Junjie Chen

Jiahao Li, Zhourun Wu, Wenhao Lin et al.

Motivation: Enhancers are important cis-regulatory elements that regulate a wide range of biological functions and enhance the transcription of target genes. Although many feature extraction methods have been proposed to improve the performance of enhancer identification, they cannot learn position-related multiscale contextual information from raw DNA sequences. Results: In this article, we propose a novel enhancer identification method (iEnhancer-ELM) based on BERT-like enhancer language models. iEnhancer-ELM tokenizes DNA sequences with multi-scale k-mers and extracts contextual information of different scale k-mers related with their positions via an multi-head attention mechanism. We first evaluate the performance of different scale k-mers, then ensemble them to improve the performance of enhancer identification. The experimental results on two popular benchmark datasets show that our model outperforms stateof-the-art methods. We further illustrate the interpretability of iEnhancer-ELM. For a case study, we discover 30 enhancer motifs via a 3-mer-based model, where 12 of motifs are verified by STREME and JASPAR, demonstrating our model has a potential ability to unveil the biological mechanism of enhancer. Availability and implementation: The models and associated code are available at https://github.com/chen-bioinfo/iEnhancer-ELM Contact: junjiechen@hit.edu.cn Supplementary information: Supplementary data are available at Bioinformatics Advances online.

Lin Yang, Junjie Chen, Shutao Gao et al.

The rapid growth of deep learning (DL) has spurred interest in enhancing log-based anomaly detection. This approach aims to extract meaning from log events (log message templates) and develop advanced DL models for anomaly detection. However, these DL methods face challenges like heavy reliance on training data, labels, and computational resources due to model complexity. In contrast, traditional machine learning and data mining techniques are less data-dependent and more efficient but less effective than DL. To make log-based anomaly detection more practical, the goal is to enhance traditional techniques to match DL's effectiveness. Previous research in a different domain (linking questions on Stack Overflow) suggests that optimized traditional techniques can rival state-of-the-art DL methods. Drawing inspiration from this concept, we conducted an empirical study. We optimized the unsupervised PCA (Principal Component Analysis), a traditional technique, by incorporating lightweight semantic-based log representation. This addresses the issue of unseen log events in training data, enhancing log representation. Our study compared seven log-based anomaly detection methods, including four DL-based, two traditional, and the optimized PCA technique, using public and industrial datasets. Results indicate that the optimized unsupervised PCA technique achieves similar effectiveness to advanced supervised/semi-supervised DL methods while being more stable with limited training data and resource-efficient. This demonstrates the adaptability and strength of traditional techniques through small yet impactful adaptations.

Junjie Chen, Xuyang Liu, Zichen Wen et al.

Large vision-language models (LVLMs) have demonstrated remarkable capabilities in multimodal understanding tasks. However, the increasing demand for high-resolution image and long-video understanding results in substantial token counts, leading to reduced inference efficiency. Token compression offers a direct solution by reducing the number of tokens to be processed, thereby improving computational efficiency. Through extensive analysis, we identify two critical limitations in existing inner-LLM token compression methods: positional bias and incompatibility with efficient operators, which hinder their practical deployment for LVLM acceleration. This paper presents the first approach from a token variation perspective, revealing that visual token variations within LLMs exhibit task-agnostic properties. We propose Variation-aware Vision Token Dropping (\textit{i.e.}, \textbf{V$^2$Drop}), which progressively removes visual tokens with minimal variation during LVLM inference, thereby enhancing computational efficiency. Extensive experiments across multiple models and benchmarks demonstrate that our V$^2$Drop is able to maintain \textbf{94.0\%} and \textbf{98.6\%} of the original model performance for image and video understanding tasks respectively, while reducing LLM generation latency by \textbf{31.5\%} and \textbf{74.2\%}. When combined with efficient operators, V$^2$Drop further reduces GPU peak memory usage.

Dong Huang, Jie M. Zhang, Qingwen Bu et al.

As the adoption of LLMs becomes more widespread in software coding ecosystems, a pressing issue has emerged: does the generated code contain social bias and unfairness, such as those related to age, gender, and race? This issue concerns the integrity, fairness, and ethical foundation of software applications that depend on the code generated by these models but are underexplored in the literature. This paper presents a novel bias testing framework that is specifically designed for code generation tasks. Based on this framework, we conduct an extensive empirical study on the biases in code generated by five widely studied LLMs (i.e., PALM-2-CodeChat-bison, Claude-instant-1, GPT-3.5-turbo, GPT-4-turbo, and GPT-4). Our findings reveal that biases are prevalent. For example, 13.47% to 49.10% of the codes generated by these LLMs have biased behaviors towards gender. Moreover, we study five bias mitigation prompt strategies that are commonly used in current code generation scenarios, i.e., zero-shot, one-shot, few-shot, and two Chain-of-Thought (CoT) prompts, with and without provided feedback-driven refinement. Our evaluation results illustrate that using direct prompt engineering strategies has limited effectiveness in mitigating bias, but our test execution feedback can help to reduce the ratio of code biases to a large extent (e.g., from 59.88% to 4.79% for GPT-4).

Xiangheng He, Junjie Chen, Georgios Rizos et al.

Emotional Voice Conversion (EVC) aims to convert the emotional style of a source speech signal to a target style while preserving its content and speaker identity information. Previous emotional conversion studies do not disentangle emotional information from emotion-independent information that should be preserved, thus transforming it all in a monolithic manner and generating audio of low quality, with linguistic distortions. To address this distortion problem, we propose a novel StarGAN framework along with a two-stage training process that separates emotional features from those independent of emotion by using an autoencoder with two encoders as the generator of the Generative Adversarial Network (GAN). The proposed model achieves favourable results in both the objective evaluation and the subjective evaluation in terms of distortion, which reveals that the proposed model can effectively reduce distortion. Furthermore, in data augmentation experiments for end-to-end speech emotion recognition, the proposed StarGAN model achieves an increase of 2% in Micro-F1 and 5% in Macro-F1 compared to the baseline StarGAN model, which indicates that the proposed model is more valuable for data augmentation.

Ensheng Shi, Yanlin Wang, Lun Du et al.

Source code summaries are important for program comprehension and maintenance. However, there are plenty of programs with missing, outdated, or mismatched summaries. Recently, deep learning techniques have been exploited to automatically generate summaries for given code snippets. To achieve a profound understanding of how far we are from solving this problem and provide suggestions to future research, in this paper, we conduct a systematic and in-depth analysis of 5 state-of-the-art neural code summarization models on 6 widely used BLEU variants, 4 pre-processing operations and their combinations, and 3 widely used datasets. The evaluation results show that some important factors have a great influence on the model evaluation, especially on the performance of models and the ranking among the models. However, these factors might be easily overlooked. Specifically, (1) the BLEU metric widely used in existing work of evaluating code summarization models has many variants. Ignoring the differences among these variants could greatly affect the validity of the claimed results. Furthermore, we conduct human evaluations and find that the metric BLEU-DC is most correlated to human perception; (2) code pre-processing choices can have a large (from -18\% to +25\%) impact on the summarization performance and should not be neglected. We also explore the aggregation of pre-processing combinations and boost the performance of models; (3) some important characteristics of datasets (corpus sizes, data splitting methods, and duplication ratios) have a significant impact on model evaluation. Based on the experimental results, we give actionable suggestions for evaluating code summarization and choosing the best method in different scenarios. We also build a shared code summarization toolbox to facilitate future research.

Akiko Aizawa, Frederic Bergeron, Junjie Chen et al.

The global pandemic of COVID-19 has made the public pay close attention to related news, covering various domains, such as sanitation, treatment, and effects on education. Meanwhile, the COVID-19 condition is very different among the countries (e.g., policies and development of the epidemic), and thus citizens would be interested in news in foreign countries. We build a system for worldwide COVID-19 information aggregation containing reliable articles from 10 regions in 7 languages sorted by topics. Our reliable COVID-19 related website dataset collected through crowdsourcing ensures the quality of the articles. A neural machine translation module translates articles in other languages into Japanese and English. A BERT-based topic-classifier trained on our article-topic pair dataset helps users find their interested information efficiently by putting articles into different categories.

Ning Xie, Ji Hu, Junjie Chen et al.

This paper concerns the problem of detecting the use of information hiding at anti-copying 2D barcodes. Prior hidden information detection schemes are either heuristicbased or Machine Learning (ML) based. The key limitation of prior heuristics-based schemes is that they do not answer the fundamental question of why the information hidden at a 2D barcode can be detected. The key limitation of prior MLbased information schemes is that they lack robustness because a printed 2D barcode is very much environmentally dependent, and thus an information hiding detection scheme trained in one environment often does not work well in another environment. In this paper, we propose two hidden information detection schemes at the existing anti-copying 2D barcodes. The first scheme is to directly use the pixel distance to detect the use of an information hiding scheme in a 2D barcode, referred as to the Pixel Distance Based Detection (PDBD) scheme. The second scheme is first to calculate the variance of the raw signal and the covariance between the recovered signal and the raw signal, and then based on the variance results, detects the use of information hiding scheme in a 2D barcode, referred as to the Pixel Variance Based Detection (PVBD) scheme. Moreover, we design advanced IC attacks to evaluate the security of two existing anti-copying 2D barcodes. We implemented our schemes and conducted extensive performance comparison between our schemes and prior schemes under different capturing devices, such as a scanner and a camera phone. Our experimental results show that the PVBD scheme can correctly detect the existence of the hidden information at both the 2LQR code and the LCAC 2D barcode. Moreover, the probability of successfully attacking of our IC attacks achieves 0.6538 for the 2LQR code and 1 for the LCAC 2D barcode.