A key challenge today lies in the ability to efficiently handle multi-omics data since such multimodal data may provide a more comprehensive overview of the underlying processes in a system. Yet it comes with challenges: multi-omics data are most often unpaired and only partially labeled, moreover only small amounts of data are available in some situation such as rare diseases. We propose MODIS which stands for Multi-Omics Data Integration for Small and unpaired datasets, a semi supervised approach to account for these particular settings. MODIS learns a probabilistic coupling of heterogeneous data modalities and learns a shared latent space where modalities are aligned. We rely on artificial data to build controlled experiments to explore how much supervision is needed for an accurate alignment of modalities, and how our approach enables dealing with new conditions for which few data are available. The code is available athttps://github.com/VILLOUTREIXLab/MODIS.
Cardiopulmonary exercise testing (CPET) provides a comprehensive assessment of functional capacity by measuring key physiological variables including oxygen consumption ($VO_2$), carbon dioxide production ($VCO_2$), and pulmonary ventilation ($VE$) during exercise. Previous research has established that parameters such as peak $VO_2$ and $VE/VCO_2$ ratio serve as robust predictors of mortality risk in chronic heart failure patients. In this study, we leverage CPET variables as surrogate mortality endpoints for patients with Congenital Heart Disease (CHD). To our knowledge, this represents the first successful implementation of an advanced machine learning approach that predicts CPET outcomes by integrating electrocardiograms (ECGs) with information derived from clinical letters. Our methodology began with extracting unstructured patient information-including intervention history, diagnoses, and medication regimens-from clinical letters using natural language processing techniques, organizing this data into a structured database. We then digitized ECGs to obtain quantifiable waveforms and established comprehensive data linkages. The core innovation of our approach lies in exploiting the Riemannian geometric properties of covariance matrices derived from both 12-lead ECGs and clinical text data to develop robust regression and classification models. Through extensive ablation studies, we demonstrated that the integration of ECG signals with clinical documentation, enhanced by covariance augmentation techniques in Riemannian space, consistently produced superior predictive performance compared to conventional approaches.
World models significantly enhance hierarchical understanding, improving data integration and learning efficiency. To explore the potential of the world model in the remote sensing (RS) field, this paper proposes a label-efficient remote sensing world model for multimodal data fusion (FusDreamer). The FusDreamer uses the world model as a unified representation container to abstract common and high-level knowledge, promoting interactions across different types of data, \emph{i.e.}, hyperspectral (HSI), light detection and ranging (LiDAR), and text data. Initially, a new latent diffusion fusion and multimodal generation paradigm (LaMG) is utilized for its exceptional information integration and detail retention capabilities. Subsequently, an open-world knowledge-guided consistency projection (OK-CP) module incorporates prompt representations for visually described objects and aligns language-visual features through contrastive learning. In this way, the domain gap can be bridged by fine-tuning the pre-trained world models with limited samples. Finally, an end-to-end multitask combinatorial optimization (MuCO) strategy can capture slight feature bias and constrain the diffusion process in a collaboratively learnable direction. Experiments conducted on four typical datasets indicate the effectiveness and advantages of the proposed FusDreamer. The corresponding code will be released at https://github.com/Cimy-wang/FusDreamer.
Efficient management of end-of-life (EoL) products is critical for advancing circularity in supply chains, particularly within the construction industry where EoL strategies are hindered by heterogenous lifecycle data and data silos. Current tools like Environmental Product Declarations (EPDs) and Digital Product Passports (DPPs) are limited by their dependency on seamless data integration and interoperability which remain significant challenges. To address these, we present the Circular Construction Product Ontology (CCPO), an applied framework designed to overcome semantic and data heterogeneity challenges in EoL decision-making for construction products. CCPO standardises vocabulary and facilitates data integration across supply chain stakeholders enabling lifecycle assessments (LCA) and robust decision-making. By aggregating disparate data into a unified product provenance, CCPO enables automated EoL recommendations through customisable SWRL rules aligned with European standards and stakeholder-specific circularity SLAs, demonstrating its scalability and integration capabilities. The adopted circular product scenario depicts CCPO's application while competency question evaluations show its superior performance in generating accurate EoL suggestions highlighting its potential to greatly improve decision-making in circular supply chains and its applicability in real-world construction environments.
Standardization of clinical reports is crucial for improving the quality of healthcare and facilitating data integration. The lack of unified standards, including format, terminology, and style, is a great challenge in clinical fundus diagnostic reports, which increases the difficulty for large language models (LLMs) to understand the data. To address this, we construct a bilingual standard terminology, containing fundus clinical terms and commonly used descriptions in clinical diagnosis. Then, we establish two models, RetSTA-7B-Zero and RetSTA-7B. RetSTA-7B-Zero, fine-tuned on an augmented dataset simulating clinical scenarios, demonstrates powerful standardization behaviors. However, it encounters a challenge of limitation to cover a wider range of diseases. To further enhance standardization performance, we build RetSTA-7B, which integrates a substantial amount of standardized data generated by RetSTA-7B-Zero along with corresponding English data, covering diverse complex clinical scenarios and achieving report-level standardization for the first time. Experimental results demonstrate that RetSTA-7B outperforms other compared LLMs in bilingual standardization task, which validates its superior performance and generalizability. The checkpoints are available at https://github.com/AB-Story/RetSTA-7B.
In the era of big data, large-scale, multi-modal datasets are increasingly ubiquitous, offering unprecedented opportunities for predictive modeling and scientific discovery. However, these datasets often exhibit complex heterogeneity, such as covariate shift, posterior drift, and missing modalities, that can hinder the accuracy of existing prediction algorithms. To address these challenges, we propose a novel Representation Retrieval ($R^2$) framework, which integrates a representation learning module (the representer) with a sparsity-induced machine learning model (the learner). Moreover, we introduce the notion of "integrativeness" for representers, characterized by the effective data sources used in learning representers, and propose a Selective Integration Penalty (SIP) to explicitly improve the property. Theoretically, we demonstrate that the $R^2$ framework relaxes the conventional full-sharing assumption in multi-task learning, allowing for partially shared structures, and that SIP can improve the convergence rate of the excess risk bound. Extensive simulation studies validate the empirical performance of our framework, and applications to two real-world datasets further confirm its superiority over existing approaches.
Open-vocabulary 3D object detection (OV-3DOD) aims at localizing and classifying novel objects beyond closed sets. The recent success of vision-language models (VLMs) has demonstrated their remarkable capabilities to understand open vocabularies. Existing works that leverage VLMs for 3D object detection (3DOD) generally resort to representations that lose the rich scene context required for 3D perception. To address this problem, we propose in this paper a hierarchical framework, named HCMA, to simultaneously learn local object and global scene information for OV-3DOD. Specifically, we first design a Hierarchical Data Integration (HDI) approach to obtain coarse-to-fine 3D-image-text data, which is fed into a VLM to extract object-centric knowledge. To facilitate the association of feature hierarchies, we then propose an Interactive Cross-Modal Alignment (ICMA) strategy to establish effective intra-level and inter-level feature connections. To better align features across different levels, we further propose an Object-Focusing Context Adjustment (OFCA) module to refine multi-level features by emphasizing object-related features. Extensive experiments demonstrate that the proposed method outperforms SOTA methods on the existing OV-3DOD benchmarks. It also achieves promising OV-3DOD results even without any 3D annotations.
High-quality, error-free datasets are a key ingredient in building reliable, accurate, and unbiased machine learning (ML) models. However, real world datasets often suffer from errors due to sensor malfunctions, data entry mistakes, or improper data integration across multiple sources that can severely degrade model performance. Detecting and correcting these issues typically require tailor-made solutions and demand extensive domain expertise. Consequently, automation is challenging, rendering the process labor-intensive and tedious. In this study, we investigate whether Large Language Models (LLMs) can help alleviate the burden of manual data cleaning. We set up an experiment in which an LLM, paired with Python, is tasked with cleaning the training dataset to improve the performance of a learning algorithm without having the ability to modify the training pipeline or perform any feature engineering. We run this experiment on multiple Kaggle datasets that have been intentionally corrupted with errors. Our results show that LLMs can identify and correct erroneous entries, such as illogical values or outlier, by leveraging contextual information from other features within the same row, as well as feedback from previous iterations. However, they struggle to detect more complex errors that require understanding data distribution across multiple rows, such as trends and biases.
Clinical trial eligibility matching is a critical yet often labor-intensive and error-prone step in medical research, as it ensures that participants meet precise criteria for safe and reliable study outcomes. Recent advances in Natural Language Processing (NLP) have shown promise in automating and improving this process by rapidly analyzing large volumes of unstructured clinical text and structured electronic health record (EHR) data. In this paper, we present a systematic overview of current NLP methodologies applied to clinical trial eligibility screening, focusing on data sources, annotation practices, machine learning approaches, and real-world implementation challenges. A comprehensive literature search (spanning Google Scholar, Mendeley, and PubMed from 2015 to 2024) yielded high-quality studies, each demonstrating the potential of techniques such as rule-based systems, named entity recognition, contextual embeddings, and ontology-based normalization to enhance patient matching accuracy. While results indicate substantial improvements in screening efficiency and precision, limitations persist regarding data completeness, annotation consistency, and model scalability across diverse clinical domains. The review highlights how explainable AI and standardized ontologies can bolster clinician trust and broaden adoption. Looking ahead, further research into advanced semantic and temporal representations, expanded data integration, and rigorous prospective evaluations is necessary to fully realize the transformative potential of NLP in clinical trial recruitment.
Combining multiple perceptual inputs and performing combinatorial reasoning in complex scenarios is a sophisticated cognitive function in humans. With advancements in multi-modal large language models, recent benchmarks tend to evaluate visual understanding across multiple images. However, they often overlook the necessity of combinatorial reasoning across multiple perceptual information. To explore the ability of advanced models to integrate multiple perceptual inputs for combinatorial reasoning in complex scenarios, we introduce two benchmarks: Clue-Visual Question Answering (CVQA), with three task types to assess visual comprehension and synthesis, and Clue of Password-Visual Question Answering (CPVQA), with two task types focused on accurate interpretation and application of visual data. For our benchmarks, we present three plug-and-play approaches: utilizing model input for reasoning, enhancing reasoning through minimum margin decoding with randomness generation, and retrieving semantically relevant visual information for effective data integration. The combined results reveal current models' poor performance on combinatorial reasoning benchmarks, even the state-of-the-art (SOTA) closed-source model achieves only 33.04% accuracy on CVQA, and drops to 7.38% on CPVQA. Notably, our approach improves the performance of models on combinatorial reasoning, with a 22.17% boost on CVQA and 9.40% on CPVQA over the SOTA closed-source model, demonstrating its effectiveness in enhancing combinatorial reasoning with multiple perceptual inputs in complex scenarios. The code will be publicly available.
Data assimilation (DA) enables hydrologic models to update their internal states using near-real-time observations for more accurate forecasts. With deep neural networks like long short-term memory (LSTM), using either lagged observations as inputs (called "data integration") or variational DA has shown success in improving forecasts. However, it is unclear which methods are performant or optimal for physics-informed machine learning ("differentiable") models, which represent only a small amount of physically-meaningful states while using deep networks to supply parameters or missing processes. Here we developed variational DA methods for differentiable models, including optimizing adjusters for just precipitation data, just model internal hydrological states, or both. Our results demonstrated that differentiable streamflow models using the CAMELS dataset can benefit strongly and equivalently from variational DA as LSTM, with one-day lead time median Nash-Sutcliffe efficiency (NSE) elevated from 0.75 to 0.82. The resulting forecast matched or outperformed LSTM with DA in the eastern, northwestern, and central Great Plains regions of the conterminous United States. Both precipitation and state adjusters were needed to achieve these results, with the latter being substantially more effective on its own, and the former adding moderate benefits for high flows. Our DA framework does not need systematic training data and could serve as a practical DA scheme for whole river networks.
In recent years, data-driven, deep learning-based approaches for precipitation nowcasting have attracted significant attention, showing promising results. However, many existing models fail to fully exploit the extensive atmospheric information available, relying primarily on precipitation data alone. This study introduces two novel deep learning architectures, SmaAt-fUsion and SmaAt-Krige-GNet, specifically designed to enhance precipitation nowcasting by integrating multi-variable weather station data with radar datasets. By leveraging additional meteorological information, these models improve representation learning in the latent space, resulting in enhanced nowcasting performance. The SmaAt-fUsion model extends the SmaAt-UNet framework by incorporating weather station data through a convolutional layer, integrating it into the bottleneck of the network. Conversely, the SmaAt-Krige-GNet model combines precipitation maps with weather station data processed using Kriging, a geo-statistical interpolation method, to generate variable-specific maps. These maps are then utilized in a dual-encoder architecture based on SmaAt-GNet, allowing multi-level data integration. Experimental evaluations were conducted using four years (2016--2019) of weather station and precipitation radar data from the Netherlands. Results demonstrate that SmaAt-Krige-GNet outperforms the standard SmaAt-UNet, which relies solely on precipitation radar data, in low precipitation scenarios, while SmaAt-fUsion surpasses SmaAt-UNet in both low and high precipitation scenarios. This highlights the potential of incorporating discrete weather station data to enhance the performance of deep learning-based weather nowcasting models.
Acute Coronary Syndromes (ACS), including ST-segment elevation myocardial infarctions (STEMI) and non-ST-segment elevation myocardial infarctions (NSTEMI), remain a leading cause of mortality worldwide. Traditional cardiovascular risk scores rely primarily on clinical data, often overlooking environmental influences like air pollution that significantly impact heart health. Moreover, integrating complex time-series environmental data with clinical records is challenging. We introduce TabulaTime, a multimodal deep learning framework that enhances ACS risk prediction by combining clinical risk factors with air pollution data. TabulaTime features three key innovations: First, it integrates time-series air pollution data with clinical tabular data to improve prediction accuracy. Second, its PatchRWKV module automatically extracts complex temporal patterns, overcoming limitations of traditional feature engineering while maintaining linear computational complexity. Third, attention mechanisms enhance interpretability by revealing interactions between clinical and environmental factors. Experimental results show that TabulaTime improves prediction accuracy by over 20% compared to conventional models such as CatBoost, Random Forest, and LightGBM, with air pollution data alone contributing over a 10% improvement. Feature importance analysis identifies critical predictors including previous angina, systolic blood pressure, PM10, and NO2. Overall, TabulaTime bridges clinical and environmental insights, supporting personalized prevention strategies and informing public health policies to mitigate ACS risk.
Knowledge graphs are an efficient method for representing and connecting information across various concepts, useful in reasoning, question answering, and knowledge base completion tasks. They organize data by linking points, enabling researchers to combine diverse information sources into a single database. This interdisciplinary approach helps uncover new research questions and ideas. Knowledge graphs create a web of data points (nodes) and their connections (edges), which enhances navigation, comprehension, and utilization of data for multiple purposes. They capture complex relationships inherent in unstructured data sources, offering a semantic framework for diverse entities and their attributes. Strategies for developing knowledge graphs include using seed data, named entity recognition, and relationship extraction. These graphs enhance chatbot accuracy and include multimedia data for richer information. Creating high-quality knowledge graphs involves both automated methods and human oversight, essential for accurate and comprehensive data representation.
This paper presents a detailed evaluation of a Retrieval-Augmented Generation (RAG) system that integrates large language models (LLMs) to enhance information retrieval and instruction generation for maintenance personnel across diverse data formats. We assessed the performance of eight LLMs, emphasizing key metrics such as response speed and accuracy, which were quantified using BLEU and METEOR scores. Our findings reveal that advanced models like GPT-4 and GPT-4o-mini significantly outperform their counterparts, particularly when addressing complex queries requiring multi-format data integration. The results validate the system's ability to deliver timely and accurate responses, highlighting the potential of RAG frameworks to optimize maintenance operations. Future research will focus on refining retrieval techniques for these models and enhancing response generation, particularly for intricate scenarios, ultimately improving the system's practical applicability in dynamic real-world environments.
Virtual knowledge graphs (VKGs) have been widely applied to access relational data with a semantic layer by using an ontology in use cases that are dynamic in nature. However, current VKG techniques focus mainly on accessing a single relational database and remain largely unstudied for data integration with several heterogeneous data sources. To overcome this limitation, we propose intermediate triple table (ITT), a general VKG architecture to access multiple and diverse data sources. Our proposal is based on data shipping and addresses heterogeneity by adopting a schema-oblivious graph representation that intervenes between the sources and the queries. We minimize data computation by just materializing a relevant subgraph for a specific query. We employ star-shaped query processing and extend this technique to mapping candidate selection. For rapid materialization of the ITT, we apply a mapping partitioning technique to parallelize mapping execution, which also guarantees duplicate-free subgraphs and reduces memory consumption. We use SPARQL-to-SQL query translation to homogeneously evaluate queries over the ITT and execute them with an in-process analytical store. We implemented ITT on top of a knowledge graph materialization engine and evaluated it with two VKG benchmarks. The experimental results show that our proposal outperforms state-of-the-art techniques for complex graph queries in terms of execution time. It also decreases the number of timeouts although it uses more memory as a trade-off. The experiments also demonstrate the source independence of the architecture on a mixed distribution of data with SQL and document stores together with various file formats.
Cancer evolves continuously over time through a complex interplay of genetic, epigenetic, microenvironmental, and phenotypic changes. This dynamic behavior drives uncontrolled cell growth, metastasis, immune evasion, and therapy resistance, posing challenges for effective monitoring and treatment. However, today's data-driven research in oncology has primarily focused on cross-sectional analysis using data from a single modality, limiting the ability to fully characterize and interpret the disease's dynamic heterogeneity. Advances in multiscale data collection and computational methods now enable the discovery of longitudinal multimodal biomarkers for precision oncology. Longitudinal data reveal patterns of disease progression and treatment response that are not evident from single-timepoint data, enabling timely abnormality detection and dynamic treatment adaptation. Multimodal data integration offers complementary information from diverse sources for more precise risk assessment and targeting of cancer therapy. In this review, we survey methods of longitudinal and multimodal modeling, highlighting their synergy in providing multifaceted insights for personalized care tailored to the unique characteristics of a patient's cancer. We summarize the current challenges and future directions of longitudinal multimodal analysis in advancing precision oncology.
Large Language Models (LLMs) are emerging as transformative tools for software vulnerability detection, addressing critical challenges in the security domain. Traditional methods, such as static and dynamic analysis, often falter due to inefficiencies, high false positive rates, and the growing complexity of modern software systems. By leveraging their ability to analyze code structures, identify patterns, and generate repair sugges- tions, LLMs, exemplified by models like GPT, BERT, and CodeBERT, present a novel and scalable approach to mitigating vulnerabilities. This paper provides a detailed survey of LLMs in vulnerability detection. It examines key aspects, including model architectures, application methods, target languages, fine-tuning strategies, datasets, and evaluation metrics. We also analyze the scope of current research problems, highlighting the strengths and weaknesses of existing approaches. Further, we address challenges such as cross-language vulnerability detection, multimodal data integration, and repository-level analysis. Based on these findings, we propose solutions for issues like dataset scalability, model interpretability, and applications in low-resource scenarios. Our contributions are threefold: (1) a systematic review of how LLMs are applied in vulnerability detection; (2) an analysis of shared patterns and differences across studies, with a unified framework for understanding the field; and (3) a summary of key challenges and future research directions. This work provides valuable insights for advancing LLM-based vulnerability detection. We also maintain and regularly update latest selected paper on https://github.com/OwenSanzas/LLM-For-Vulnerability-Detection
Deep learning-based medical image segmentation models, such as U-Net, rely on high-quality annotated datasets to achieve accurate predictions. However, the increasing use of generative models for synthetic data augmentation introduces potential risks, particularly in the absence of rigorous quality control. In this paper, we investigate the impact of synthetic MRI data on the robustness and segmentation accuracy of U-Net models for brain tumor segmentation. Specifically, we generate synthetic T1-contrast-enhanced (T1-Ce) MRI scans using a GAN-based model with a shared encoding-decoding framework and shortest-path regularization. To quantify the effect of synthetic data contamination, we train U-Net models on progressively "poisoned" datasets, where synthetic data proportions range from 16.67% to 83.33%. Experimental results on a real MRI validation set reveal a significant performance degradation as synthetic data increases, with Dice coefficients dropping from 0.8937 (33.33% synthetic) to 0.7474 (83.33% synthetic). Accuracy and sensitivity exhibit similar downward trends, demonstrating the detrimental effect of synthetic data on segmentation robustness. These findings underscore the importance of quality control in synthetic data integration and highlight the risks of unregulated synthetic augmentation in medical image analysis. Our study provides critical insights for the development of more reliable and trustworthy AI-driven medical imaging systems.
The machine learning (ML) training over disparate data sources traditionally involves materialization, which can impose substantial time and space overhead due to data movement and replication. Factorized learning, which leverages direct computation on disparate sources through linear algebra (LA) rewriting, has emerged as a viable alternative to improve computational efficiency. However, the adaptation of factorized learning to leverage the full capabilities of modern LA-friendly hardware like GPUs has been limited, often requiring manual intervention for algorithm compatibility. This paper introduces Ilargi, a novel factorized learning framework that utilizes matrix-represented data integration (DI) metadata to facilitate automatic factorization across CPU and GPU environments without the need for costly relational joins. Ilargi incorporates an ML-based cost estimator to intelligently selects between factorization and materialization based on data properties, algorithm complexity, hardware environments, and their interactions. This strategy ensures up to 8.9x speedups on GPUs and achieves over 20% acceleration in batch ML training workloads, thereby enhancing the practicability of ML training across diverse data integration scenarios and hardware platforms. To our knowledge, this work is the very first effort in GPU-compatible factorized learning.