arXiv subjects

Wenjie Du

Publications and source records attributed to Wenjie Du.

36 records · Page 2Linked to original sources

arXiv2025

ModuLM: Enabling Modular and Multimodal Molecular Relational Learning with Large Language Models

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.

cs.LG↗

arXiv2025

Deep Learning for Multivariate Time Series Imputation: A Survey

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.

cs.LG↗

arXiv2025

LLM-Explorer: Towards Efficient and Affordable LLM-based Exploration for Mobile Apps

Large language models (LLMs) have opened new opportunities for automated mobile app exploration, an important and challenging problem that used to suffer from the difficulty of generating meaningful UI interactions. However, existing LLM-based exploration approaches rely heavily on LLMs to generate actions in almost every step, leading to a huge cost of token fees and computational resources. We argue that such extensive usage of LLMs is neither necessary nor effective, since many actions during exploration do not require, or may even be biased by the abilities of LLMs. Further, based on the insight that a precise and compact knowledge plays the central role for effective exploration, we introduce LLM-Explorer, a new exploration agent designed for efficiency and affordability. LLM-Explorer uses LLMs primarily for maintaining the knowledge instead of generating actions, and knowledge is used to guide action generation in a LLM-less manner. Based on a comparison with 5 strong baselines on 20 typical apps, LLM-Explorer was able to achieve the fastest and highest coverage among all automated app explorers, with over 148x lower cost than the state-of-the-art LLM-based approach.

cs.SE↗

arXiv2025

Soft causal learning for generalized molecule property prediction: An environment perspective

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.

cs.LG↗

arXiv2025

AutoDroid-V2: Boosting SLM-based GUI Agents via Code Generation

Large language models (LLMs) have brought exciting new advances to mobile UI agents, a long-standing research field that aims to complete arbitrary natural language tasks through mobile UI interactions. However, existing UI agents usually demand powerful large language models that are difficult to be deployed locally on end-users' devices, raising huge concerns about user privacy and centralized serving cost. Inspired by the remarkable coding abilities of recent small language models (SLMs), we propose to convert the UI task automation problem to a code generation problem, which can be effectively solved by an on-device SLM and efficiently executed with an on-device code interpreter. Unlike normal coding tasks that can be extensively pre-trained with public datasets, generating UI automation code is challenging due to the diversity, complexity, and variability of target apps. Therefore, we adopt a document-centered approach that automatically builds fine-grained API documentation for each app and generates diverse task samples based on this documentation. By guiding the agent with the synthetic documents and task samples, it learns to generate precise and efficient scripts to complete unseen tasks. Based on detailed comparisons with state-of-the-art mobile UI agents, our approach effectively improves the mobile task automation with significantly higher success rates and lower latency/token consumption. Code is open-sourced at https://github.com/MobileLLM/AutoDroid-V2.

cs.AI↗

arXiv2025

Beyond Random Missingness: Clinically Rethinking for Healthcare Time Series Imputation

This study investigates the impact of masking strategies on time series imputation models in healthcare settings. While current approaches predominantly rely on random masking for model evaluation, this practice fails to capture the structured nature of missing patterns in clinical data. Using the PhysioNet Challenge 2012 dataset, we analyse how different masking implementations affect both imputation accuracy and downstream clinical predictions across eleven imputation methods. Our results demonstrate that masking choices significantly influence model performance, while recurrent architectures show more consistent performance across strategies. Analysis of downstream mortality prediction reveals that imputation accuracy doesn't necessarily translate to optimal clinical prediction capabilities. Our findings emphasise the need for clinically-informed masking strategies that better reflect real-world missing patterns in healthcare data, suggesting current evaluation frameworks may need reconsideration for reliable clinical deployment.

cs.LG↗

arXiv2024

NovoBench: Benchmarking Deep Learning-based De Novo Peptide Sequencing Methods in Proteomics

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the high-throughput analysis of protein composition in biological tissues. Many deep learning methods have been developed for \emph{de novo} peptide sequencing task, i.e., predicting the peptide sequence for the observed mass spectrum. However, two key challenges seriously hinder the further advancement of this important task. Firstly, since there is no consensus for the evaluation datasets, the empirical results in different research papers are often not comparable, leading to unfair comparison. Secondly, the current methods are usually limited to amino acid-level or peptide-level precision and recall metrics. In this work, we present the first unified benchmark NovoBench for \emph{de novo} peptide sequencing, which comprises diverse mass spectrum data, integrated models, and comprehensive evaluation metrics. Recent impressive methods, including DeepNovo, PointNovo, Casanovo, InstaNovo, AdaNovo and $π$-HelixNovo are integrated into our framework. In addition to amino acid-level and peptide-level precision and recall, we evaluate the models' performance in terms of identifying post-tranlational modifications (PTMs), efficiency and robustness to peptide length, noise peaks and missing fragment ratio, which are important influencing factors while seldom be considered. Leveraging this benchmark, we conduct a large-scale study of current methods, report many insightful findings that open up new possibilities for future development.

q-bio.QM↗

arXiv2024

TSI-Bench: Benchmarking Time Series Imputation

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.

cs.LG↗

arXiv2024

FlexMol: A Flexible Toolkit for Benchmarking Molecular Relational Learning

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.

cs.LG↗

arXiv2024

Text-guided Diffusion Model for 3D Molecule Generation

The de novo generation of molecules with targeted properties is crucial in biology, chemistry, and drug discovery. Current generative models are limited to using single property values as conditions, struggling with complex customizations described in detailed human language. To address this, we propose the text guidance instead, and introduce TextSMOG, a new Text-guided Small Molecule Generation Approach via 3D Diffusion Model which integrates language and diffusion models for text-guided small molecule generation. This method uses textual conditions to guide molecule generation, enhancing both stability and diversity. Experimental results show TextSMOG's proficiency in capturing and utilizing information from textual descriptions, making it a powerful tool for generating 3D molecular structures in response to complex textual customizations.

cs.LG↗

arXiv2024

MolTC: Towards Molecular Relational Modeling In Language Models

Molecular Relational Learning (MRL), aiming to understand interactions between molecular pairs, plays a pivotal role in advancing biochemical research. Recently, the adoption of large language models (LLMs), known for their vast knowledge repositories and advanced logical inference capabilities, has emerged as a promising way for efficient and effective MRL. Despite their potential, these methods predominantly rely on the textual data, thus not fully harnessing the wealth of structural information inherent in molecular graphs. Moreover, the absence of a unified framework exacerbates the issue of information underutilization, as it hinders the sharing of interaction mechanism learned across diverse datasets. To address these challenges, this work proposes a novel LLM-based multi-modal framework for Molecular inTeraction prediction following Chain-of-Thought (CoT) theory, termed MolTC, which effectively integrate graphical information of two molecules in pair. To train MolTC efficiently, we introduce a Multi-hierarchical CoT concept to refine its training paradigm, and conduct a comprehensive Molecular Interactive Instructions dataset for the development of biochemical LLMs involving MRL. Our experiments, conducted across various datasets involving over 4,000,000 molecular pairs, exhibit the superiority of our method over current GNN and LLM-based baselines. Code is available at https://github.com/MangoKiller/MolTC.

q-bio.QM↗

arXiv2024

AdaNovo: Adaptive \emph{De Novo} Peptide Sequencing with Conditional Mutual Information

Tandem mass spectrometry has played a pivotal role in advancing proteomics, enabling the analysis of protein composition in biological samples. Despite the development of various deep learning methods for identifying amino acid sequences (peptides) responsible for observed spectra, challenges persist in \emph{de novo} peptide sequencing. Firstly, prior methods struggle to identify amino acids with post-translational modifications (PTMs) due to their lower frequency in training data compared to canonical amino acids, further resulting in decreased peptide-level identification precision. Secondly, diverse types of noise and missing peaks in mass spectra reduce the reliability of training data (peptide-spectrum matches, PSMs). To address these challenges, we propose AdaNovo, a novel framework that calculates conditional mutual information (CMI) between the spectrum and each amino acid/peptide, using CMI for adaptive model training. Extensive experiments demonstrate AdaNovo's state-of-the-art performance on a 9-species benchmark, where the peptides in the training set are almost completely disjoint from the peptides of the test sets. Moreover, AdaNovo excels in identifying amino acids with PTMs and exhibits robustness against data noise. The supplementary materials contain the official code.

q-bio.QM↗

arXiv2023

Trusta: Reasoning about Assurance Cases with Formal Methods and Large Language Models

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.

cs.SE↗

arXiv2023

SAITS: Self-Attention-based Imputation for Time Series

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.

cs.LG↗

arXiv2022

Forecasting Loss of Signal in Optical Networks with Machine Learning

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.

cs.NI↗

arXiv2015

Modal Characterisations of Behavioural Pseudometrics

For the model of probabilistic labelled transition systems that allow for the co-existence of nondeterminism and probabilities, we present two notions of bisimulation metrics: one is state-based and the other is distribution-based. We provide a sound and complete modal characterisation for each of them, using real-valued modal logics based on the Hennessy-Milner logic. The logic for characterising the state-based metric is much simpler than an earlier logic by Desharnais et al. as it uses only two non-expansive operators rather than the general class of non-expansive operators.

cs.LO↗

arXiv2011

Logical, Metric, and Algorithmic Characterisations of Probabilistic Bisimulation

Many behavioural equivalences or preorders for probabilistic processes involve a lifting operation that turns a relation on states into a relation on distributions of states. We show that several existing proposals for lifting relations can be reconciled to be different presentations of essentially the same lifting operation. More interestingly, this lifting operation nicely corresponds to the Kantorovich metric, a fundamental concept used in mathematics to lift a metric on states to a metric on distributions of states, besides the fact the lifting operation is related to the maximum flow problem in optimisation theory. The lifting operation yields a neat notion of probabilistic bisimulation, for which we provide logical, metric, and algorithmic characterisations. Specifically, we extend the Hennessy-Milner logic and the modal mu-calculus with a new modality, resulting in an adequate and an expressive logic for probabilistic bisimilarity, respectively. The correspondence of the lifting operation and the Kantorovich metric leads to a natural characterisation of bisimulations as pseudometrics which are post-fixed points of a monotone function. We also present an "on the fly" algorithm to check if two states in a finitary system are related by probabilistic bisimilarity, exploiting the close relationship between the lifting operation and the maximum flow problem.

cs.LO↗

arXiv2008

Study of Bc -> BP,BV Decays with QCD Factorization

The Bc -> BP,BV decays are studied with the QCD factorization approach (where P and V denote pseudoscalar and vector mesons, respectively). Considering the contributions of both current-current and penguin operators, the amplitudes of branching ratios are estimated at the leading approximation. We find that the contributions of the penguin operators are very small due to the serious suppression by the CKM elements. The most promising decay modes are Bc -> Bs Pi, Bs rho, which might be easily detected at hadron colliders.

hep-ph↗