The real-time demand for web security makes Security Information and Event Management (SIEM) platforms and their applied security rule an integral part of the intrusion detection life-cycle. However, the heterogeneity of vendor-specific rules (e.g., Splunk SPL, Microsoft KQL, IBM AQL, Google YARA-L, and RSA ESA) makes cross-platform rule reuse extremely difficult, requiring deep domain knowledge for reliable conversion. As a result, an autonomous and accurate rule conversion framework can significantly lead to effort savings, preserving the value of existing rules. In this paper, we propose ARuleCon, an agentic SIEM-rule conversion approach. Using ARuleCon, the security professionals do not need to distill the source rules' logic and re-map it to target vendors, instead, they provide the source rules, the documentation of the target rules and ARuleCon can purposely convert to the target vendors without more intervention. To achieve this, ARuleCon is equipped with intermediate representation (IR) that aligns core detection logic into vendor-neutral layer, agentic RAG pipeline that retrieves authoritative official vendor documentation to address the convension/schema mismatches, and Python-based consistency check that running both source and target rules in controlled test environments to mitigate subtle semantic drifts. We present a comprehensive evaluation of ARuleCon ranging from textual alignment between the source and target rules, and the execution success of target rules, showcasing ARuleCon can convert rules with higher fidelity, outperforming the baseline LLM models by 15% averagely. Finally, we perform a case study and interview with our industry collaborators 1, which showcases that ARuleCon can significantly save the expert's time on understanding the cross-SIEM's documentation and remapping the logic.

Accumulating evidence indicates that long noncoding RNAs (lncRNAs) play important roles in molecular and cellular biology. Although many algorithms have been developed to reveal their associations with complex diseases by using downstream targets, the upstream (epi)genetic regulatory information has not been sufficiently leveraged to predict the function of lncRNAs in various biological processes. Therefore, we present FunlncModel, a machine learning-based interpretable computational framework, which aims to screen out functional lncRNAs by integrating a large number of (epi)genetic features and functional genomic features from their upstream/downstream multi-omic regulatory networks. We adopted the random forest method to mine nearly 60 features in three categories from >2000 datasets across 11 data types, including transcription factors (TFs), histone modifications, typical enhancers, super-enhancers, methylation sites, and mRNAs. FunlncModel outperformed alternative methods for classification performance in human embryonic stem cell (hESC) (0.95 Area Under Curve (AUROC) and 0.97 Area Under the Precision-Recall Curve (AUPRC)). It could not only infer the most known lncRNAs that influence the states of stem cells, but also discover novel high-confidence functional lncRNAs. We extensively validated FunlncModel's efficacy by up to 27 cancer-related functional prediction tasks, which involved multiple cancer cell growth processes and cancer hallmarks. Meanwhile, we have also found that (epi)genetic regulatory features, such as TFs and histone modifications, serve as strong predictors for revealing the function of lncRNAs. Overall, FunlncModel is a strong and stable prediction model for identifying functional lncRNAs in specific cellular contexts. FunlncModel is available as a web server at https://bio.liclab.net/FunlncModel/.

In the realm of large vision language models (LVLMs), jailbreak attacks serve as a red-teaming approach to bypass guardrails and uncover safety implications. Existing jailbreaks predominantly focus on the visual modality, perturbing solely visual inputs in the prompt for attacks. However, they fall short when confronted with aligned models that fuse visual and textual features simultaneously for generation. To address this limitation, this paper introduces the Bi-Modal Adversarial Prompt Attack (BAP), which executes jailbreaks by optimizing textual and visual prompts cohesively. Initially, we adversarially embed universally adversarial perturbations in an image, guided by a few-shot query-agnostic corpus (e.g., affirmative prefixes and negative inhibitions). This process ensures that the adversarial image prompt LVLMs to respond positively to harmful queries. Subsequently, leveraging the image, we optimize textual prompts with specific harmful intent. In particular, we utilize a large language model to analyze jailbreak failures and employ chain-of-thought reasoning to refine textual prompts through a feedback-iteration manner. To validate the efficacy of our approach, we conducted extensive evaluations on various datasets and LVLMs, demonstrating that our BAP significantly outperforms other methods by large margins (+29.03% in attack success rate on average). Additionally, we showcase the potential of our attacks on black-box commercial LVLMs, such as GPT-4o and Gemini.

MOTIVATION: DNA methylation within gene body and promoters in cancer cells is well documented. An increasing number of studies showed that cytosine-phosphate-guanine (CpG) sites falling within other regulatory elements could also regulate target gene activation, mainly by affecting transcription factors (TFs) binding in human cancers. This led to the urgent need for comprehensively and effectively collecting distinct cis-regulatory elements and TF-binding sites (TFBS) to annotate DNA methylation regulation. RESULTS: We developed a database (CanMethdb, http://meth.liclab.net/CanMethdb/) that focused on the upstream and downstream annotations for CpG-genes in cancers. This included upstream cis-regulatory elements, especially those involving distal regions to genes, and TFBS annotations for the CpGs and downstream functional annotations for the target genes, computed through integrating abundant DNA methylation and gene expression profiles in diverse cancers. Users could inquire CpG-target gene pairs for a cancer type through inputting a genomic region, a CpG, a gene name, or select hypo/hypermethylated CpG sets. The current version of CanMethdb documented a total of 38 986 060 CpG-target gene pairs (with 6 769 130 unique pairs), involving 385 217 CpGs and 18 044 target genes, abundant cis-regulatory elements and TFs for 33 TCGA cancer types. CanMethdb might help biologists perform in-depth studies of target gene regulations based on DNA methylations in cancer. AVAILABILITY AND IMPLEMENTATION: The main program is available at https://github.com/chunquanlipathway/CanMethdb. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The rapid development of genomic high-throughput sequencing has identified a large number of DNA regulatory elements with abundant epigenetics markers, which promotes the rapid accumulation of functional genomic region data. The comprehensively understanding and research of human functional genomic regions is still a relatively urgent work at present. However, the existing analysis tools lack extensive annotation and enrichment analytical abilities for these regions. Here, we designed a novel software, Genomic Region sets Enrichment Analysis Platform (GREAP), which provides comprehensive region annotation and enrichment analysis capabilities. Currently, GREAP supports 85 370 genomic region reference sets, which cover 634 681 107 regions across 11 different data types, including super enhancers, transcription factors, accessible chromatins, etc. GREAP provides widespread annotation and enrichment analysis of genomic regions. To reflect the significance of enrichment analysis, we used the hypergeometric test and also provided a Locus Overlap Analysis. In summary, GREAP is a powerful platform that provides many types of genomic region sets for users and supports genomic region annotations and enrichment analyses. In addition, we developed a customizable genome browser containing >400 000 000 customizable tracks for visualization. The platform is freely available at http://www.liclab.net/Greap/view/index.