The design of alloys is a multi-scale problem that requires a holistic approach that involves retrieving relevant knowledge, applying advanced computational methods, conducting experimental validations, and analyzing the results, a process that is typically reserved for human experts. Machine learning (ML) can help accelerate this process, for instance, through the use of deep surrogate models that connect structural features to material properties, or vice versa. However, existing data-driven models often target specific material objectives, offering limited flexibility to integrate out-of-domain knowledge and cannot adapt to new, unforeseen challenges. Here, we overcome these limitations by leveraging the distinct capabilities of multiple AI agents that collaborate autonomously within a dynamic environment to solve complex materials design tasks. The proposed physics-aware generative AI platform, AtomAgents, synergizes the intelligence of large language models (LLM) the dynamic collaboration among AI agents with expertise in various domains, including knowledge retrieval, multi-modal data integration, physics-based simulations, and comprehensive results analysis across modalities that includes numerical data and images of physical simulation results. The concerted effort of the multi-agent system allows for addressing complex materials design problems, as demonstrated by examples that include autonomously designing metallic alloys with enhanced properties compared to their pure counterparts. Our results enable accurate prediction of key characteristics across alloys and highlight the crucial role of solid solution alloying to steer the development of advanced metallic alloys. Our framework enhances the efficiency of complex multi-objective design tasks and opens new avenues in fields such as biomedical materials engineering, renewable energy, and environmental sustainability.
Purpose: Federated training is often hindered by heterogeneous datasets due to divergent data storage options, inconsistent naming schemes, varied annotation procedures, and disparities in label quality. This is particularly evident in the emerging multi-modal learning paradigms, where dataset harmonization including a uniform data representation and filtering options are of paramount importance. Methods: DICOM structured reports enable the standardized linkage of arbitrary information beyond the imaging domain and can be used within Python deep learning pipelines with highdicom. Building on this, we developed an open platform for data integration and interactive filtering capabilities that simplifies the process of assembling multi-modal datasets. Results: In this study, we extend our prior work by showing its applicability to more and divergent data types, as well as streamlining datasets for federated training within an established consortium of eight university hospitals in Germany. We prove its concurrent filtering ability by creating harmonized multi-modal datasets across all locations for predicting the outcome after minimally invasive heart valve replacement. The data includes DICOM data (i.e. computed tomography images, electrocardiography scans) as well as annotations (i.e. calcification segmentations, pointsets and pacemaker dependency), and metadata (i.e. prosthesis and diagnoses). Conclusion: Structured reports bridge the traditional gap between imaging systems and information systems. Utilizing the inherent DICOM reference system arbitrary data types can be queried concurrently to create meaningful cohorts for clinical studies. The graphical interface as well as example structured report templates will be made publicly available.
X-ray images are vital in medical diagnostics, but their effectiveness is limited without clinical context. Radiologists often find chest X-rays insufficient for diagnosing underlying diseases, necessitating the integration of structured clinical features with radiology reports. To address this, we introduce DALL-M, a novel framework that enhances clinical datasets by generating contextual synthetic data. DALL-M augments structured patient data, including vital signs (e.g., heart rate, oxygen saturation), radiology findings (e.g., lesion presence), and demographic factors. It integrates this tabular data with contextual knowledge extracted from radiology reports and domain-specific resources (e.g., Radiopaedia, Wikipedia), ensuring clinical consistency and reliability. DALL-M follows a three-phase process: (i) clinical context storage, (ii) expert query generation, and (iii) context-aware feature augmentation. Using large language models (LLMs), it generates both contextual synthetic values for existing clinical features and entirely new, clinically relevant features. Applied to 799 cases from the MIMIC-IV dataset, DALL-M expanded the original 9 clinical features to 91. Empirical validation with machine learning models (including Decision Trees, Random Forests, XGBoost, and TabNET) demonstrated a 16.5% improvement in F1 score and a 25% increase in Precision and Recall. DALL-M bridges an important gap in clinical data augmentation by preserving data integrity while enhancing predictive modeling in healthcare. Our results show that integrating LLM-generated synthetic features significantly improves model performance, making DALL-M a scalable and practical approach for AI-driven medical diagnostics.
Despite the wealth of single-cell multi-omics data, it remains challenging to predict the consequences of novel genetic and chemical perturbations in the human body. It requires knowledge of molecular interactions at all biological levels, encompassing disease models and humans. Current machine learning methods primarily establish statistical correlations between genotypes and phenotypes but struggle to identify physiologically significant causal factors, limiting their predictive power. Key challenges in predictive modeling include scarcity of labeled data, generalization across different domains, and disentangling causation from correlation. In light of recent advances in multi-omics data integration, we propose a new artificial intelligence (AI)-powered biology-inspired multi-scale modeling framework to tackle these issues. This framework will integrate multi-omics data across biological levels, organism hierarchies, and species to predict causal genotype-environment-phenotype relationships under various conditions. AI models inspired by biology may identify novel molecular targets, biomarkers, pharmaceutical agents, and personalized medicines for presently unmet medical needs.
Sepsis poses a major global health threat, accounting for millions of deaths annually and significant economic costs. Accurately predicting the risk of mortality in sepsis patients enables early identification, promotes the efficient allocation of medical resources, and facilitates timely interventions, thereby improving patient outcomes. Current methods typically utilize only one type of data--either constant, temporal, or ICD codes. This study introduces a novel approach, the Time-Constant Kolmogorov-Arnold Network (TCKAN), which uniquely integrates temporal data, constant data, and ICD codes within a single predictive model. Unlike existing methods that typically rely on one type of data, TCKAN leverages a multi-modal data integration strategy, resulting in superior predictive accuracy and robustness in identifying high-risk sepsis patients. Validated against the MIMIC-III and MIMIC-IV datasets, TCKAN surpasses existing machine learning and deep learning methods in accuracy, sensitivity, and specificity. Notably, TCKAN achieved AUCs of 87.76% and 88.07%, demonstrating superior capability in identifying high-risk patients. Additionally, TCKAN effectively combats the prevalent issue of data imbalance in clinical settings, improving the detection of patients at elevated risk of mortality and facilitating timely interventions. These results confirm the model's effectiveness and its potential to transform patient management and treatment optimization in clinical practice. Although the TCKAN model has already incorporated temporal, constant, and ICD code data, future research could include more diverse medical data types, such as imaging and laboratory test results, to achieve a more comprehensive data integration and further improve predictive accuracy.
Integrated satellite, aerial, and terrestrial networks (ISATNs) represent a sophisticated convergence of diverse communication technologies to ensure seamless connectivity across different altitudes and platforms. This paper explores the transformative potential of integrating Large Language Models (LLMs) into ISATNs, leveraging advanced Artificial Intelligence (AI) and Machine Learning (ML) capabilities to enhance these networks. We outline the current architecture of ISATNs and highlight the significant role LLMs can play in optimizing data flow, signal processing, and network management to advance 5G/6G communication technologies through advanced predictive algorithms and real-time decision-making. A comprehensive analysis of ISATN components is conducted, assessing how LLMs can effectively address traditional data transmission and processing bottlenecks. The paper delves into the network management challenges within ISATNs, emphasizing the necessity for sophisticated resource allocation strategies, traffic routing, and security management to ensure seamless connectivity and optimal performance under varying conditions. Furthermore, we examine the technical challenges and limitations associated with integrating LLMs into ISATNs, such as data integration for LLM processing, scalability issues, latency in decision-making processes, and the design of robust, fault-tolerant systems. The study also identifies key future research directions for fully harnessing LLM capabilities in ISATNs, which is crucial for enhancing network reliability, optimizing performance, and achieving a truly interconnected and intelligent global network system.
Detecting dynamic patterns of task-specific responses shared across heterogeneous datasets is an essential and challenging problem in many scientific applications in medical science and neuroscience. In our motivating example of rodent electrophysiological data, identifying the dynamical patterns in neuronal activity associated with ongoing cognitive demands and behavior is key to uncovering the neural mechanisms of memory. One of the greatest challenges in investigating a cross-subject biological process is that the systematic heterogeneity across individuals could significantly undermine the power of existing machine learning methods to identify the underlying biological dynamics. In addition, many technically challenging neurobiological experiments are conducted on only a handful of subjects where rich longitudinal data are available for each subject. The low sample sizes of such experiments could further reduce the power to detect common dynamic patterns among subjects. In this paper, we propose a novel heterogeneous data integration framework based on optimal transport to extract shared patterns in complex biological processes. The key advantages of the proposed method are that it can increase discriminating power in identifying common patterns by reducing heterogeneity unrelated to the signal by aligning the extracted latent spatiotemporal information across subjects. Our approach is effective even with a small number of subjects, and does not require auxiliary matching information for the alignment. In particular, our method can align longitudinal data across heterogeneous subjects in a common latent space to capture the dynamics of shared patterns while utilizing temporal dependency within subjects.
Embedding high-dimensional data into a low-dimensional space is an indispensable component of data analysis. In numerous applications, it is necessary to align and jointly embed multiple datasets from different studies or experimental conditions. Such datasets may share underlying structures of interest but exhibit individual distortions, resulting in misaligned embeddings using traditional techniques. In this work, we propose \textit{Entropic Optimal Transport (EOT) eigenmaps}, a principled approach for aligning and jointly embedding a pair of datasets with theoretical guarantees. Our approach leverages the leading singular vectors of the EOT plan matrix between two datasets to extract their shared underlying structure and align the datasets accordingly in a common embedding space. We interpret our approach as an inter-data variant of the classical Laplacian eigenmaps and diffusion maps embeddings, showing that it enjoys many favorable analogous properties. We then analyze a data-generative model where two observed high-dimensional datasets share latent variables on a common low-dimensional manifold, but each dataset is subject to data-specific translation, scaling, nuisance structures, and noise. We show that in a high-dimensional asymptotic regime, the EOT plan recovers the shared manifold structure by approximating a kernel function evaluated at the locations of the latent variables. Subsequently, we provide a geometric interpretation of our embedding by relating it to the eigenfunctions of population-level operators encoding the density and geometry of the shared manifold. Finally, we showcase the performance of our approach for data integration and embedding through simulations and analyses of real-world biological data, demonstrating its advantages over alternative methods in challenging scenarios.
The widespread adoption of synthetic data raises new questions about how models generating the data can influence other large language models (LLMs) via distilled data. To start, our work exhaustively characterizes the impact of passive inheritance of model properties by systematically studying the consequences of synthetic data integration. We provide one of the most comprehensive studies to-date of how the source of synthetic data shapes models' internal biases, calibration and generations' textual attributes and preferences. We find that models are surprisingly sensitive towards certain attributes even when the synthetic data prompts appear "neutral". which invites the question whether this sensitivity can be exploited for good. Our findings invite the question can we explicitly steer the models towards the properties we want at test time by exploiting the data generation process? This would have historically been considered infeasible due to the cost of collecting data with a specific characteristic or objective in mind. However, improvement in the quality of synthetic data, as well as a shift towards general-purpose models designed to follow a diverse way of instructions, means this question is timely. We propose active inheritance as a term to describe intentionally constraining synthetic data according to a non-differentiable objective. We demonstrate how active inheritance can steer the generation profiles of models towards desirable non-differentiable attributes, e.g. high lexical diversity or low toxicity.
The essence of precision oncology lies in its commitment to tailor targeted treatments and care measures to each patient based on the individual characteristics of the tumor. The inherent heterogeneity of tumors necessitates gathering information from diverse data sources to provide valuable insights from various perspectives, fostering a holistic comprehension of the tumor. Over the past decade, multimodal data integration technology for precision oncology has made significant strides, showcasing remarkable progress in understanding the intricate details within heterogeneous data modalities. These strides have exhibited tremendous potential for improving clinical decision-making and model interpretation, contributing to the advancement of cancer care and treatment. Given the rapid progress that has been achieved, we provide a comprehensive overview of about 300 papers detailing cutting-edge multimodal data integration techniques in precision oncology. In addition, we conclude the primary clinical applications that have reaped significant benefits, including early assessment, diagnosis, prognosis, and biomarker discovery. Finally, derived from the findings of this survey, we present an in-depth analysis that explores the pivotal challenges and reveals essential pathways for future research in the field of multimodal data integration for precision oncology.
Inferring parameters of models of biochemical kinetics from single-cell data remains challenging because of the uncertainty arising from the intractability of the likelihood function of stochastic reaction networks. Such uncertainty falls beyond current error quantification measures, which focus on the effects of finite sample size and identifiability but lack theoretical guarantees when likelihood approximations are needed. Here, we propose a method for the inference of parameters of stochastic reaction networks that works for both steady-state and time-resolved data and is applicable to networks with non-linear and rational propensities. Our approach provides bounds on the parameters via convex optimisation over sets constrained by moment equations and moment matrices by taking observations to form moment intervals, which are then used to constrain parameters through convex sets. The bounds on the parameters contain the true parameters under the condition that the moment intervals contain the true moments, thus providing uncertainty quantification and error guarantees. Our approach does not need to predict moments and distributions for given parameters (i.e., it avoids solving or simulating the forward problem), and hence circumvents intractable likelihood computations or computationally expensive simulations. We demonstrate its use for uncertainty quantification, data integration and prediction of latent species statistics through synthetic data from common non-linear biochemical models including the Schl\"ogl model and the toggle switch, a model of post-transcriptional regulation at steady state, and a birth-death model with time-dependent data.
In the era of Industry 4.0, artificial intelligence (AI) is assuming an increasingly pivotal role within industrial systems. Despite the recent trend within various industries to adopt AI, the actual adoption of AI is not as developed as perceived. A significant factor contributing to this lag is the data issues in AI implementation. How to address these data issues stands as a significant concern confronting both industry and academia. To address data issues, the first step involves mapping out these issues. Therefore, this study conducts a meta-review to explore data issues and methods within the implementation of industrial AI. Seventy-two data issues are identified and categorized into various stages of the data lifecycle, including data source and collection, data access and storage, data integration and interoperation, data pre-processing, data processing, data security and privacy, and AI technology adoption. Subsequently, the study analyzes the data requirements of various AI algorithms. Building on the aforementioned analyses, it proposes a data management framework, addressing how data issues can be systematically resolved at every stage of the data lifecycle. Finally, the study highlights future research directions. In doing so, this study enriches the existing body of knowledge and provides guidelines for professionals navigating the complex landscape of achieving data usability and usefulness in industrial AI.
Patchwork learning arises as a new and challenging data collection paradigm where both samples and features are observed in fragmented subsets. Due to technological limits, measurement expense, or multimodal data integration, such patchwork data structures are frequently seen in neuroscience, healthcare, and genomics, among others. Instead of analyzing each data patch separately, it is highly desirable to extract comprehensive knowledge from the whole data set. In this work, we focus on the clustering problem in patchwork learning, aiming at discovering clusters amongst all samples even when some are never jointly observed for any feature. We propose a novel spectral clustering method called Cluster Quilting, consisting of (i) patch ordering that exploits the overlapping structure amongst all patches, (ii) patchwise SVD, (iii) sequential linear mapping of top singular vectors for patch overlaps, followed by (iv) k-means on the combined and weighted singular vectors. Under a sub-Gaussian mixture model, we establish theoretical guarantees via a non-asymptotic misclustering rate bound that reflects both properties of the patch-wise observation regime as well as the clustering signal and noise dependencies. We also validate our Cluster Quilting algorithm through extensive empirical studies on both simulated and real data sets in neuroscience and genomics, where it discovers more accurate and scientifically more plausible clusters than other approaches.
Sustainable Development Goals (SDGs) give the UN a road map for development with Agenda 2030 as a target. SDG3 "Good Health and Well-Being" ensures healthy lives and promotes well-being for all ages. Digital technologies can support SDG3. Burnout and even depression could be reduced by encouraging better preventive health. Due to the lack of patient knowledge and focus to take care of their health, it is necessary to help patients before it is too late. New trends such as positive psychology and mindfulness are highly encouraged in the USA. Digital Twins (DTs) can help with the continuous monitoring of emotion using physiological signals (e.g., collected via wearables). DTs facilitate monitoring and provide constant health insight to improve quality of life and well-being with better personalization. Healthcare DTs challenges are standardizing data formats, communication protocols, and data exchange mechanisms. As an example, ISO has the ISO/IEC JTC 1/SC 41 Internet of Things (IoT) and DTs Working Group, with standards such as "ISO/IEC 21823-3:2021 IoT - Interoperability for IoT Systems - Part 3 Semantic interoperability", "ISO/IEC CD 30178 - IoT - Data format, value and coding". To achieve those data integration and knowledge challenges, we designed the Mental Health Knowledge Graph (ontology and dataset) to boost mental health. As an example, explicit knowledge is described such as chocolate contains magnesium which is recommended for depression. The Knowledge Graph (KG) acquires knowledge from ontology-based mental health projects classified within the LOV4IoT ontology catalog (Emotion, Depression, and Mental Health). Furthermore, the KG is mapped to standards when possible. Standards from ETSI SmartM2M can be used such as SAREF4EHAW to represent medical devices and sensors, but also ITU/WHO, ISO, W3C, NIST, and IEEE standards relevant to mental health can be considered.
Severe convective weather events, such as hail, tornadoes, and thunderstorms, often occur quickly yet cause significant damage, costing billions of dollars every year. This highlights the importance of forecasting severe weather threats hours in advance to better prepare meteorologists and residents in at-risk areas. Can modern large foundation models perform such forecasting? Existing weather benchmarks typically focus only on predicting time-series changes in certain weather parameters (e.g., temperature, moisture) with text-only features. In this work, we introduce WeatherQA, the first multimodal dataset designed for machines to reason about complex combinations of weather parameters (a.k.a., ingredients) and predict severe weather in real-world scenarios. The dataset includes over 8,000 (multi-images, text) pairs for diverse severe weather events. Each pair contains rich information crucial for forecasting -- the images describe the ingredients capturing environmental instability, surface observations, and radar reflectivity, and the text contains forecast analyses written by human experts. With WeatherQA, we evaluate state-of-the-art vision language models, including GPT4, Claude3.5, Gemini-1.5, and a fine-tuned Llama3-based VLM, by designing two challenging tasks: (1) multi-choice QA for predicting affected area and (2) classification of the development potential of severe convection. These tasks require deep understanding of domain knowledge (e.g., atmospheric dynamics) and complex reasoning over multimodal data (e.g., interactions between weather parameters). We show a substantial gap between the strongest VLM, GPT4o, and human reasoning. Our comprehensive case study with meteorologists further reveals the weaknesses of the models, suggesting that better training and data integration are necessary to bridge this gap. WeatherQA link: https://github.com/chengqianma/WeatherQA.
Cancer clinics capture disease data at various scales, from genetic to organ level. Current bioinformatic methods struggle to handle the heterogeneous nature of this data, especially with missing modalities. We propose PARADIGM, a Graph Neural Network (GNN) framework that learns from multimodal, heterogeneous datasets to improve clinical outcome prediction. PARADIGM generates embeddings from multi-resolution data using foundation models, aggregates them into patient-level representations, fuses them into a unified graph, and enhances performance for tasks like survival analysis. We train GNNs on pan-Squamous Cell Carcinomas and validate our approach on Moffitt Cancer Center lung SCC data. Multimodal GNN outperforms other models in patient survival prediction. Converging individual data modalities across varying scales provides a more insightful disease view. Our solution aims to understand the patient's circumstances comprehensively, offering insights on heterogeneous data integration and the benefits of converging maximum data views.
Currently, a variety of pipeline tools are available for use in data engineering. Data scientists can use these tools to resolve data wrangling issues associated with data and accomplish some data engineering tasks from data ingestion through data preparation to utilization as input for machine learning (ML). Some of these tools have essential built-in components or can be combined with other tools to perform desired data engineering operations. While some tools are wholly or partly commercial, several open-source tools are available to perform expert-level data engineering tasks. This survey examines the broad categories and examples of pipeline tools based on their design and data engineering intentions. These categories are Extract Transform Load/Extract Load Transform (ETL/ELT), pipelines for Data Integration, Ingestion, and Transformation, Data Pipeline Orchestration and Workflow Management, and Machine Learning Pipelines. The survey also provides a broad outline of the utilization with examples within these broad groups and finally, a discussion is presented with case studies indicating the usage of pipeline tools for data engineering. The studies present some first-user application experiences with sample data, some complexities of the applied pipeline, and a summary note of approaches to using these tools to prepare data for machine learning.
We introduce Semantic Parsing in Contextual Environments (SPICE), a task designed to enhance artificial agents' contextual awareness by integrating multimodal inputs with prior contexts. SPICE goes beyond traditional semantic parsing by offering a structured, interpretable framework for dynamically updating an agent's knowledge with new information, mirroring the complexity of human communication. We develop the VG-SPICE dataset, crafted to challenge agents with visual scene graph construction from spoken conversational exchanges, highlighting speech and visual data integration. We also present the Audio-Vision Dialogue Scene Parser (AViD-SP) developed for use on VG-SPICE. These innovations aim to improve multimodal information processing and integration. Both the VG-SPICE dataset and the AViD-SP model are publicly available.
Transformer-based and MLP-based methods have emerged as leading approaches in time series forecasting (TSF). While Transformer-based methods excel in capturing long-range dependencies, they suffer from high computational complexities and tend to overfit. Conversely, MLP-based methods offer computational efficiency and adeptness in modeling temporal dynamics, but they struggle with capturing complex temporal patterns effectively. To address these challenges, we propose a novel MLP-based Adaptive Multi-Scale Decomposition (AMD) framework for TSF. Our framework decomposes time series into distinct temporal patterns at multiple scales, leveraging the Multi-Scale Decomposable Mixing (MDM) block to dissect and aggregate these patterns in a residual manner. Complemented by the Dual Dependency Interaction (DDI) block and the Adaptive Multi-predictor Synthesis (AMS) block, our approach effectively models both temporal and channel dependencies and utilizes autocorrelation to refine multi-scale data integration. Comprehensive experiments demonstrate that our AMD framework not only overcomes the limitations of existing methods but also consistently achieves state-of-the-art performance in both long-term and short-term forecasting tasks across various datasets, showcasing superior efficiency. Code is available at \url{https://github.com/TROUBADOUR000/AMD}
We present an approach for modeling and imputation of nonignorable missing data. Our approach uses Bayesian data integration to combine (1) a Gaussian copula model for all study variables and missingness indicators, which allows arbitrary marginal distributions, nonignorable missingess, and other dependencies, and (2) auxiliary information in the form of marginal quantiles for some study variables. We prove that, remarkably, one only needs a small set of accurately-specified quantiles to estimate the copula correlation consistently. The remaining marginal distribution functions are inferred nonparametrically and jointly with the copula parameters using an efficient MCMC algorithm. We also characterize the (additive) nonignorable missingness mechanism implied by the copula model. Simulations confirm the effectiveness of this approach for multivariate imputation with nonignorable missing data. We apply the model to analyze associations between lead exposure and end-of-grade test scores for 170,000 North Carolina students. Lead exposure has nonignorable missingness: children with higher exposure are more likely to be measured. We elicit marginal quantiles for lead exposure using statistics provided by the Centers for Disease Control and Prevention. Multiple imputation inferences under our model support stronger, more adverse associations between lead exposure and educational outcomes relative to complete case and missing-at-random analyses.