Zhi Quan Zhou

Zhi Quan Zhou, Dave Towey, Tsong Yueh Chen

Large language models (LLMs) are increasingly used to generate requirements specifications, design documents, code, and test cases. In contrast, much less attention has been given to a more difficult assurance problem: statically verifying whether implemented code satisfies requirements written in natural language. Conventional static analysis tools are effective at detecting coding defects and known vulnerability patterns, but they cannot determine whether program behavior matches intended business logic. Detecting such defects requires reasoning over the specification rather than the code alone. Software testing can expose some of these mismatches, but its effectiveness depends heavily on test design, executable artifacts, and runtime environments. This article presents a two-stage LLM-based workflow for addressing this challenge in an intelligent-vehicle cybersecurity case study. In the first stage, an AI-based rule miner extracts verifiable rules from natural-language requirements while explicitly identifying ambiguity, self-contradiction, and other non-verifiable statements. In the second stage, an AI-based code auditor checks implementation evidence against the extracted rules. Instead of asking a single LLM to directly verify code against lengthy natural-language specifications, the workflow introduces a structured intermediate representation to reduce hallucination, output variability, limited explainability, and context loss. The resulting approach is a requirement-aware and semantics-aware form of static analysis that complements software testing. By analyzing requirements and source code without requiring compilation, execution, or runtime environments, the method shifts verification and validation activities left in the development lifecycle. This LLM-based static analysis is also a new approach to addressing the test oracle problem.

Pratik Dutta, Matthew Obusan, Rekha Sathian et al.

Whole-genome sequencing (WGS) has revealed numerous non-coding short variants whose functional impacts remain poorly understood. Despite recent advances in deep-learning genomic approaches, accurately predicting and prioritizing clinically relevant mutations in gene regulatory regions remains a major challenge. Here we introduce Deep VRegulome, a deep-learning method for prediction and interpretation of functionally disruptive variants in the human regulome, which combines 700 DNABERT fine-tuned models, trained on vast amounts of ENCODE gene regulatory regions, with variant scoring, motif analysis, attention-based visualization, and survival analysis. We showcase its application on TCGA glioblastoma WGS dataset in prioritizing survival-associated mutations and regulatory regions. The analysis identified 572 splice-disrupting and 9,837 transcription-factor binding site altering mutations occurring in greater than 10% of glioblastoma samples. Survival analysis linked 1352 mutations and 563 disrupted regulatory regions to patient outcomes, enabling stratification via non-coding mutation signatures. All the code, fine-tuned models, and an interactive data portal are publicly available.

Jun Feng, Zixin Wang, Zhentao Zhang et al.

Multimodal Large Language Models (MLLMs) have demonstrated remarkable capabilities in visual mathematical reasoning across various existing benchmarks. However, these benchmarks are predominantly based on clean or processed multimodal inputs, without incorporating the images provided by real-world Kindergarten through 12th grade (K-12) educational users. To address this gap, we introduce MathReal, a meticulously curated dataset comprising 2,000 mathematical questions with images captured by handheld mobile devices in authentic scenarios. Each question is an image, containing the question text and visual element. We systematically classify the real images into three primary categories: image quality degradation, perspective variation, and irrelevant content interference, which are further delineated into 14 subcategories. Additionally, MathReal spans five core knowledge and ability categories, which encompass three question types and are divided into three difficulty levels. To comprehensively evaluate the multimodal mathematical reasoning abilities of state-of-the-art MLLMs in real-world scenarios, we design six experimental settings that enable a systematic analysis of their performance. Through extensive experimentation, we find that the problem-solving abilities of existing MLLMs are significantly challenged in realistic educational contexts. Based on this, we conduct a thorough analysis of their performance and error patterns, providing insights into their recognition, comprehension, and reasoning capabilities, and outlining directions for future improvements. Data and code: https://github.com/junfeng0288/MathReal.

Hao-Zhe Tan, Zhi Zhou, Yu-Feng Li et al.

Pre-trained Vision-Language Models (VLMs) are becoming increasingly popular across various visual tasks, and several open-sourced VLM variants have been released. However, selecting the best-performing pre-trained VLM for a specific downstream task is challenging since no single VLM can achieve promising performance on all downstream tasks, and evaluating all available VLMs is impossible due to time and data limitations. To address this problem, this paper proposes a novel paradigm to select and reuse VLM for downstream tasks, called Model Label Learning (MLL). The proposal contains three key modules: \emph{model labeling}, which assigns labels to each VLM to describe their specialty and utility; \emph{model selection}, which matches the requirements of the target task with model labels; and \emph{model reuse}, which applies selected VLMs to the target task in an ensemble manner. The proposal is highly computationally efficient and growable since the model labeling process is completed target task independent and the ability could grow with the number of candidate VLMs. We also introduce a new benchmark for evaluating VLM selection methods, including 49 VLMs and 17 target task datasets. Experimental results clearly demonstrate the effectiveness of the proposed method for selecting and reusing VLMs.

Zhi Zhou, Kun-Yang Yu, Lan-Zhe Guo et al.

Tabular data plays a vital role in various real-world scenarios and finds extensive applications. Although recent deep tabular models have shown remarkable success, they still struggle to handle data distribution shifts, leading to performance degradation when testing distributions change. To remedy this, a robust tabular model must adapt to generalize to unknown distributions during testing. In this paper, we investigate the problem of fully test-time adaptation (FTTA) for tabular data, where the model is adapted using only the testing data. We identify three key challenges: the existence of label and covariate distribution shifts, the lack of effective data augmentation, and the sensitivity of adaptation, which render existing FTTA methods ineffective for tabular data. To this end, we propose the Fully Test-time Adaptation for Tabular data, namely FTAT, which enables FTTA methods to robustly optimize the label distribution of predictions, adapt to shifted covariate distributions, and suit a variety of tasks and models effectively. We conduct comprehensive experiments on six benchmark datasets, which are evaluated using three metrics. The experimental results demonstrate that FTAT outperforms state-of-the-art methods by a margin.

Shi-Yu Tian, Zhi Zhou, Kun-Yang Yu et al.

Large language models (LLMs) have demonstrated impressive performance on reasoning tasks, including mathematical reasoning. However, the current evaluation mostly focuses on carefully constructed benchmarks and neglects the consideration of real-world reasoning problems that present missing or contradictory conditions, known as ill-defined problems. To further study this problem, we develop a largescale benchmark called Problems with Missing and Contradictory conditions (PMC) containing over 5,000 validated ill-defined mathematical problems. Our preliminary experiments through PMC reveal two challenges about existing methods: (1) traditional methods exhibit a trade-off between solving accuracy and rejection capabilities, and (2) formal methods struggle with modeling complex problems. To address these challenges, We develop Variable-Constraint Search (VCSEARCH), a trainingfree framework that leverages formal language to detect ill-defined problems, where a variableconstraint pair search strategy is incorporated to improve the modeling capability of formal language. Extensive experiments demonstrate that VCSEARCH improves the accuracy of identifying unsolvable problems by at least 12% across different LLMs, thus achieving stronger robust mathematical reasoning ability.

Liming Xu, Dave Towey, Andrew French et al.

Software testing is often hindered where it is impossible or impractical to determine the correctness of the behaviour or output of the software under test (SUT), a situation known as the oracle problem. An example of an area facing the oracle problem is automatic image classification, using machine learning to classify an input image as one of a set of predefined classes. An approach to software testing that alleviates the oracle problem is metamorphic testing (MT). While traditional software testing examines the correctness of individual test cases, MT instead examines the relations amongst multiple executions of test cases and their outputs. These relations are called metamorphic relations (MRs): if an MR is found to be violated, then a fault must exist in the SUT. This paper examines the problem of classifying images containing visually hidden markers called Artcodes, and applies MT to verify and enhance the trained classifiers. This paper further examines two MRs, Separation and Occlusion, and reports on their capability in verifying the image classification using one-way analysis of variance (ANOVA) in conjunction with three other statistical analysis methods: t-test (for unequal variances), Kruskal-Wallis test, and Dunnett's test. In addition to our previously-studied classifier, that used Random Forests, we introduce a new classifier that uses a support vector machine, and present its MR-augmented version. Experimental evaluations across a number of performance metrics show that the augmented classifiers can achieve better performance than non-augmented classifiers. This paper also analyses how the enhanced performance is obtained.