Wenjie Du

Zezhong Chen, Yuxin Deng, Wenjie Du

Assurance cases can be used to argue for the safety of products in safety engineering. In safety-critical areas, the construction of assurance cases is indispensable. Trustworthiness Derivation Trees (TDTs) enhance assurance cases by incorporating formal methods, rendering it possible for automatic reasoning about assurance cases. We present Trustworthiness Derivation Tree Analyzer (Trusta), a desktop application designed to automatically construct and verify TDTs. The tool has a built-in Prolog interpreter in its backend, and is supported by the constraint solvers Z3 and MONA. Therefore, it can solve constraints about logical formulas involving arithmetic, sets, Horn clauses etc. Trusta also utilizes large language models to make the creation and evaluation of assurance cases more convenient. It allows for interactive human examination and modification. We evaluated top language models like ChatGPT-3.5, ChatGPT-4, and PaLM 2 for generating assurance cases. Our tests showed a 50%-80% similarity between machine-generated and human-created cases. In addition, Trusta can extract formal constraints from text in natural languages, facilitating an easier interpretation and validation process. This extraction is subject to human review and correction, blending the best of automated efficiency with human insight. To our knowledge, this marks the first integration of large language models in automatic creating and reasoning about assurance cases, bringing a novel approach to a traditional challenge. Through several industrial case studies, Trusta has proven to quickly find some subtle issues that are typically missed in manual inspection, demonstrating its practical value in enhancing the assurance case development process.

Jun Wang, Wenjie Du, Yiyuan Yang et al.

Missing values are ubiquitous in multivariate time series (MTS) data, posing significant challenges for accurate analysis and downstream applications. In recent years, deep learning-based methods have successfully handled missing data by leveraging complex temporal dependencies and learned data distributions. In this survey, we provide a comprehensive summary of deep learning approaches for multivariate time series imputation (MTSI) tasks. We propose a novel taxonomy that categorizes existing methods based on two key perspectives: imputation uncertainty and neural network architecture. Furthermore, we summarize existing MTSI toolkits with a particular emphasis on the PyPOTS Ecosystem, which provides an integrated and standardized foundation for MTSI research. Finally, we discuss key challenges and future research directions, which give insight for further MTSI research. This survey aims to serve as a valuable resource for researchers and practitioners in the field of time series analysis and missing data imputation tasks.A well-maintained MTSI paper and tool list are available at https://github.com/WenjieDu/Awesome_Imputation.

Wenjie Du, Jun Wang, Linglong Qian et al.

Effective imputation is a crucial preprocessing step for time series analysis. Despite the development of numerous deep learning algorithms for time series imputation, the community lacks standardized and comprehensive benchmark platforms to effectively evaluate imputation performance across different settings. Moreover, although many deep learning forecasting algorithms have demonstrated excellent performance, whether their modelling achievements can be transferred to time series imputation tasks remains unexplored. To bridge these gaps, we develop TSI-Bench, the first (to our knowledge) comprehensive benchmark suite for time series imputation utilizing deep learning techniques. The TSI-Bench pipeline standardizes experimental settings to enable fair evaluation of imputation algorithms and identification of meaningful insights into the influence of domain-appropriate missing rates and patterns on model performance. Furthermore, TSI-Bench innovatively provides a systematic paradigm to tailor time series forecasting algorithms for imputation purposes. Our extensive study across 34,804 experiments, 28 algorithms, and 8 datasets with diverse missingness scenarios demonstrates TSI-Bench's effectiveness in diverse downstream tasks and potential to unlock future directions in time series imputation research and analysis. All source code and experiment logs are released at https://github.com/WenjieDu/AwesomeImputation.

Wenjie Du, Yiyuan Yang, Linglong Qian et al.

PyPOTS is an open-source Python library dedicated to data mining and analysis on multivariate partially-observed time series with missing values. Particularly, it provides easy access to diverse algorithms categorized into five tasks: imputation, forecasting, anomaly detection, classification, and clustering. The included models represent a diverse set of methodological paradigms, offering a unified and well-documented interface suitable for both academic research and practical applications. With robustness and scalability in its design philosophy, best practices of software construction, for example, unit testing, continuous integration and continuous delivery, code coverage, maintainability evaluation, interactive tutorials, and parallelization, are carried out as principles during the development of PyPOTS. The toolbox is available on PyPI, Anaconda, and Docker. PyPOTS is open source and publicly available on GitHub https://github.com/WenjieDu/PyPOTS.

Wenjie Du, David Cote, Yan Liu

Missing data in time series is a pervasive problem that puts obstacles in the way of advanced analysis. A popular solution is imputation, where the fundamental challenge is to determine what values should be filled in. This paper proposes SAITS, a novel method based on the self-attention mechanism for missing value imputation in multivariate time series. Trained by a joint-optimization approach, SAITS learns missing values from a weighted combination of two diagonally-masked self-attention (DMSA) blocks. DMSA explicitly captures both the temporal dependencies and feature correlations between time steps, which improves imputation accuracy and training speed. Meanwhile, the weighted-combination design enables SAITS to dynamically assign weights to the learned representations from two DMSA blocks according to the attention map and the missingness information. Extensive experiments quantitatively and qualitatively demonstrate that SAITS outperforms the state-of-the-art methods on the time-series imputation task efficiently and reveal SAITS' potential to improve the learning performance of pattern recognition models on incomplete time-series data from the real world. The code is open source on GitHub at https://github.com/WenjieDu/SAITS.

Sizhe Liu, Jun Xia, Lecheng Zhang et al.

Molecular relational learning (MRL) is crucial for understanding the interaction behaviors between molecular pairs, a critical aspect of drug discovery and development. However, the large feasible model space of MRL poses significant challenges to benchmarking, and existing MRL frameworks face limitations in flexibility and scope. To address these challenges, avoid repetitive coding efforts, and ensure fair comparison of models, we introduce FlexMol, a comprehensive toolkit designed to facilitate the construction and evaluation of diverse model architectures across various datasets and performance metrics. FlexMol offers a robust suite of preset model components, including 16 drug encoders, 13 protein sequence encoders, 9 protein structure encoders, and 7 interaction layers. With its easy-to-use API and flexibility, FlexMol supports the dynamic construction of over 70, 000 distinct combinations of model architectures. Additionally, we provide detailed benchmark results and code examples to demonstrate FlexMol's effectiveness in simplifying and standardizing MRL model development and comparison.

Limin Li, Kuo Yang, Wenjie Du et al.

Learning on molecule graphs has become an increasingly important topic in AI for science, which takes full advantage of AI to facilitate scientific discovery. Existing solutions on modeling molecules utilize Graph Neural Networks (GNNs) to achieve representations but they mostly fail to adapt models to out-of-distribution (OOD) samples. Although recent advances on OOD-oriented graph learning have discovered the invariant rationale on graphs, they still ignore three important issues, i.e., 1) the expanding atom patterns regarding environments on graphs lead to failures of invariant rationale based models, 2) the associations between discovered molecular subgraphs and corresponding properties are complex where causal substructures cannot fully interpret the labels. 3) the interactions between environments and invariances can influence with each other thus are challenging to be modeled. To this end, we propose a soft causal learning framework, to tackle the unresolved OOD challenge in molecular science, from the perspective of fully modeling the molecule environments and bypassing the invariant subgraphs. Specifically, we first incorporate chemistry theories into our graph growth generator to imitate expaned environments, and then devise an GIB-based objective to disentangle environment from whole graphs and finally introduce a cross-attention based soft causal interaction, which allows dynamic interactions between environments and invariances. We perform experiments on seven datasets by imitating different kinds of OOD generalization scenarios. Extensive comparison, ablation experiments as well as visualized case studies demonstrate well generalization ability of our proposal.

Zhuo Chen, Yizhen Zheng, Huan Yee Koh et al.

Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies have explored the integration of MRL with LLMs and achieved promising results. However, the increasing availability of diverse LLMs and molecular structure encoders has significantly expanded the model space, presenting major challenges for benchmarking. Currently, there is no LLM framework that supports both flexible molecular input formats and dynamic architectural switching. To address these challenges, reduce redundant coding, and ensure fair model comparison, we propose ModuLM, a framework designed to support flexible LLM-based model construction and diverse molecular representations. ModuLM provides a rich suite of modular components, including 8 types of 2D molecular graph encoders, 11 types of 3D molecular conformation encoders, 7 types of interaction layers, and 7 mainstream LLM backbones. Owing to its highly flexible model assembly mechanism, ModuLM enables the dynamic construction of over 50,000 distinct model configurations. In addition, we provide comprehensive results to demonstrate the effectiveness of ModuLM in supporting LLM-based MRL tasks.

Wenjie Du, David Cote, Chris Barber et al.

Loss of Signal (LOS) represents a significant cost for operators of optical networks. By studying large sets of real-world Performance Monitoring (PM) data collected from six international optical networks, we find that it is possible to forecast LOS events with good precision 1-7 days before they occur, albeit at relatively low recall, with supervised machine learning (ML). Our study covers twelve facility types, including 100G lines and ETH10G clients. We show that the precision for a given network improves when training on multiple networks simultaneously relative to training on an individual network. Furthermore, we show that it is possible to forecast LOS from all facility types and all networks with a single model, whereas fine-tuning for a particular facility or network only brings modest improvements. Hence our ML models remain effective for optical networks previously unknown to the model, which makes them usable for commercial applications.