Jinbo Li

Jinbo Li, Hesam Izakian, Witold Pedrycz et al.

Multivariate time series data come as a collection of time series describing different aspects of a certain temporal phenomenon. Anomaly detection in this type of data constitutes a challenging problem yet with numerous applications in science and engineering because anomaly scores come from the simultaneous consideration of the temporal and variable relationships. In this paper, we propose a clustering-based approach to detect anomalies concerning the amplitude and the shape of multivariate time series. First, we use a sliding window to generate a set of multivariate subsequences and thereafter apply an extended fuzzy clustering to reveal a structure present within the generated multivariate subsequences. Finally, a reconstruction criterion is employed to reconstruct the multivariate subsequences with the optimal cluster centers and the partition matrix. We construct a confidence index to quantify a level of anomaly detected in the series and apply Particle Swarm Optimization as an optimization vehicle for the problem of anomaly detection. Experimental studies completed on several synthetic and six real-world datasets suggest that the proposed methods can detect the anomalies in multivariate time series. With the help of available clusters revealed by the extended fuzzy clustering, the proposed framework can detect anomalies in the multivariate time series and is suitable for identifying anomalous amplitude and shape patterns in various application domains such as health care, weather data analysis, finance, and disease outbreak detection.

Jinbo Li, Witold Pedrycz, Iqbal Jamal

In this study, we develop an approach to multivariate time series anomaly detection focused on the transformation of multivariate time series to univariate time series. Several transformation techniques involving Fuzzy C-Means (FCM) clustering and fuzzy integral are studied. In the sequel, a Hidden Markov Model (HMM), one of the commonly encountered statistical methods, is engaged here to detect anomalies in multivariate time series. We construct HMM-based anomaly detectors and in this context compare several transformation methods. A suite of experimental studies along with some comparative analysis is reported.

Jinbo Li, Peng Liu, Long Chen et al.

The integration of different learning paradigms has long been a focus of machine learning research, aimed at overcoming the inherent limitations of individual methods. Fuzzy rule-based models excel in interpretability and have seen widespread application across diverse fields. However, they face challenges such as complex design specifications and scalability issues with large datasets. The fusion of different techniques and strategies, particularly Gradient Boosting, with Fuzzy Rule-Based Models offers a robust solution to these challenges. This paper proposes an Integrated Fusion Framework that merges the strengths of both paradigms to enhance model performance and interpretability. At each iteration, a Fuzzy Rule-Based Model is constructed and controlled by a dynamic factor to optimize its contribution to the overall ensemble. This control factor serves multiple purposes: it prevents model dominance, encourages diversity, acts as a regularization parameter, and provides a mechanism for dynamic tuning based on model performance, thus mitigating the risk of overfitting. Additionally, the framework incorporates a sample-based correction mechanism that allows for adaptive adjustments based on feedback from a validation set. Experimental results substantiate the efficacy of the presented gradient boosting framework for fuzzy rule-based models, demonstrating performance enhancement, especially in terms of mitigating overfitting and complexity typically associated with many rules. By leveraging an optimal factor to govern the contribution of each model, the framework improves performance, maintains interpretability, and simplifies the maintenance and update of the models.

Jiang Liu, Ge Qiu, Hao Fei et al.

With the rapid development of large language models (LLMs), more and more researchers have paid attention to information extraction based on LLMs. However, there are still some spaces to improve in the existing related methods. First, existing multimodal information extraction (MIE) methods usually employ natural language templates as the input and output of LLMs, which mismatch with the characteristics of information tasks that mostly include structured information such as entities and relations. Second, although a few methods have adopted structured and more IE-friendly code-style templates, they just explored their methods on text-only IE rather than multimodal IE. Moreover, their methods are more complex in design, requiring separate templates to be designed for each task. In this paper, we propose a Code-style Multimodal Information Extraction framework (Code-MIE) which formalizes MIE as unified code understanding and generation. Code-MIE has the following novel designs: (1) Entity attributes such as gender, affiliation are extracted from the text to guide the model to understand the context and role of entities. (2) Images are converted into scene graphs and visual features to incorporate rich visual information into the model. (3) The input template is constructed as a Python function, where entity attributes, scene graphs and raw text compose of the function parameters. In contrast, the output template is formalized as Python dictionaries containing all extraction results such as entities, relations, etc. To evaluate Code-MIE, we conducted extensive experiments on the M$^3$D, Twitter-15, Twitter-17, and MNRE datasets. The results show that our method achieves state-of-the-art performance compared to six competing baseline models, with 61.03\% and 60.49\% on the English and Chinese datasets of M$^3$D, and 76.04\%, 88.07\%, and 73.94\% on the other three datasets.

Tian Lan, Hao Duong Le, Jinbo Li et al.

Time series anomaly detection (TSAD) is a critical task, but developing models that generalize to unseen data in a zero-shot manner remains a major challenge. Prevailing foundation models for TSAD predominantly rely on reconstruction-based objectives, which suffer from a fundamental objective mismatch: they struggle to identify subtle anomalies while often misinterpreting complex normal patterns, leading to high rates of false negatives and positives. To overcome these limitations, we introduce \texttt{TimeRCD}, a novel foundation model for TSAD built upon a new pre-training paradigm: Relative Context Discrepancy (RCD). Instead of learning to reconstruct inputs, \texttt{TimeRCD} is explicitly trained to identify anomalies by detecting significant discrepancies between adjacent time windows. This relational approach, implemented with a standard Transformer architecture, enables the model to capture contextual shifts indicative of anomalies that reconstruction-based methods often miss. To facilitate this paradigm, we develop a large-scale, diverse synthetic corpus with token-level anomaly labels, providing the rich supervisory signal necessary for effective pre-training. Extensive experiments demonstrate that \texttt{TimeRCD} significantly outperforms existing general-purpose and anomaly-specific foundation models in zero-shot TSAD across diverse datasets. Our results validate the superiority of the RCD paradigm and establish a new, effective path toward building robust and generalizable foundation models for time series anomaly detection.

Rongbin Li, Wenbo Chen, Jinbo Li et al.

By leveraging GPT-4 for ontology narration, we developed GPTON to infuse structured knowledge into LLMs through verbalized ontology terms, achieving accurate text and ontology annotations for over 68% of gene sets in the top five predictions. Manual evaluations confirm GPTON's robustness, highlighting its potential to harness LLMs and structured knowledge to significantly advance biomedical research beyond gene set annotation.

Rongbin Li, Wenbo Chen, Zhao Li et al.

Single-cell RNA sequencing has transformed our ability to identify diverse cell types and their transcriptomic signatures. However, annotating these signatures-especially those involving poorly characterized genes-remains a major challenge. Traditional methods, such as Gene Set Enrichment Analysis (GSEA), depend on well-curated annotations and often perform poorly in these contexts. Large Language Models (LLMs) offer a promising alternative but struggle to represent complex biological knowledge within structured ontologies. To address this, we present BRAINCELL-AID (BRAINCELL-AID: https://biodataai.uth.edu/BRAINCELL-AID), a novel multi-agent AI system that integrates free-text descriptions with ontology labels to enable more accurate and robust gene set annotation. By incorporating retrieval-augmented generation (RAG), we developed a robust agentic workflow that refines predictions using relevant PubMed literature, reducing hallucinations and enhancing interpretability. Using this workflow, we achieved correct annotations for 77% of mouse gene sets among their top predictions. Applying this approach, we annotated 5,322 brain cell clusters from the comprehensive mouse brain cell atlas generated by the BRAIN Initiative Cell Census Network, enabling novel insights into brain cell function by identifying region-specific gene co-expression patterns and inferring functional roles of gene ensembles. BRAINCELL-AID also identifies Basal Ganglia-related cell types with neurologically meaningful descriptions. Hence, we create a valuable resource to support community-driven cell type annotation.

Tian Lan, Hao Duong Le, Jinbo Li et al.

Time-series anomaly detection (TSAD) increasingly demands explanations that articulate not only if an anomaly occurred, but also what pattern it exhibits and why it is anomalous. Leveraging the impressive explanatory capabilities of Large Language Models (LLMs), recent works have attempted to treat time series as text for explainable TSAD. However, this approach faces a fundamental challenge: LLMs operate on discrete tokens and struggle to directly process long, continuous signals. Consequently, naive time-to-text serialization suffers from a lack of contextual grounding and representation alignment between the two modalities. To address this gap, we introduce AXIS, a framework that conditions a frozen LLM for nuanced time-series understanding. Instead of direct serialization, AXIS enriches the LLM's input with three complementary hints derived from the series: (i) a symbolic numeric hint for numerical grounding, (ii) a context-integrated, step-aligned hint distilled from a pretrained time-series encoder to capture fine-grained dynamics, and (iii) a task-prior hint that encodes global anomaly characteristics. Furthermore, to facilitate robust evaluation of explainability, we introduce a new benchmark featuring multi-format questions and rationales that supervise contextual grounding and pattern-level semantics. Extensive experiments, including both LLM-based and human evaluations, demonstrate that AXIS yields explanations of significantly higher quality and achieves competitive detection accuracy compared to general-purpose LLMs, specialized time-series LLMs, and time-series Vision Language Models.