Zhiyuan Chen

Zhiyuan Chen, Tianhao Chen, Chenggang Xie et al.

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

Yang Qin, Chao Chen, Zhihang Fu et al.

Despite the significant advancements in Text-to-SQL (Text2SQL) facilitated by large language models (LLMs), the latest state-of-the-art techniques are still trapped in the in-context learning of closed-source LLMs (e.g., GPT-4), which limits their applicability in open scenarios. To address this challenge, we propose a novel RObust mUltitask Tuning and collaboration mEthod (ROUTE) to improve the comprehensive capabilities of open-source LLMs for Text2SQL, thereby providing a more practical solution. Our approach begins with multi-task supervised fine-tuning (SFT) using various synthetic training data related to SQL generation. Unlike existing SFT-based Text2SQL methods, we introduced several additional SFT tasks, including schema linking, noise correction, and continuation writing. Engaging in a variety of SQL generation tasks enhances the model's understanding of SQL syntax and improves its ability to generate high-quality SQL queries. Additionally, inspired by the collaborative modes of LLM agents, we introduce a Multitask Collaboration Prompting (MCP) strategy. This strategy leverages collaboration across several SQL-related tasks to reduce hallucinations during SQL generation, thereby maximizing the potential of enhancing Text2SQL performance through explicit multitask capabilities. Extensive experiments and in-depth analyses have been performed on eight open-source LLMs and five widely-used benchmarks. The results demonstrate that our proposal outperforms the latest Text2SQL methods and yields leading performance.

Zhiyuan Chen, Guang Yao, Wennan Ma et al.

Many efforts have been devoted to designing sampling, mining, and weighting strategies in high-level deep metric learning (DML) loss objectives. However, little attention has been paid to low-level but essential data transformation. In this paper, we develop a novel mechanism, the independent domain embedding augmentation learning ({IDEAL}) method. It can simultaneously learn multiple independent embedding spaces for multiple domains generated by predefined data transformations. Our IDEAL is orthogonal to existing DML techniques and can be seamlessly combined with prior DML approaches for enhanced performance. Empirical results on visual retrieval tasks demonstrate the superiority of the proposed method. For example, the IDEAL improves the performance of MS loss by a large margin, 84.5\% $\rightarrow$ 87.1\% on Cars-196, and 65.8\% $\rightarrow$ 69.5\% on CUB-200 at Recall$@1$. Our IDEAL with MS loss also achieves the new state-of-the-art performance on three image retrieval benchmarks, \ie, \emph{Cars-196}, \emph{CUB-200}, and \emph{SOP}. It outperforms the most recent DML approaches, such as Circle loss and XBM, significantly. The source code and pre-trained models of our method will be available at\emph{\url{https://github.com/emdata-ailab/IDEAL}}.

Zhiyuan Chen, Wei Lu, Radhika Bhong et al.

A stable, reliable, and controllable orbit lock system is crucial to an electron (or ion) accelerator because the beam orbit and beam energy instability strongly affect the quality of the beam delivered to experimental halls. Currently, when the orbit lock system fails operators must manually intervene. This paper develops a Machine Learning based fault detection methodology to identify orbit lock anomalies and notify accelerator operations staff of the off-normal behavior. Our method is unsupervised, so it does not require labeled data. It uses Long-Short Memory Networks (LSTM) Auto Encoder to capture normal patterns and predict future values of monitoring sensors in the orbit lock system. Anomalies are detected when the prediction error exceeds a threshold. We conducted experiments using monitoring data from Jefferson Lab's Continuous Electron Beam Accelerator Facility (CEBAF). The results are promising: the percentage of real anomalies identified by our solution is 68.6%-89.3% using monitoring data of a single component in the orbit lock control system. The accuracy can be as high as 82%.

Siyuan Li, Zicheng Liu, Zelin Zang et al.

Unsupervised representation learning (URL), which learns compact embeddings of high-dimensional data without supervision, has made remarkable progress recently. However, the development of URLs for different requirements is independent, which limits the generalization of the algorithms, especially prohibitive as the number of tasks grows. For example, dimension reduction methods, t-SNE, and UMAP optimize pair-wise data relationships by preserving the global geometric structure, while self-supervised learning, SimCLR, and BYOL focus on mining the local statistics of instances under specific augmentations. To address this dilemma, we summarize and propose a unified similarity-based URL framework, GenURL, which can smoothly adapt to various URL tasks. In this paper, we regard URL tasks as different implicit constraints on the data geometric structure that help to seek optimal low-dimensional representations that boil down to data structural modeling (DSM) and low-dimensional transformation (LDT). Specifically, DMS provides a structure-based submodule to describe the global structures, and LDT learns compact low-dimensional embeddings with given pretext tasks. Moreover, an objective function, General Kullback-Leibler divergence (GKL), is proposed to connect DMS and LDT naturally. Comprehensive experiments demonstrate that GenURL achieves consistent state-of-the-art performance in self-supervised visual learning, unsupervised knowledge distillation (KD), graph embeddings (GE), and dimension reduction.

Kasra Babaei, ZhiYuan Chen, Tomas Maul

This paper proposes an autoencoder (AE) that is used for improving the performance of once-class classifiers for the purpose of detecting anomalies. Traditional one-class classifiers (OCCs) perform poorly under certain conditions such as high-dimensionality and sparsity. Also, the size of the training set plays an important role on the performance of one-class classifiers. Autoencoders have been widely used for obtaining useful latent variables from high-dimensional datasets. In the proposed approach, the AE is capable of deriving meaningful features from high-dimensional datasets while doing data augmentation at the same time. The augmented data is used for training the OCC algorithms. The experimental results show that the proposed approach enhance the performance of OCC algorithms and also outperforms other well-known approaches.

Pooja Parameshwarappa, Zhiyuan Chen, Gunes Koru

Publishing physical activity data can facilitate reproducible health-care research in several areas such as population health management, behavioral health research, and management of chronic health problems. However, publishing such data also brings high privacy risks related to re-identification which makes anonymization necessary. One of the challenges in anonymizing physical activity data collected periodically is its sequential nature. The existing anonymization techniques work sufficiently for cross-sectional data but have high computational costs when applied directly to sequential data. This paper presents an effective anonymization approach, Multi-level Clustering based anonymization to anonymize physical activity data. Compared with the conventional methods, the proposed approach improves time complexity by reducing the clustering time drastically. While doing so, it preserves the utility as much as the conventional approaches.

Ashwinkumar Ganesan, Pooja Parameshwarappa, Akshay Peshave et al.

Evolving cybersecurity threats are a persistent challenge for systemadministrators and security experts as new malwares are continu-ally released. Attackers may look for vulnerabilities in commercialproducts or execute sophisticated reconnaissance campaigns tounderstand a targets network and gather information on securityproducts like firewalls and intrusion detection / prevention systems(network or host-based). Many new attacks tend to be modificationsof existing ones. In such a scenario, rule-based systems fail to detectthe attack, even though there are minor differences in conditions /attributes between rules to identify the new and existing attack. Todetect these differences the IDS must be able to isolate the subset ofconditions that are true and predict the likely conditions (differentfrom the original) that must be observed. In this paper, we proposeaprobabilistic abductive reasoningapproach that augments an exist-ing rule-based IDS (snort [29]) to detect these evolved attacks by (a)Predicting rule conditions that are likely to occur (based on existingrules) and (b) able to generate new snort rules when provided withseed rule (i.e. a starting rule) to reduce the burden on experts toconstantly update them. We demonstrate the effectiveness of theapproach by generating new rules from the snort 2012 rules set andtesting it on the MACCDC 2012 dataset [6].