Entity matching (EM) is a critical step in entity resolution (ER). Recently, entity matching based on large language models (LLMs) has shown great promise. However, current LLM-based entity matching approaches typically follow a binary matching paradigm that ignores the global consistency among record relationships. In this paper, we investigate various methodologies for LLM-based entity matching that incorporate record interactions from different perspectives. Specifically, we comprehensively compare three representative strategies: matching, comparing, and selecting, and analyze their respective advantages and challenges in diverse scenarios. Based on our findings, we further design a compound entity matching framework (ComEM) that leverages the composition of multiple strategies and LLMs. ComEM benefits from the advantages of different sides and achieves improvements in both effectiveness and efficiency. Experimental results on 8 ER datasets and 10 LLMs verify the superiority of incorporating record interactions through the selecting strategy, as well as the further cost-effectiveness brought by ComEM.

Data-driven modeling methods for industrial quality index prediction often face the challenge of limited data representation. Using process variable snapshots from a single time step is insufficient for building high-performance soft sensors. Moreover, during online prediction, the performance of soft sensors is affected by diverse operating conditions and concept drift in industrial data streams, leading to performance degradation . To address these challenges, this paper proposes a Temporal Feature Extraction and Incremental Variational Bayesian Regression Ensemble (TFE-IVBRE) framework, which provides a general solution for various online industrial quality index prediction tasks. The TFE-IVBRE framework combines the temporal feature extraction capabilities of deep neural networks , the ability of ensemble learning to handle diverse operating conditions, and the online learning features of variational Bayesian models . An incremental update strategy is also incorporated to maintain consistent prediction performance. Experiments in the Debutanizer Column and Sulfur Recovery Unit scenarios show that the prediction performance of TFE-IVBRE significantly outperforms other static and online comparison models, with the effectiveness of its components validated through ablation studies. Finally, the overall model also demonstrates good robustness. These results offer valuable insights for the advancement of industrial soft sensor development.

Protein structure prediction is a longstanding issue crucial for identifying new drug targets and providing a mechanistic understanding of protein functions. To enhance the progress in this field, a spectrum of computational methodologies has been cultivated. AlphaFold2 has exhibited exceptional precision in predicting wild-type protein structures, with performance exceeding that of other methods. However, predicting the structures of missense mutant proteins using AlphaFold2 remains challenging due to the intricate and substantial structural alterations caused by minor sequence variations in the mutant proteins. Molecular dynamics (MD) has been validated for precisely capturing changes in amino acid interactions attributed to protein mutations. Therefore, for the first time, a strategy entitled 'MoDAFold' was proposed to improve the accuracy and reliability of missense mutant protein structure prediction by combining AlphaFold2 with MD. Multiple case studies have confirmed the superior performance of MoDAFold compared to other methods, particularly AlphaFold2.

Accurate Urban SpatioTemporal Prediction (USTP) is of great importance to the development and operation of the smart city. As an emerging building block, multi-sourced urban data are usually integrated as urban knowledge graphs (UrbanKGs) to provide critical knowledge for urban spatiotemporal prediction models. However, existing UrbanKGs are often tailored for specific downstream prediction tasks and are not publicly available, which limits the potential advancement. This paper presents UUKG, the unified urban knowledge graph dataset for knowledge-enhanced urban spatiotemporal predictions. Specifically, we first construct UrbanKGs consisting of millions of triplets for two metropolises by connecting heterogeneous urban entities such as administrative boroughs, POIs, and road segments. Moreover, we conduct qualitative and quantitative analysis on constructed UrbanKGs and uncover diverse high-order structural patterns, such as hierarchies and cycles, that can be leveraged to benefit downstream USTP tasks. To validate and facilitate the use of UrbanKGs, we implement and evaluate 15 KG embedding methods on the KG completion task and integrate the learned KG embeddings into 9 spatiotemporal models for five different USTP tasks. The extensive experimental results not only provide benchmarks of knowledge-enhanced USTP models under different task settings but also highlight the potential of state-of-the-art high-order structure-aware UrbanKG embedding methods. We hope the proposed UUKG fosters research on urban knowledge graphs and broad smart city applications. The dataset and source code are available at https://github.com/usail-hkust/UUKG/.

MOTIVATION: With the rapid advances of RNA sequencing and microarray technologies in non-coding RNA (ncRNA) research, functional tools that perform enrichment analysis for ncRNAs are needed. On the one hand, because of the rapidly growing interest in circRNAs, snoRNAs, and piRNAs, it is essential to develop tools for enrichment analysis for these newly emerged ncRNAs. On the other hand, due to the key role of ncRNAs' interacting target in the determination of their function, the interactions between ncRNA and its corresponding target should be fully considered in functional enrichment. Based on the ncRNA-mRNA/protein-function strategy, some tools have been developed to functionally analyze a single type of ncRNA (the majority focuses on miRNA); in addition, some tools adopt predicted target data and lead to only low-confidence results. RESULTS: Herein, an online tool named RNAenrich was developed to enable the comprehensive and accurate enrichment analysis of ncRNAs. It is unique in (i) realizing the enrichment analysis for various RNA types in humans and mice, such as miRNA, lncRNA, circRNA, snoRNA, piRNA, and mRNA; (ii) extending the analysis by introducing millions of experimentally validated data of RNA-target interactions as a built-in database; and (iii) providing a comprehensive interacting network among various ncRNAs and targets to facilitate the mechanistic study of ncRNA function. Importantly, RNAenrich led to a more comprehensive and accurate enrichment analysis in a COVID-19-related miRNA case, which was largely attributed to its coverage of comprehensive ncRNA-target interactions. AVAILABILITY AND IMPLEMENTATION: RNAenrich is now freely accessible at https://idrblab.org/rnaenr/.

Designing efficient tools for modeling and analyzing transportation trajectories help improve various smart city services, e.g., location prediction, business recommendation and traffic forecasting. Yet with limited historical travel data, conventional tools are faced with challenges in representing the sophisticated contextual and spatiotemporal relationships inherent in transportation trajectories, while such trajectories have strong functional, geographical and time-specific characteristics. In this work, we propose an imitative transportation trajectory generation framework with multi-source urban knowledge enhancement. Specifically, we first construct Know-ST, an urban knowledge fusion framework that captures cross-domain knowledge (i.e., road network, point of interest, etc.) via tailored urban knowledge graph representation learning. The Know-ST preserves the temporal characteristics of trajectories and can continuously adapt to newly arriving trajectories. Moreover, we formulate the trajectory generation problem as a sequential imitation learning process, where an adversarially trained generator network is equipped to autonomously capture both the spatiotemporal and contextual information within individual transportation trajectories. Extensive experiments on real-world dataset show Know-ST outperforms multiple baselines under a variety of benchmarks, indicating the effectiveness of the proposed framework.

The discovery of proper molecular signature from OMIC data is indispensable for determining biological state, physiological condition, disease etiology, and therapeutic response. However, the identified signature is reported to be highly inconsistent, and there is little overlap among the signatures identified from different biological datasets. Such inconsistency raises doubts about the reliability of reported signatures and significantly hampers its biological and clinical applications. Herein, an online tool, ConSIG, was constructed to realize consistent discovery of gene/protein signature from any uploaded transcriptomic/proteomic data. This tool is unique in a) integrating a novel strategy capable of significantly enhancing the consistency of signature discovery, b) determining the optimal signature by collective assessment, and c) confirming the biological relevance by enriching the disease/gene ontology. With the increasingly accumulated concerns about signature consistency and biological relevance, this online tool is expected to be used as an essential complement to other existing tools for OMIC-based signature discovery. ConSIG is freely accessible to all users without login requirement at https://idrblab.org/consig/.

In a drug formulation (DFM), the major components by mass are not Active Pharmaceutical Ingredient (API) but rather Drug Inactive Ingredients (DIGs). DIGs can reach much higher concentrations than that achieved by API, which raises great concerns about their clinical toxicities. Therefore, the biological activities of DIG on physiologically relevant target are widely demanded by both clinical investigation and pharmaceutical industry. However, such activity data are not available in any existing pharmaceutical knowledge base, and their potentials in predicting the DIG-target interaction have not been evaluated yet. In this study, the comprehensive assessment and analysis on the biological activities of DIGs were therefore conducted. First, the largest number of DIGs and DFMs were systematically curated and confirmed based on all drugs approved by US Food and Drug Administration. Second, comprehensive activities for both DIGs and DFMs were provided for the first time to pharmaceutical community. Third, the biological targets of each DIG and formulation were fully referenced to available databases that described their pharmaceutical/biological characteristics. Finally, a variety of popular artificial intelligence techniques were used to assess the predictive potential of DIGs' activity data, which was the first evaluation on the possibility to predict DIG's activity. As the activities of DIGs are critical for current pharmaceutical studies, this work is expected to have significant implications for the future practice of drug discovery and precision medicine.

In recent years, sequential learning has been of great interest due to the advance of deep learning with applications in time-series forecasting, natural language processing, and speech recognition. Recurrent neural networks (RNNs) have achieved superior performance in single-view and synchronous multi-view sequential learning comparing to traditional machine learning models. However, the method remains less explored in asynchronous multi-view sequential learning, and the unalignment nature of multiple sequences poses a great challenge to learn the inter-view interactions. We develop an AMANet (Attention and Memory-Augmented Networks) architecture by integrating both attention and memory to solve asynchronous multi-view learning problem in general, and we focus on experiments in dual-view sequences in this paper. Self-attention and inter-attention are employed to capture intra-view interaction and inter-view interaction, respectively. History attention memory is designed to store the historical information of a specific object, which serves as local knowledge storage. Dynamic external memory is used to store global knowledge for each view. We evaluate our model in three tasks: medication recommendation from a patient's medical records, diagnosis-related group (DRG) classification from a hospital record, and invoice fraud detection through a company's taxation behaviors. The results demonstrate that our model outperforms all baselines and other state-of-the-art models in all tasks. Moreover, the ablation study of our model indicates that the inter-attention mechanism plays a key role in the model and it can boost the predictive power by effectively capturing the inter-view interactions from asynchronous views.