Anomaly-Based Intrusion Detection Systems (IDSs) have been extensively researched for their ability to detect zero-day attacks. These systems establish a baseline of normal behavior using benign traffic data and flag deviations from this norm as potential threats. They generally experience higher false alarm rates than signature-based IDSs. Unlike image data, where the observed features provide immediate utility, raw network traffic necessitates additional processing for effective detection. It is challenging to learn useful patterns directly from raw traffic data or simple traffic statistics (e.g., connection duration, package inter-arrival time) as the complex relationships are difficult to distinguish. Therefore, some feature engineering becomes imperative to extract and transform raw data into new feature representations that can directly improve the detection capability and reduce the false positive rate. We propose a geometric feature learning method to optimize the feature extraction process. We employ contrastive feature learning to learn a feature space where normal traffic instances reside in a compact cluster. We further utilize H-Score feature learning to maximize the compactness of the cluster representing the normal behavior, enhancing the subsequent anomaly detection performance. Our evaluations using the NSL-KDD and N-BaloT datasets demonstrate that the proposed IDS powered by feature learning can consistently outperform state-of-the-art anomaly-based IDS methods by significantly lowering the false positive rate. Furthermore, we deploy the proposed IDS on a Raspberry Pi 4 and demonstrate its applicability on resource-constrained Internet of Things (IoT) devices, highlighting its versatility for diverse application scenarios.

This study benchmarks the robustness and resilience of computational deconvolution methods for estimating cell-type proportions in bulk tissues, with a focus on comparing reference-based and reference-free methods. Robustness is evaluated by generating in silico pseudo-bulk tissue RNA sequencing data from cell-level gene expression profiles derived from four different tissue types, with simulated cellular composition at varying levels of heterogeneity. To assess resilience, we intentionally alter single-cell RNA profiles to create pseudo-bulk tissue RNA-seq data. Deconvolution estimates are compared with ground truth using Pearson's correlation coefficient, root mean squared deviation, and mean absolute deviation. The results show that reference-based methods are more robust when reliable reference data are available, whereas reference-free methods excel in scenarios lacking suitable reference data. Furthermore, variations in cell-level transcriptomic profiles and cell composition have emerged as critical factors influencing the performance of deconvolution methods. This study provides significant insights into the factors affecting bulk tissue deconvolution performance, which are essential for guiding users and advancing the development of more powerful and reliable algorithms in the future.

Artificial neural networks have recently gained significant attention in biomedical research. However, their utility in survival analysis still faces many challenges. In addition to designing models for high accuracy, it is essential to optimize models that provide biologically meaningful insights. With these considerations in mind, we developed a deep neural network model, MaskedNet, to identify genes and pathways whose expression at the time of diagnosis is associated with overall survival. MaskedNet was trained using TCGA breast cancer transcriptome and clinical data, and the model’s final output was the predicted logarithm of the hazard ratio for death. The trained model was interpreted using SHapley Additive exPlanations (SHAP), a technique grounded in robust mathematical principles that assigns importance scores to input features. Compared to traditional Cox proportional hazards regression, MaskedNet had higher accuracy, as measured by Harrell’s C-index. We also found that aggregating outputs from several model runs identified multiple genes and pathways associated with overall survival, including IFNG and PIK3CA genes , along with their related pathways. To further elucidate the role of the IFNG gene, tumors were partitioned into two groups based on low and high IFNG SHAP values, respectively. Tumors with lower IFNG SHAP values exhibited higher IFNG expression and better overall survival, which were linked to more abundant presence of M1 macrophages and activated CD4+ and CD8+ T cells in the tumor microenvironment. The association of the IFNG pathway with overall survival was validated in the trastuzumab arm of the NCCTG-N9831 trial, an independent breast cancer study.

[This corrects the article PMC11643596.].

Blockchain’s decentralization, transparency, and tamper-resistance properties have facilitated the system’s use in various application fields. However, the low throughput and high confirmation latency hinder the widespread adoption of Blockchain. Many solutions have been proposed to address these issues, including first-layer solutions (or on-chain solutions) and second-layer solutions (or off-chain solutions). Among the proposed solutions, the blockchain sharding system is the most scalable one, where the nodes in the network are divided into several groups. The nodes in different shards work in parallel to validate the transactions and add them to the blocks, and in such a way, the throughput increases significantly. However, previous works have not adequately summarized the latest achievements in blockchain sharding, nor have they fully showcased its state-of-the-art. Our study provides a systemization of knowledge of public blockchain sharding, including the core components of sharding systems, challenges, limitations, and mechanisms of the latest sharding protocols. We also compare their performance and discuss current constraints and future research directions.

The adaptive fuzzy logic position and force control scheme are proposed for multimanipulators with nonlinear uncertainties, external disturbances, and input dead-zone nonlinearities. Specifically, the adaptive fuzzy logic system is employed for approximating the nonlinear dynamics of the manipulator, and the approximation error is compensated online by the designed robust control terms. In addition, to address the nonlinear input dead-zone effect, a new theorem is presented to stabilize the system without using specific Nussbaum functions. Consequently, the proposed robust control algorithm exhibits strong applicability. Finally, the stability of the multimanipulator tracking system is verified using a Lyapunov function. Simulation results demonstrate the effectiveness of this strategy.

Knowledge Graph (KG), as a side-information, tends to be utilized to supplement the collaborative filtering (CF) based recommendation model. By mapping items with the entities in KGs, prior studies mostly extract the knowledge information from the KGs and inject it into the representations of users and items. Despite their remarkable performance, they fail to model the user preference on attribute in the KG, since they ignore that (1) the structure information of KG may hinder the user preference learning, and (2) the user's interacted attributes will result in the bias issue on the similarity scores. With the help of causality tools, we construct the causal-effect relation between the variables in KG-based recommendation and identify the reasons causing the mentioned challenges. Accordingly, we develop a new framework, termed Knowledge Graph-based Causal Recommendation (KGCR), which implements the deconfounded user preference learning and adopts counterfactual inference to eliminate bias in the similarity scoring. Ultimately, we evaluate our proposed model on three datasets, including Amazon-book, LastFM, and Yelp2018 datasets. By conducting extensive experiments on the datasets, we demonstrate that KGCR outperforms several state-of-the-art baselines, such as KGNN-LS (Wang et al., 2019), KGAT (Wang et al., 2019) and KGIN (Wang et al., 2021).

With the advancement of biotechniques, a vast amount of genomic data is generated with no limit. Predicting a disease trait based on these data offers a cost-effective and time-efficient way for early disease screening. Here we proposed a composite kernel partial least squares (CKPLS) regression model for quantitative disease trait prediction focusing on genomic data. It can efficiently capture nonlinear relationships among features compared with linear learning algorithms such as Least Absolute Shrinkage and Selection Operator or ridge regression. We proposed to optimize the kernel parameters and kernel weights with the genetic algorithm (GA). In addition to improved performance for parameter optimization, the proposed GA-CKPLS approach also has better learning capacity and generalization ability compared with single kernel-based KPLS method as well as other nonlinear prediction models such as the support vector regression. Extensive simulation studies demonstrated that GA-CKPLS had better prediction performance than its counterparts under different scenarios. The utility of the method was further demonstrated through two case studies. Our method provides an efficient quantitative platform for disease trait prediction based on increasing volume of omics data.

In a trust network, two users who are connected by a trust relationship tend to have similar interests. Based on this observation, existing trust-aware recommendation methods predict ratings for a target user on unseen items by referencing to ratings of those users who are reachable from the target user in the forward direction of trustor-trustee relationship through the trust network. However, these methods have overlooked the possibility of utilizing the ratings of those users reachable in the backward direction, which may also have similar interests. In this paper, we investigate this possibility by identifying and adding these users to the existing methods when predicting ratings for the target user. We perform a series of experiments and observe that our approach improves the coverage while preserving the accuracy.

MOTIVATION: Tumors exhibit numerous genomic lesions such as copy number variations, structural variations and sequence variations. It is difficult to determine whether a specific constellation of lesions observed across a cohort of multiple tumors provides statistically significant evidence that the lesions target a set of genes that may be located across different chromosomes but yet are all involved in a single specific biological process or function. RESULTS: We introduce the genomic random interval (GRIN) statistical model and analysis method that evaluates the statistical significance of the abundance of genomic lesions that overlap a specific locus or a pre-defined set of biologically related loci. The GRIN model retains certain biologically important properties of genomic lesions that are ignored by other methods. In a simulation study and two example analyses of leukemia genomic lesion data, GRIN more effectively identified important loci as significant than did three methods based on a permutation-of-markers model. GRIN also identified biologically relevant pathways with a significant abundance of lesions in both examples. AVAILABILITY: An R package will be freely available at CRAN and www.stjuderesearch.org/site/depts/biostats/software.

Recently, product review sitesthat contain user ratings and trust statements such as Epinions.com have become popular, and many attempts have been made to analyze user behavior on those sites. In this paper, we first define three different user groups for each user, i.e. Trustee, Trust or, and Irrelevance which describe different kinds of trust statements. Then we investigate the relationship between each user and users in his/her different user groups by comparing how their ratings are similar on Epinions data sets. Most existing works simply ignored Trust or group when considering a certain user. However, our observations suggest that Trust or group still meaningful that should not be simply disregarded.