A posterior probability based Bayesian method for single-cell RNA-seq data imputation

Computational Methods for Data Integration and Imputation of Missing Values in Omics Datasets

Molecular profiling of different omic-modalities (e.g., DNA methylomics, transcriptomics, proteomics) in biological systems represents the basis for research and clinical decision-making. Measurement-specific biases, so-called batch effects, often hinder the integration of independently acquired datasets, and missing values further hamper the applicability of typical data processing algorithms. In addition to careful experimental design, well-defined standards in data acquisition and data exchange, the alleviation of these phenomena particularly requires a dedicated data integration and preprocessing pipeline. This review aims to give a comprehensive overview of computational methods for data integration and missing value imputation for omic data analyses. We provide formal definitions for missing value mechanisms and propose a novel statistical taxonomy for batch effects, especially in the presence of missing data. Based on an automated document search and systematic literature review, we describe 32 distinct data integration methods from five main methodological categories, as well as 37 algorithms for missing value imputation from five separate categories. Additionally, this review highlights multiple quantitative evaluation methods to aid researchers in selecting a suitable set of methods for their work. Finally, this work provides an integrated discussion of the relevance of batch effects and missing values in omics with corresponding method recommendations. We then propose a comprehensive three-step workflow from the study conception to final data analysis and deduce perspectives for future research. Eventually, we present a comprehensive flow chart as well as exemplary decision trees to aid practitioners in the selection of specific approaches for imputation and data integration in their studies.

Terrorism group prediction using feature combination and BiGRU with self-attention mechanism

The world faces the ongoing challenge of terrorism and extremism, which threaten the stability of nations, the security of their citizens, and the integrity of political, economic, and social systems. Given the complexity and multifaceted nature of this phenomenon, combating it requires a collective effort, with tailored methods to address its various aspects. Identifying the terrorist organization responsible for an attack is a critical step in combating terrorism. Historical data plays a pivotal role in this process, providing insights that can inform prevention and response strategies. With advancements in technology and artificial intelligence (AI), particularly in military applications, there is growing interest in utilizing these developments to enhance national and regional security against terrorism. Central to this effort are terrorism databases, which serve as rich resources for data on armed organizations, extremist entities, and terrorist incidents. The Global Terrorism Database (GTD) stands out as one of the most widely used and accessible resources for researchers. Recent progress in machine learning (ML), deep learning (DL), and natural language processing (NLP) offers promising avenues for improving the identification and classification of terrorist organizations. This study introduces a framework designed to classify and predict terrorist groups using bidirectional recurrent units and self-attention mechanisms, referred to as BiGRU-SA. This approach utilizes the comprehensive data in the GTD by integrating textual features extracted by DistilBERT with features that show a high correlation with terrorist organizations. Additionally, the Synthetic Minority Over-sampling Technique with Tomek links (SMOTE-T) was employed to address data imbalance and enhance the robustness of our predictions. The BiGRU-SA model captures temporal dependencies and contextual information within the data. By processing data sequences in both forward and reverse directions, BiGRU-SA offers a comprehensive view of the temporal dynamics, significantly enhancing classification accuracy. To evaluate the effectiveness of our framework, we compared ten models, including six traditional ML models and four DL algorithms. The proposed BiGRU-SA framework demonstrated outstanding performance in classifying 36 terrorist organizations responsible for terrorist attacks, achieving an accuracy of 98.68%, precision of 96.06%, sensitivity of 96.83%, specificity of 99.50%, and a Matthews correlation coefficient of 97.50%. Compared to state-of-the-art methods, the proposed model outperformed others, confirming its effectiveness and accuracy in the classification and prediction of terrorist organizations.

invMap: a sensitive mapping tool for long noisy reads with inversion structural variants

MOTIVATION

Longer reads produced by PacBio or Oxford Nanopore sequencers could more frequently span the breakpoints of structural variations (SVs) than shorter reads. Therefore, existing long-read mapping methods often generate wrong alignments and variant calls. Compared to deletions and insertions, inversion events are more difficult to be detected since the anchors in inversion regions are nonlinear to those in SV-free regions. To address this issue, this study presents a novel long-read mapping algorithm (named as invMap).

RESULTS

For each long noisy read, invMap first locates the aligned region with a specifically designed scoring method for chaining, then checks the remaining anchors in the aligned region to discover potential inversions. We benchmark invMap on simulated datasets across different genomes and sequencing coverages, experimental results demonstrate that invMap is more accurate to locate aligned regions and call SVs for inversions than the competing methods. The real human genome sequencing dataset of NA12878 illustrates that invMap can effectively find more candidate variant calls for inversions than the competing methods.

AVAILABILITY AND IMPLEMENTATION

The invMap software is available at https://github.com/zhang134/invMap.git.