Weicai Long

Shuo Yang, Xinran Zheng, Xinchen Zhang et al.

Large Language Models (LLMs) have revolutionized various fields with their exceptional capabilities in understanding, processing, and generating human-like text. This paper investigates the potential of LLMs in advancing Network Intrusion Detection Systems (NIDS), analyzing current challenges, methodologies, and future opportunities. It begins by establishing a foundational understanding of NIDS and LLMs, exploring the enabling technologies that bridge the gap between intelligent and cognitive systems in AI-driven NIDS. While Intelligent NIDS leverage machine learning and deep learning to detect threats based on learned patterns, they often lack contextual awareness and explainability. In contrast, Cognitive NIDS integrate LLMs to process both structured and unstructured security data, enabling deeper contextual reasoning, explainable decision-making, and automated response for intrusion behaviors. Practical implementations are then detailed, highlighting LLMs as processors, detectors, and explainers within a comprehensive AI-driven NIDS pipeline. Furthermore, the concept of an LLM-centered Controller is proposed, emphasizing its potential to coordinate intrusion detection workflows, optimizing tool collaboration and system performance. Finally, this paper identifies critical challenges and opportunities, aiming to foster innovation in developing reliable, adaptive, and explainable NIDS. By presenting the transformative potential of LLMs, this paper seeks to inspire advancement in next-generation network security systems.

Weicai Long, Yusen Hou, Junning Feng et al.

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However, existing benchmarks either focus on specialized DNA models trained for sequence prediction or evaluate biological knowledge using text-only questions, leaving the behavior of general-purpose LLMs when directly exposed to raw genome sequences underexplored. We introduce GenomeQA, a benchmark designed to provide a controlled evaluation setting for general-purpose LLMs on sequence-based genome inference tasks. GenomeQA comprises 5,200 samples drawn from multiple biological databases, with sequence lengths ranging from 6 to 1,000 base pairs (bp), spanning six task families: Enhancer and Promoter Identification, Splice Site Identification, Taxonomic Classification, Histone Mark Prediction, Transcription Factor Binding Site Prediction, and TF Motif Prediction. Across six frontier LLMs, we find that models consistently outperform random baselines and can exploit local sequence signals such as GC content and short motifs, while performance degrades on tasks that require more indirect or multi-step inference over sequence patterns. GenomeQA establishes a diagnostic benchmark for studying and improving the use of general-purpose LLMs on raw genomic sequences.

Yusen Hou, Weicai Long, Haitao Hu et al.

Bacteriophages, often referred to as the dark matter of the biosphere, play a critical role in regulating microbial ecosystems and in antibiotic alternatives. Thus, accurate interpretation of their genomes holds significant scientific and practical value. While general-purpose Large Language Models (LLMs) excel at understanding biological texts, their ability to directly interpret raw nucleotide sequences and perform biological reasoning remains underexplored. To address this, we introduce PhageBench, the first benchmark designed to evaluate phage genome understanding by mirroring the workflow of bioinformatics experts. The dataset contains 5,600 high-quality samples covering five core tasks across three stages: Screening, Quality Control, and Phenotype Annotation. Our evaluation of eight LLMs reveals that general-purpose reasoning models significantly outperform random baselines in phage contig identification and host prediction, demonstrating promising potential for genomic understanding. However, they exhibit significant limitations in complex reasoning tasks involving long-range dependencies and fine-grained functional localization. These findings highlight the necessity of developing next-generation models with enhanced reasoning capabilities for biological sequences.