The advent of single-cell RNA sequencing (scRNA-seq) has offering unprecedented insights at the single-cell level. This groundbreaking technology has opened new pathways for understanding cellular diversity and revealing novel insights into disease mechanisms. However, the analysis of scRNA-seq data is challenging, primarily due to dropout events caused by technical noise. Developing effective imputation methods is crucial for the reliable and informative analysis of scRNA-seq data. While deep learning-based approaches have been proposed for scRNA-seq data imputation, they often fall short of optimal performance, especially in identifying rare cell types. Here we propose a novel self-supervised deep learning model named scGANCL for scRNA-seq data imputation. scGANCL combines bidirectional generative adversarial network (BiGAN) with contrastive learning (CL) to enhance imputation performance. To fully exploit gene expression profiles, a contrastive learning module is introduced to enhance the representation learning of cells by minimizing the discrepancy between the distributions of real and generated data. Comprehensive experiments have been conducted on ten simulated and seven real datasets to validate scGANCL's effectiveness. The results demonstrated scGANCL consistently outperformed seven state-of-the-art methods across various downstream tasks. Ablation studies further validated the contribution of each component to the overall performance of the model.

MOTIVATION: Single-cell RNA-sequencing (scRNA-seq) is widely used to reveal cellular heterogeneity, complex disease mechanisms and cell differentiation processes. Due to high sparsity and complex gene expression patterns, scRNA-seq data present a large number of dropout events, affecting downstream tasks such as cell clustering and pseudo-time analysis. Restoring the expression levels of genes is essential for reducing technical noise and facilitating downstream analysis. However, existing scRNA-seq data imputation methods ignore the topological structure information of scRNA-seq data and cannot comprehensively utilize the relationships between cells. RESULTS: Here, we propose a single-cell Graph Contrastive Learning method for scRNA-seq data imputation, named scGCL, which integrates graph contrastive learning and Zero-inflated Negative Binomial (ZINB) distribution to estimate dropout values. scGCL summarizes global and local semantic information through contrastive learning and selects positive samples to enhance the representation of target nodes. To capture the global probability distribution, scGCL introduces an autoencoder based on the ZINB distribution, which reconstructs the scRNA-seq data based on the prior distribution. Through extensive experiments, we verify that scGCL outperforms existing state-of-the-art imputation methods in clustering performance and gene imputation on 14 scRNA-seq datasets. Further, we find that scGCL can enhance the expression patterns of specific genes in Alzheimer's disease datasets. AVAILABILITY AND IMPLEMENTATION: The code and data of scGCL are available on Github: https://github.com/zehaoxiong123/scGCL. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

single-cell RNA-sequencing (scRNA-seq) technology can reveal cellular heterogeneity with high throughput and resolution, facilitating the profiling of single-cell transcriptomes. However, due to some experimental factors, a large number of missing values are generated in scRNA-seq data, which are called dropout events, and this phenomenon affects the downstream analysis. Imputation is an effective denoising method, but existing imputation methods still face a huge challenge: lack of interpretability. In this study, we propose single-cell Self-Attention Generative Adversarial Networks(scSAGAN), a semi-supervised imputation method for scRNA-seq data. scSAGAN mainly uses Semi-Supervised Learning (SSL) and Probabilistic Latent Semantic Analysis (PLSA), which can not only learn the potential characteristics of different types of cells but explain their imputation behavior. In clustering experiments, scSAGAN exhibits better clustering performance than all baselines on 7 datasets. Next, we interpret the imputation behavior of scSAGAN on datasets such as Alzheimer’s disease and find causative genes associated with the corresponding datasets. scSAGAN is currently an open-source method, available at https://github.com/zehaoxiongl23/scSAGAN.

MOTIVATION: Cell-type annotation plays a crucial role in single-cell RNA-seq (scRNA-seq) data analysis. As more and more well-annotated scRNA-seq reference data are publicly available, automatical label transference algorithms are gaining popularity over manual marker gene-based annotation methods. However, most existing methods fail to unify cell-type annotation with dimensionality reduction and are unable to generate deep latent representation from the perspective of data generation. RESULTS: In this article, we propose scSemiGAN, a single-cell semi-supervised cell-type annotation and dimensionality reduction framework based on a generative adversarial network, to overcome these challenges, modeling scRNA-seq data from the aspect of data generation. Our proposed scSemiGAN is capable of performing deep latent representation learning and cell-type label prediction simultaneously. Through extensive comparison with four state-of-the-art annotation methods on diverse simulated and real scRNA-seq datasets, scSemiGAN achieves competitive or superior performance in multiple downstream tasks including cell-type annotation, latent representation visualization, confounding factor removal and enrichment analysis. AVAILABILITY AND IMPLEMENTATION: The code and data of scSemiGAN are available on GitHub: https://github.com/rafa-nadal/scSemiGAN. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Attribute-based access control (ABAC) provides a high level of flexibility that promotes security and information sharing. ABAC policy mining algorithms have potential to significantly reduce the cost of migration to ABAC, by partially automating the development of an ABAC policy from an access control list (ACL) policy or role-based access control (RBAC) policy with accompanying attribute data. This paper presents an ABAC policy mining algorithm. To the best of our knowledge, it is the first ABAC policy mining algorithm. Our algorithm iterates over tuples in the given user-permission relation, uses selected tuples as seeds for constructing candidate rules, and attempts to generalize each candidate rule to cover additional tuples in the user-permission relation by replacing conjuncts in attribute expressions with constraints. Our algorithm attempts to improve the policy by merging and simplifying candidate rules, and then it selects the highest-quality candidate rules for inclusion in the generated policy.

In large organizations, access control policies are managed by multiple users (administrators). An administrative policy specifies how each user in an enterprise may change the policy. Fully understanding the consequences of an administrative policy in an enterprise system can be difficult, because of the scale and complexity of the access control policy and the administrative policy, and because sequences of changes by different users may interact in unexpected ways. Administrative policy analysis helps by answering questions such as user-permission reachability, which asks whether specified users can together change the policy in a way that achieves a specified goal, namely, granting a specified permission to a specified user. This paper presents a rule-based access control policy language, a rule-based administrative policy model that controls addition and removal of facts and rules, and an abductive analysis algorithm for user-permission reachability. Abductive analysis means that the algorithm can analyze policy rules even if the facts initially in the policy (e.g., information about users) are unavailable. The algorithm does this by computing minimal sets of facts that, if present in the initial policy, imply reachability of the goal.

Role-based access control (RBAC) offers significant advantages over lower-level access control policy representations, such as access control lists (ACLs). However, the effort required for a large organization to migrate from ACLs to RBAC can be a significant obstacle to adoption of RBAC. Role mining algorithms partially automate the construction of an RBAC policy from an ACL policy and possibly other information. These algorithms can significantly reduce the cost of migration to RBAC.

Role-based access control (RBAC) offers significant advantages over lower-level access control policy representations, such as access control lists (ACLs). However, the effort required for a large organization to migrate from ACLs to RBAC can be a significant obstacle to adoption of RBAC. Role mining algorithms partially automate the construction of an RBAC policy from an ACL policy and possibly other information, such as user attributes. These algorithms can significantly reduce the cost of migration to RBAC.

We define a new temporal logic called CTL[k-QDDC]. It extends CTL with the ability to specify branching pasts and quantitative temporal properties by combining CTL with the logic Quantified Discrete-time Duration Calculus (QDDC). The idea of bounded model checking is also used in this logic. Compared to CTL, the added expressive power is necessary for specification and verification of real-time distributed software and hardware systems. We give the syntax and semantics of CTL[k-QDDC], discuss its expressive power, and propose an explicit model checking algorithm for Kripke structure. CTL[k-QDDC] is considered as a foundation of some more complex logics for specifying and verifying continuous-time properties in some appropriate structures.

This paper discusses speaker-independent isolated word recognition using fuzzy set theory. In the case of a small training sample set, a second-level fuzzy clustering method (clustering algorithm based on a fuzzy equivalent relation combined with the fuzzy ISODATA algorithm) is presented for obtaining initial reference templates. In the course of recognition, the self-updating algorithm of the reference templates and weighted vector is used. >