate E-values, as likelihood ratios falling into the null hypothesis over the entire parameter space, for DMR detection in RRBS data. We also provide the R package 'metevalue' as a user-friendly interface to implement E-value calculations into various DMR detection tools. To evaluate the performance of E-values, we generated various RRBS benchmarking datasets using our simulator 'RRBSsim' with eight samples in each experimental group. Our comprehensive benchmarking analyses showed that using E-values not only significantly improved accuracy, area under ROC curve and power, over that of P-values or adjusted P-values, but also reduced false discovery rates and type I errors. In applications using real RRBS data of CRL rats and a clinical trial on low-salt diet, the use of E-values detected biologically more relevant DMRs and also improved the negative association between DNA methylation and gene expression.

Building a good feature space is essential for the metric-based few-shot algorithms to recognize a novel class with only a few samples. The feature space is often built by Convolutional Neural Networks (CNNs). However, CNNs primarily focus on local information with the limited receptive field, and the global information generated by distant pixels is not well used. Meanwhile, having a global understanding of the current task and focusing on distinct regions of the same sample for different queries are important for the few-shot classification. To tackle these problems, we propose the Cross Non-Local Neural Network (CNL) for capturing the long-range dependency of the samples and the current task. CNL extracts the task-specific and context-aware features dynamically by strengthening the features of the sample at a position via aggregating information from all positions of itself and the current task. To reduce losing important information, we maximize the mutual information between the original and refined features as a constraint. Moreover, we add a task-specific scaling to deal with multi-scale and task-specific features extracted by CNL. We conduct extensive experiments for validating our proposed algorithm, which achieves new state-of-the-art performances on two public benchmarks.

Few-shot learning can recognize a novel category based on only a few samples because it learns to learn from a lot of labeled samples during the training process. When data is insufficient, the performance is affected. And it is expensive to obtain a large-scale finegrained dataset with annotation. In this paper, we adopt domain- specific knowledge to fill the gap of insufficient annotated data. We propose a cross-modal knowledge distillation (CMKD) framework to do fine-grained one-shot classification and propose the Spatial Relation Loss (SRL) to transfer cross-modal information, which can tackle the semantic gap between multimodal features. The teacher network distills the spatial relationship of the samples as a soft target for training a unimodal student network. Notably, the student network makes predictions only based on a few samples without any external knowledge in the application. This model-agnostic framework will be well adapted to other few-shot models. Extensive experimental results on benchmarks demonstrate that CMKD can make full use of cross-modal knowledge in image and text few-shot classification. CKMD improves the performances of the student networks significantly, even if it is a state-of-the-art student network.

Conducting fraud transactions has become popular among e-commerce sellers to make their products favorable to the platform and buyers, which decreases the utilization efficiency of buyer impressions and jeopardizes the business environment. Fraud detection techniques are necessary but not enough for the platform since it is impossible to recognize all the fraud transactions. In this paper, we focus on improving the platform's impression allocation mechanism to maximize its profit and reduce the sellers' fraudulent behaviors simultaneously. First, we learn a seller behavior model to predict the sellers' fraudulent behaviors from the real-world data provided by one of the largest e-commerce company in the world. Then, we formulate the platform's impression allocation problem as a continuous Markov Decision Process (MDP) with unbounded action space. In order to make the action executable in practice and facilitate learning, we propose a novel deep reinforcement learning algorithm DDPG-ANP that introduces an action norm penalty to the reward function. Experimental results show that our algorithm significantly outperforms existing baselines in terms of scalability and solution quality.

UNLABELLED: : Next-Generation Sequencing (NGS) technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent differences from their corresponding mature reference sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). These isomiRs mainly originate via the imprecise and alternative cleavage during the pre-miRNA processing and post-transcriptional modifications that influence miRNA stability, their sub-cellular localization and target selection. Although several tools for the identification of isomiR have been reported, no bioinformatics resource dedicated to gather isomiRs from public NGS data and to provide functional analysis of these isomiRs is available to date. Thus, a free online database, IsomiR Bank has been created to integrate isomiRs detected by our previously published algorithm CPSS. In total, 2727 samples (Small RNA NGS data downloaded from ArrayExpress) from eight species (Arabidopsis thaliana, Drosophila melanogaster, Danio rerio, Homo sapiens, Mus musculus, Oryza sativa, Solanum lycopersicum and Zea mays) are analyzed. At present, 308 919 isomiRs from 4706 mature miRNAs are collected into IsomiR Bank. In addition, IsomiR Bank provides target prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. AVAILABILITY AND IMPLEMENTATION: IsomiR Bank is implemented in PHP/PERL + MySQL + R format and can be freely accessed at http://mcg.ustc.edu.cn/bsc/isomir/ CONTACTS: : [email protected] or [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

UNLABELLED: Next generation sequencing (NGS) techniques have been widely used to document the small ribonucleic acids (RNAs) implicated in a variety of biological, physiological and pathological processes. An integrated computational tool is needed for handling and analysing the enormous datasets from small RNA deep sequencing approach. Herein, we present a novel web server, CPSS (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. Small RNA NGS data can be submitted to this server with analysis results being returned in two parts: (i) annotation analysis, which provides the most comprehensive analysis for small RNA transcriptome, including length distribution and genome mapping of sequencing reads, small RNA quantification, prediction of novel miRNAs, identification of differentially expressed miRNAs, piwi-interacting RNAs and other non-coding small RNAs between paired samples and detection of miRNA editing and modifications and (ii) functional analysis, including prediction of miRNA targeted genes by multiple tools, enrichment of gene ontology terms, signalling pathway involvement and protein-protein interaction analysis for the predicted genes. CPSS, a ready-to-use web server that integrates most functions of currently available bioinformatics tools, provides all the information wanted by the majority of users from small RNA deep sequencing datasets. AVAILABILITY: CPSS is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/db/cpss/index.html or http://mcg.ustc.edu.cn/sdap1/cpss/index.html.

UNLABELLED: High-throughput deep-sequencing technology has generated an unprecedented number of expressed short sequence reads, presenting not only an opportunity but also a challenge for prediction of novel microRNAs. To verify the existence of candidate microRNAs, we have to show that these short sequences can be processed from candidate pre-microRNAs. However, it is laborious and time consuming to verify these using existing experimental techniques. Therefore, here, we describe a new method, miRD, which is constructed using two feature selection strategies based on support vector machines (SVMs) and boosting method. It is a high-efficiency tool for novel pre-microRNA prediction with accuracy up to 94.0% among different species. AVAILABILITY: miRD is implemented in PHP/PERL+MySQL+R and can be freely accessed at http://mcg.ustc.edu.cn/rpg/mird/mird.php.