Cancer research is increasingly driven by the integration of diverse data modalities, spanning from genomics and proteomics to imaging and clinical factors. However, extracting actionable insights from these vast and heterogeneous datasets remains a key challenge. The rise of foundation models (FMs) -- large deep-learning models pretrained on extensive amounts of data serving as a backbone for a wide range of downstream tasks -- offers new avenues for discovering biomarkers, improving diagnosis, and personalizing treatment. This paper presents a comprehensive review of widely adopted integration strategies of multimodal data to assist advance the computational approaches for data-driven discoveries in oncology. We examine emerging trends in machine learning (ML) and deep learning (DL), including methodological frameworks, validation protocols, and open-source resources targeting cancer subtype classification, biomarker discovery, treatment guidance, and outcome prediction. This study also comprehensively covers the shift from traditional ML to FMs for multimodal integration. We present a holistic view of recent FMs advancements and challenges faced during the integration of multi-omics with advanced imaging data. We identify the state-of-the-art FMs, publicly available multi-modal repositories, and advanced tools and methods for data integration. We argue that current state-of-the-art integrative methods provide the essential groundwork for developing the next generation of large-scale, pre-trained models poised to further revolutionize oncology. To the best of our knowledge, this is the first review to systematically map the transition from conventional ML to advanced FM for multimodal data integration in oncology, while also framing these developments as foundational for the forthcoming era of large-scale AI models in cancer research.
Recent achievements in implantable brain-computer interfaces (iBCIs) have demonstrated the potential to decode cognitive and motor behaviors with intracranial brain recordings; however, individual physiological and electrode implantation heterogeneities have constrained current approaches to neural decoding within single individuals, rendering interindividual neural decoding elusive. Here, we present Multi-individual Brain Region-Aggregated Network (MIBRAIN), a neural decoding framework that constructs a whole functional brain network model by integrating intracranial neurophysiological recordings across multiple individuals. MIBRAIN leverages self-supervised learning to derive generalized neural prototypes and supports group-level analysis of brain-region interactions and inter-subject neural synchrony. To validate our framework, we recorded stereoelectroencephalography (sEEG) signals from a cohort of individuals performing Mandarin syllable articulation. Both real-time online and offline decoding experiments demonstrated significant improvements in both audible and silent articulation decoding, enhanced decoding accuracy with increased multi-subject data integration, and effective generalization to unseen subjects. Furthermore, neural predictions for regions without direct electrode coverage were validated against authentic neural data. Overall, this framework paves the way for robust neural decoding across individuals and offers insights for practical clinical applications.
This study explores the effectiveness of predictive maintenance models and the optimization of intelligent Operation and Maintenance (O&M) systems in improving wind power generation efficiency. Through qualitative research, structured interviews were conducted with five wind farm engineers and maintenance managers, each with extensive experience in turbine operations. Using thematic analysis, the study revealed that while predictive maintenance models effectively reduce downtime by identifying major faults, they often struggle with detecting smaller, gradual failures. Key challenges identified include false positives, sensor malfunctions, and difficulties in integrating new models with older turbine systems. Advanced technologies such as digital twins, SCADA systems, and condition monitoring have significantly enhanced turbine maintenance practices. However, these technologies still require improvements, particularly in AI refinement and real-time data integration. The findings emphasize the need for continuous development to fully optimize wind turbine performance and support the broader adoption of renewable energy.
Data-driven agriculture, which integrates technology and data into agricultural practices, has the potential to improve crop yield, disease resilience, and long-term soil health. However, privacy concerns, such as adverse pricing, discrimination, and resource manipulation, deter farmers from sharing data, as it can be used against them. To address this barrier, we propose a privacy-preserving framework that enables secure data sharing and collaboration for research and development while mitigating privacy risks. The framework combines dimensionality reduction techniques (like Principal Component Analysis (PCA)) and differential privacy by introducing Laplacian noise to protect sensitive information. The proposed framework allows researchers to identify potential collaborators for a target farmer and train personalized machine learning models either on the data of identified collaborators via federated learning or directly on the aggregated privacy-protected data. It also allows farmers to identify potential collaborators based on similarities. We have validated this on real-life datasets, demonstrating robust privacy protection against adversarial attacks and utility performance comparable to a centralized system. We demonstrate how this framework can facilitate collaboration among farmers and help researchers pursue broader research objectives. The adoption of the framework can empower researchers and policymakers to leverage agricultural data responsibly, paving the way for transformative advances in data-driven agriculture. By addressing critical privacy challenges, this work supports secure data integration, fostering innovation and sustainability in agricultural systems.
Foundation models (FMs), large neural networks pretrained on extensive and diverse datasets, have revolutionized artificial intelligence and shown significant promise in medical imaging by enabling robust performance with limited labeled data. Although numerous surveys have reviewed the application of FM in healthcare care, brain imaging remains underrepresented, despite its critical role in the diagnosis and treatment of neurological diseases using modalities such as MRI, CT, and PET. Existing reviews either marginalize brain imaging or lack depth on the unique challenges and requirements of FM in this domain, such as multimodal data integration, support for diverse clinical tasks, and handling of heterogeneous, fragmented datasets. To address this gap, we present the first comprehensive and curated review of FMs for brain imaging. We systematically analyze 161 brain imaging datasets and 86 FM architectures, providing information on key design choices, training paradigms, and optimizations driving recent advances. Our review highlights the leading models for various brain imaging tasks, summarizes their innovations, and critically examines current limitations and blind spots in the literature. We conclude by outlining future research directions to advance FM applications in brain imaging, with the aim of fostering progress in both clinical and research settings.
The Medical Information Mart for Intensive Care (MIMIC) datasets have become the Kernel of Digital Health Research by providing freely accessible, deidentified records from tens of thousands of critical care admissions, enabling a broad spectrum of applications in clinical decision support, outcome prediction, and healthcare analytics. Although numerous studies and surveys have explored the predictive power and clinical utility of MIMIC based models, critical challenges in data integration, representation, and interoperability remain underexplored. This paper presents a comprehensive survey that focuses uniquely on open problems. We identify persistent issues such as data granularity, cardinality limitations, heterogeneous coding schemes, and ethical constraints that hinder the generalizability and real-time implementation of machine learning models. We highlight key progress in dimensionality reduction, temporal modelling, causal inference, and privacy preserving analytics, while also outlining promising directions including hybrid modelling, federated learning, and standardized preprocessing pipelines. By critically examining these structural limitations and their implications, this survey offers actionable insights to guide the next generation of MIMIC powered digital health innovations.
Diabetes is a chronic metabolic disease characterized by elevated blood glucose levels, leading to complications like heart disease, kidney failure, and nerve damage. Accurate state-level predictions are vital for effective healthcare planning and targeted interventions, but in many cases, data for necessary analyses are incomplete. This study begins with a data engineering process to integrate diabetes-related datasets from 2011 to 2021 to create a comprehensive feature set. We then introduce an enhanced bagging ensemble regression model (EBMBag+) for time series forecasting to predict diabetes prevalence across U.S. cities. Several baseline models, including SVMReg, BDTree, LSBoost, NN, LSTM, and ERMBag, were evaluated for comparison with our EBMBag+ algorithm. The experimental results demonstrate that EBMBag+ achieved the best performance, with an MAE of 0.41, RMSE of 0.53, MAPE of 4.01, and an R2 of 0.9.
We present Ring-lite, a Mixture-of-Experts (MoE)-based large language model optimized via reinforcement learning (RL) to achieve efficient and robust reasoning capabilities. Built upon the publicly available Ling-lite model, a 16.8 billion parameter model with 2.75 billion activated parameters, our approach matches the performance of state-of-the-art (SOTA) small-scale reasoning models on challenging benchmarks (e.g., AIME, LiveCodeBench, GPQA-Diamond) while activating only one-third of the parameters required by comparable models. To accomplish this, we introduce a joint training pipeline integrating distillation with RL, revealing undocumented challenges in MoE RL training. First, we identify optimization instability during RL training, and we propose Constrained Contextual Computation Policy Optimization(C3PO), a novel approach that enhances training stability and improves computational throughput via algorithm-system co-design methodology. Second, we empirically demonstrate that selecting distillation checkpoints based on entropy loss for RL training, rather than validation metrics, yields superior performance-efficiency trade-offs in subsequent RL training. Finally, we develop a two-stage training paradigm to harmonize multi-domain data integration, addressing domain conflicts that arise in training with mixed dataset. We will release the model, dataset, and code.
Single-cell omics technologies have transformed our understanding of cellular diversity by enabling high-resolution profiling of individual cells. However, the unprecedented scale and heterogeneity of these datasets demand robust frameworks for data integration and annotation. The Cell Ontology (CL) has emerged as a pivotal resource for achieving FAIR (Findable, Accessible, Interoperable, and Reusable) data principles by providing standardized, species-agnostic terms for canonical cell types - forming a core component of a wide range of platforms and tools. In this paper, we describe the wide variety of uses of CL in these platforms and tools and detail ongoing work to improve and extend CL content including the addition of transcriptomically defined types, working closely with major atlasing efforts including the Human Cell Atlas and the Brain Initiative Cell Atlas Network to support their needs. We cover the challenges and future plans for harmonising classical and transcriptomic cell type definitions, integrating markers and using Large Language Models (LLMs) to improve content and efficiency of CL workflows.
Accurate near-real-time precipitation retrieval has been enhanced by satellite-based technologies. However, infrared-based algorithms have low accuracy due to weak relations with surface precipitation, whereas passive microwave and radar-based methods are more accurate but limited in range. This challenge motivates the Precipitation Retrieval Expansion (PRE) task, which aims to enable accurate, infrared-based full-disc precipitation retrievals beyond the scanning swath. We introduce Multimodal Knowledge Expansion, a two-stage pipeline with the proposed PRE-Net model. In the Swath-Distilling stage, PRE-Net transfers knowledge from a multimodal data integration model to an infrared-based model within the scanning swath via Coordinated Masking and Wavelet Enhancement (CoMWE). In the Full-Disc Adaptation stage, Self-MaskTune refines predictions across the full disc by balancing multimodal and full-disc infrared knowledge. Experiments on the introduced PRE benchmark demonstrate that PRE-Net significantly advanced precipitation retrieval performance, outperforming leading products like PERSIANN-CCS, PDIR, and IMERG. The code will be available at https://github.com/Zjut-MultimediaPlus/PRE-Net.
Constructing real-world data-to-insight pipelines often involves data extraction from data lakes, data integration across heterogeneous data sources, and diverse operations from data cleaning to analysis. The design and implementation of data science pipelines require domain knowledge, technical expertise, and even project-specific insights. AI systems have shown remarkable reasoning, coding, and understanding capabilities. However, it remains unclear to what extent these capabilities translate into successful design and execution of such complex pipelines. We introduce KRAMABENCH: a benchmark composed of 104 manually-curated real-world data science pipelines spanning 1700 data files from 24 data sources in 6 different domains. We show that these pipelines test the end-to-end capabilities of AI systems on data processing, requiring data discovery, wrangling and cleaning, efficient processing, statistical reasoning, and orchestrating data processing steps given a high-level task. Our evaluation tests 5 general models and 3 code generation models using our reference framework, DS-GURU, which instructs the AI model to decompose a question into a sequence of subtasks, reason through each step, and synthesize Python code that implements the proposed design. Our results on KRAMABENCH show that, although the models are sufficiently capable of solving well-specified data science code generation tasks, when extensive data processing and domain knowledge are required to construct real-world data science pipelines, existing out-of-box models fall short. Progress on KramaBench represents crucial steps towards developing autonomous data science agents for real-world applications. Our code, reference framework, and data are available at https://github.com/mitdbg/KramaBench.
Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present scSSL-Bench, a comprehensive benchmark that evaluates nineteen SSL methods. Our evaluation spans nine datasets and focuses on three common downstream tasks: batch correction, cell type annotation, and missing modality prediction. Furthermore, we systematically assess various data augmentation strategies. Our analysis reveals task-specific trade-offs: the specialized single-cell frameworks, scVI, CLAIRE, and the finetuned scGPT excel at uni-modal batch correction, while generic SSL methods, such as VICReg and SimCLR, demonstrate superior performance in cell typing and multi-modal data integration. Random masking emerges as the most effective augmentation technique across all tasks, surpassing domain-specific augmentations. Notably, our results indicate the need for a specialized single-cell multi-modal data integration framework. scSSL-Bench provides a standardized evaluation platform and concrete recommendations for applying SSL to single-cell analysis, advancing the convergence of deep learning and single-cell genomics.
Multi-task learning (MTL) has become an essential machine learning tool for addressing multiple learning tasks simultaneously and has been effectively applied across fields such as healthcare, marketing, and biomedical research. However, to enable efficient information sharing across tasks, it is crucial to leverage both shared and heterogeneous information. Despite extensive research on MTL, various forms of heterogeneity, including distribution and posterior heterogeneity, present significant challenges. Existing methods often fail to address these forms of heterogeneity within a unified framework. In this paper, we propose a dual-encoder framework to construct a heterogeneous latent factor space for each task, incorporating a task-shared encoder to capture common information across tasks and a task-specific encoder to preserve unique task characteristics. Additionally, we explore the intrinsic similarity structure of the coefficients corresponding to learned latent factors, allowing for adaptive integration across tasks to manage posterior heterogeneity. We introduce a unified algorithm that alternately learns the task-specific and task-shared encoders and coefficients. In theory, we investigate the excess risk bound for the proposed MTL method using local Rademacher complexity and apply it to a new but related task. Through simulation studies, we demonstrate that the proposed method outperforms existing data integration methods across various settings. Furthermore, the proposed method achieves superior predictive performance for time to tumor doubling across five distinct cancer types in PDX data.
The growing need to integrate information from a large number of diverse sources poses significant scalability challenges for data integration systems. These systems often rely on manually written schema mappings, which are complex, source-specific, and costly to maintain as sources evolve. While recent advances suggest that large language models (LLMs) can assist in automating schema matching by leveraging both structural and natural language cues, key challenges remain. In this paper, we identify three core issues with using LLMs for schema mapping: (1) inconsistent outputs due to sensitivity to input phrasing and structure, which we propose methods to address through sampling and aggregation techniques; (2) the need for more expressive mappings (e.g., GLaV), which strain the limited context windows of LLMs; and (3) the computational cost of repeated LLM calls, which we propose to mitigate through strategies like data type prefiltering.
As a leading online platform with a vast global audience, YouTube's extensive reach also makes it susceptible to hosting harmful content, including disinformation and conspiracy theories. This study explores the use of open-weight Large Language Models (LLMs), both text-only and multimodal, for identifying conspiracy theory videos shared on YouTube. Leveraging a labeled dataset of thousands of videos, we evaluate a variety of LLMs in a zero-shot setting and compare their performance to a fine-tuned RoBERTa baseline. Results show that text-based LLMs achieve high recall but lower precision, leading to increased false positives. Multimodal models lag behind their text-only counterparts, indicating limited benefits from visual data integration. To assess real-world applicability, we evaluate the most accurate models on an unlabeled dataset, finding that RoBERTa achieves performance close to LLMs with a larger number of parameters. Our work highlights the strengths and limitations of current LLM-based approaches for online harmful content detection, emphasizing the need for more precise and robust systems.
Knowledge Graphs (KGs) are increasingly adopted as a foundational technology for integrating heterogeneous data in domains such as climate science, cultural heritage, and the life sciences. Declarative mapping languages like R2RML and RML have played a central role in enabling scalable and reusable KG construction, offering a transparent means of transforming structured and semi-structured data into RDF. In this paper, we present PyRML, a lightweight, Python-native library for building Knowledge Graphs through declarative mappings. PyRML supports core RML constructs and provides a programmable interface for authoring, executing, and testing mappings directly within Python environments. It integrates with popular data and semantic web libraries (e.g., Pandas and RDFlib), enabling transparent and modular workflows. By lowering the barrier to entry for KG creation and fostering reproducible, ontology-aligned data integration, PyRML bridges the gap between declarative semantics and practical KG engineering.
With the increasing availability of meteorological data from various sensors, numerical models and reanalysis products, the need for efficient data integration methods has become paramount for improving weather forecasts and hydrometeorological studies. In this work, we propose a data fusion approach for precipitation nowcasting by integrating data from meteorological and rain gauge stations in Rio de Janeiro metropolitan area with ERA5 reanalysis data and GFS numerical weather prediction. We employ the spatiotemporal deep learning architecture called STConvS2S, leveraging a structured dataset covering a 9 x 11 grid. The study spans from January 2011 to October 2024, and we evaluate the impact of integrating three surface station systems. Among the tested configurations, the fusion-based model achieves an F1-score of 0.2033 for forecasting heavy precipitation events (greater than 25 mm/h) at a one-hour lead time. Additionally, we present an ablation study to assess the contribution of each station network and propose a refined inference strategy for precipitation nowcasting, integrating the GFS numerical weather prediction (NWP) data with in-situ observations.
The electrification of transportation and the increased adoption of decentralized renewable energy generation have added complexity to managing Renewable Energy Communities (RECs). Integrating Electric Vehicle (EV) charging with building energy systems like heating, ventilation, air conditioning (HVAC), photovoltaic (PV) generation, and battery storage presents significant opportunities but also practical challenges. Reinforcement learning (RL), particularly MultiAgent Deep Deterministic Policy Gradient (MADDPG) algorithms, have shown promising results in simulation, outperforming heuristic control strategies. However, translating these successes into real-world deployments faces substantial challenges, including incomplete and noisy data, integration of heterogeneous subsystems, synchronization issues, unpredictable occupant behavior, and missing critical EV state-of-charge (SoC) information. This paper introduces a framework designed explicitly to handle these complexities and bridge the simulation to-reality gap. The framework incorporates EnergAIze, a MADDPG-based multi-agent control strategy, and specifically addresses challenges related to real-world data collection, system integration, and user behavior modeling. Preliminary results collected from a real-world operational REC with four residential buildings demonstrate the practical feasibility of our approach, achieving an average 9% reduction in daily peak demand and a 5% decrease in energy costs through optimized load scheduling and EV charging behaviors. These outcomes underscore the framework's effectiveness, advancing the practical deployment of intelligent energy management solutions in RECs.
This research explores the application of Multimodal Generative AI to enhance story point estimation in Agile software development. By integrating text, image, and categorical data using advanced models like BERT, CNN, and XGBoost, our approach surpasses the limitations of traditional single-modal estimation methods. The results demonstrate strong accuracy for simpler story points, while also highlighting challenges in more complex categories due to data imbalance. This study further explores the impact of categorical data, particularly severity, on the estimation process, emphasizing its influence on model performance. Our findings emphasize the transformative potential of multimodal data integration in refining AI-driven project management, paving the way for more precise, adaptable, and domain-specific AI capabilities. Additionally, this work outlines future directions for addressing data variability and enhancing the robustness of AI in Agile methodologies.
Fine-grained economic mapping through urban representation learning has emerged as a crucial tool for evidence-based economic decisions. While existing methods primarily rely on supervised or unsupervised approaches, they often overlook semi-supervised learning in data-scarce scenarios and lack unified multi-task frameworks for comprehensive sectoral economic analysis. To address these gaps, we propose SemiGTX, an explainable semi-supervised graph learning framework for sectoral economic mapping. The framework is designed with dedicated fusion encoding modules for various geospatial data modalities, seamlessly integrating them into a cohesive graph structure. It introduces a semi-information loss function that combines spatial self-supervision with locally masked supervised regression, enabling more informative and effective region representations. Through multi-task learning, SemiGTX concurrently maps GDP across primary, secondary, and tertiary sectors within a unified model. Extensive experiments conducted in the Pearl River Delta region of China demonstrate the model's superior performance compared to existing methods, achieving R2 scores of 0.93, 0.96, and 0.94 for the primary, secondary and tertiary sectors, respectively. Cross-regional experiments in Beijing and Chengdu further illustrate its generality. Systematic analysis reveals how different data modalities influence model predictions, enhancing explainability while providing valuable insights for regional development planning. This representation learning framework advances regional economic monitoring through diverse urban data integration, providing a robust foundation for precise economic forecasting.