Many, if not most, systems of interest in science are naturally described as nonlinear dynamical systems. Empirically, we commonly access these systems through time series measurements. Often such time series may consist of discrete random variables rather than continuous measurements, or may be composed of measurements from multiple data modalities observed simultaneously. For instance, in neuroscience we may have behavioral labels in addition to spike counts and continuous physiological recordings. While by now there is a burgeoning literature on deep learning for dynamical systems reconstruction (DSR), multimodal data integration has hardly been considered in this context. Here we provide such an efficient and flexible algorithmic framework that rests on a multimodal variational autoencoder for generating a sparse teacher signal that guides training of a reconstruction model, exploiting recent advances in DSR training techniques. It enables to combine various sources of information for optimal reconstruction, even allows for reconstruction from symbolic data (class labels) alone, and connects different types of observations within a common latent dynamics space. In contrast to previous multimodal data integration techniques for scientific applications, our framework is fully \textit{generative}, producing, after training, trajectories with the same geometrical and temporal structure as those of the ground truth system.
As modern data pipelines continue to collect, produce, and store a variety of data formats, extracting and combining value from traditional and context-rich sources such as strings, text, video, audio, and logs becomes a manual process where such formats are unsuitable for RDBMS. To tap into the dark data, domain experts analyze and extract insights and integrate them into the data repositories. This process can involve out-of-DBMS, ad-hoc analysis, and processing resulting in ETL, engineering effort, and suboptimal performance. While AI systems based on ML models can automate the analysis process, they often further generate context-rich answers. Using multiple sources of truth, for either training the models or in the form of knowledge bases, further exacerbates the problem of consolidating the data of interest. We envision an analytical engine co-optimized with components that enable context-rich analysis. Firstly, as the data from different sources or resulting from model answering cannot be cleaned ahead of time, we propose using online data integration via model-assisted similarity operations. Secondly, we aim for a holistic pipeline cost- and rule-based optimization across relational and model-based operators. Thirdly, with increasingly heterogeneous hardware and equally heterogeneous workloads ranging from traditional relational analytics to generative model inference, we envision a system that just-in-time adapts to the complex analytical query requirements. To solve increasingly complex analytical problems, ML offers attractive solutions that must be combined with traditional analytical processing and benefit from decades of database community research to achieve scalability and performance effortless for the end user.
In recent years the importance of Smart Healthcare cannot be overstated. The current work proposed to expand the state-of-art of smart healthcare in integrating solutions for Obsessive Compulsive Disorder (OCD). Identification of OCD from oxidative stress biomarkers (OSBs) using machine learning is an important development in the study of OCD. However, this process involves the collection of OCD class labels from hospitals, collection of corresponding OSBs from biochemical laboratories, integrated and labeled dataset creation, use of suitable machine learning algorithm for designing OCD prediction model, and making these prediction models available for different biochemical laboratories for OCD prediction for unlabeled OSBs. Further, from time to time, with significant growth in the volume of the dataset with labeled samples, redesigning the prediction model is required for further use. The whole process requires distributed data collection, data integration, coordination between the hospital and biochemical laboratory, dynamic machine learning OCD prediction mode design using a suitable machine learning algorithm, and making the machine learning model available for the biochemical laboratories. Keeping all these things in mind, Accu-Help a fully automated, smart, and accurate OCD detection conceptual model is proposed to help the biochemical laboratories for efficient detection of OCD from OSBs. OSBs are classified into three classes: Healthy Individual (HI), OCD Affected Individual (OAI), and Genetically Affected Individual (GAI). The main component of this proposed framework is the machine learning OCD prediction model design. In this Accu-Help, a neural network-based approach is presented with an OCD prediction accuracy of 86 percent.
Synergetic use of sensors for soil moisture retrieval is attracting considerable interest due to the different advantages of different sensors. Active, passive, and optic data integration could be a comprehensive solution for exploiting the advantages of different sensors aimed at preparing soil moisture maps. Typically, pixel-based methods are used for multi-sensor fusion. Since, different applications need different scales of soil moisture maps, pixel-based approaches are limited for this purpose. Object-based image analysis employing an image object instead of a pixel could help us to meet this need. This paper proposes a segment-based image fusion framework to evaluate the possibility of preparing a multi-scale soil moisture map through integrated Sentinel-1, Sentinel-2, and Soil Moisture Active Passive (SMAP) data. The results confirmed that the proposed methodology was able to improve soil moisture estimation in different scales up to 20% better compared to pixel-based fusion approach.
International initiatives such as METABRIC (Molecular Taxonomy of Breast Cancer International Consortium) have collected several multigenomic and clinical data sets to identify the undergoing molecular processes taking place throughout the evolution of various cancers. Numerous Machine Learning and statistical models have been designed and trained to analyze these types of data independently, however, the integration of such differently shaped and sourced information streams has not been extensively studied. To better integrate these data sets and generate meaningful representations that can ultimately be leveraged for cancer detection tasks could lead to giving well-suited treatments to patients. Hence, we propose a novel learning pipeline comprising three steps - the integration of cancer data modalities as graphs, followed by the application of Graph Neural Networks in an unsupervised setting to generate lower-dimensional embeddings from the combined data, and finally feeding the new representations on a cancer sub-type classification model for evaluation. The graph construction algorithms are described in-depth as METABRIC does not store relationships between the patient modalities, with a discussion of their influence over the quality of the generated embeddings. We also present the models used to generate the lower-latent space representations: Graph Neural Networks, Variational Graph Autoencoders and Deep Graph Infomax. In parallel, the pipeline is tested on a synthetic dataset to demonstrate that the characteristics of the underlying data, such as homophily levels, greatly influence the performance of the pipeline, which ranges between 51\% to 98\% accuracy on artificial data, and 13\% and 80\% on METABRIC. This project has the potential to improve cancer data understanding and encourages the transition of regular data sets to graph-shaped data.
Many optimization algorithm benchmarking platforms allow users to share their experimental data to promote reproducible and reusable research. However, different platforms use different data models and formats, which drastically complicates the identification of relevant datasets, their interpretation, and their interoperability. Therefore, a semantically rich, ontology-based, machine-readable data model that can be used by different platforms is highly desirable. In this paper, we report on the development of such an ontology, which we call OPTION (OPTImization algorithm benchmarking ONtology). Our ontology provides the vocabulary needed for semantic annotation of the core entities involved in the benchmarking process, such as algorithms, problems, and evaluation measures. It also provides means for automatic data integration, improved interoperability, and powerful querying capabilities, thereby increasing the value of the benchmarking data. We demonstrate the utility of OPTION, by annotating and querying a corpus of benchmark performance data from the BBOB collection of the COCO framework and from the Yet Another Black-Box Optimization Benchmark (YABBOB) family of the Nevergrad environment. In addition, we integrate features of the BBOB functional performance landscape into the OPTION knowledge base using publicly available datasets with exploratory landscape analysis. Finally, we integrate the OPTION knowledge base into the IOHprofiler environment and provide users with the ability to perform meta-analysis of performance data.
Deep learning-based linkage of records across different databases is becoming increasingly useful in data integration and mining applications to discover new insights from multiple sources of data. However, due to privacy and confidentiality concerns, organisations often are not willing or allowed to share their sensitive data with any external parties, thus making it challenging to build/train deep learning models for record linkage across different organizations' databases. To overcome this limitation, we propose the first deep learning-based multi-party privacy-preserving record linkage (PPRL) protocol that can be used to link sensitive databases held by multiple different organisations. In our approach, each database owner first trains a local deep learning model, which is then uploaded to a secure environment and securely aggregated to create a global model. The global model is then used by a linkage unit to distinguish unlabelled record pairs as matches and non-matches. We utilise differential privacy to achieve provable privacy protection against re-identification attacks. We evaluate the linkage quality and scalability of our approach using several large real-world databases, showing that it can achieve high linkage quality while providing sufficient privacy protection against existing attacks.
We build a new class of generative algorithms capable of efficiently learning an arbitrary target distribution from possibly scarce, high-dimensional data and subsequently generate new samples. These generative algorithms are particle-based and are constructed as gradient flows of Lipschitz-regularized Kullback-Leibler or other $f$-divergences, where data from a source distribution can be stably transported as particles, towards the vicinity of the target distribution. As a highlighted result in data integration, we demonstrate that the proposed algorithms correctly transport gene expression data points with dimension exceeding 54K, while the sample size is typically only in the hundreds.
Cellular functions crucially depend on the precise execution of complex biochemical reactions taking place on the chromatin fiber in the tightly packed environment of the cell nucleus. Despite the availability of large data sets probing this process from multiple angles, we still lack a bottom-up framework which can incorporate the sequence-specific nature of biochemistry in a unified model of 3D chromatin dynamics. Here we propose SEMPER (Sequence Enhanced Magnetic PolymER), a novel stochastic polymer model which naturally incorporates observational data about sequence-driven biochemical processes, such as binding of transcription factor proteins, in a 3D model of chromatin structure. By introducing a new algorithm for approximate Bayesian inference, we discuss how to estimate in a robust manner the relative importance of biochemical vs. polymer signals in the determination of the chromatin epigenetic states which is leading to a significant revision of the interpretation of previous models. Furthermore we show that, without additional input from the genome 3D structure, our model can predict with reasonable accuracy some notable and non trivial conformational features of chromatin folding within the nucleus. Our work highlights the importance of introducing physically realistic statistical models for predicting chromatin states from epigenetic data, and opens the way to a new class of more systematic approaches to interpret epigenomic data.
Structured and unstructured data and facts about drugs, genes, protein, viruses, and their mechanism are spread across a huge number of scientific articles. These articles are a large-scale knowledge source and can have a huge impact on disseminating knowledge about the mechanisms of certain biological processes. A knowledge graph (KG) can be constructed by integrating such facts and data and be used for data integration, exploration, and federated queries. However, exploration and querying large-scale KGs is tedious for certain groups of users due to a lack of knowledge about underlying data assets or semantic technologies. A question-answering (QA) system allows the answer of natural language questions over KGs automatically using triples contained in a KG. Recently, the use and adaption of digital assistants are getting wider owing to their capability at enabling users to voice commands to control smart systems or devices. This paper is about using Amazon Alexa's voice-enabled interface for QA over KGs. As a proof-of-concept, we use the well-known DisgeNET KG, which contains knowledge covering 1.13 million gene-disease associations between 21,671 genes and 30,170 diseases, disorders, and clinical or abnormal human phenotypes. Our study shows how Alex could be of help to find facts about certain biological entities from large-scale knowledge bases.
A key challenge for Industry 4.0 applications is to develop control systems for automated manufacturing services that are capable of addressing both data integration and semantic interoperability issues, as well as monitoring and decision making tasks. To address such an issue in advanced manufacturing systems, principled knowledge representation approaches based on formal ontologies have been proposed as a foundation to information management and maintenance in presence of heterogeneous data sources. In addition, ontologies provide reasoning and querying capabilities to aid domain experts and end users in the context of constraint validation and decision making. Finally, ontology-based approaches to advanced manufacturing services can support the explainability and interpretability of the behaviour of monitoring, control, and simulation systems that are based on black-box machine learning algorithms. In this work, we provide a novel ontology for the classification of process-induced defects known from the metal additive manufacturing literature. Together with a formal representation of the characterising features and sources of defects, we integrate our knowledge base with state-of-the-art ontologies in the field. Our knowledge base aims at enhancing the modelling capabilities of additive manufacturing ontologies by adding further defect analysis terminology and diagnostic inference features.
More and more, with the growing focus on large scale analytics, we are confronted with the need of integrating data from multiple sources. The problem is that these data are impossible to reuse as-is. The net result is high cost, with the further drawback that the resulting integrated data will again be hardly reusable as-is. iTelos is a general purpose methodology aiming at minimizing the effects of this process. The intuition is that data will be treated differently based on their popularity: the more a certain set of data have been reused, the more they will be reused and the less they will be changed across reuses, thus decreasing the overall data preprocessing costs, while increasing backward compatibility and future sharing
Industrial analytics that includes among others equipment diagnosis and anomaly detection heavily relies on integration of heterogeneous production data. Knowledge Graphs (KGs) as the data format and ontologies as the unified data schemata are a prominent solution that offers high quality data integration and a convenient and standardised way to exchange data and to layer analytical applications over it. However, poor design of ontologies of high degree of mismatch between them and industrial data naturally lead to KGs of low quality that impede the adoption and scalability of industrial analytics. Indeed, such KGs substantially increase the training time of writing queries for users, consume high volume of storage for redundant information, and are hard to maintain and update. To address this problem we propose an ontology reshaping approach to transform ontologies into KG schemata that better reflect the underlying data and thus help to construct better KGs. In this poster we present a preliminary discussion of our on-going research, evaluate our approach with a rich set of SPARQL queries on real-world industry data at Bosch and discuss our findings.
Single-cell RNA-seq datasets are growing in size and complexity, enabling the study of cellular composition changes in various biological/clinical contexts. Scalable dimensionality reduction techniques are in need to disentangle biological variation in them, while accounting for technical and biological confounders. In this work, we extend a popular approach for probabilistic non-linear dimensionality reduction, the Gaussian process latent variable model, to scale to massive single-cell datasets while explicitly accounting for technical and biological confounders. The key idea is to use an augmented kernel which preserves the factorisability of the lower bound allowing for fast stochastic variational inference. We demonstrate its ability to reconstruct latent signatures of innate immunity recovered in Kumasaka et al. (2021) with 9x lower training time. We further analyze a COVID dataset and demonstrate across a cohort of 130 individuals, that this framework enables data integration while capturing interpretable signatures of infection. Specifically, we explore COVID severity as a latent dimension to refine patient stratification and capture disease-specific gene expression.
Interoperability issues concerning observational data have gained attention in recent times. Automated data integration is important when it comes to the scientific analysis of observational data from different sources. However, it is hampered by various data interoperability issues. We focus exclusively on semantic interoperability issues for observational characteristics. We propose a use-case-driven approach to identify general classes of interoperability issues. In this paper, this is exemplarily done for the use-case of citizen science fireball observations. We derive key concepts for the identified interoperability issues that are generalizable to observational data in other fields of science. These key concepts contain several modeling challenges, and we broadly describe each modeling challenges associated with its interoperability issue. We believe, that addressing these challenges with a set of ontology design patterns will be an effective means for unified semantic modeling, paving the way for a unified approach for resolving interoperability issues in observational data. We demonstrate this with one design pattern, highlighting the importance and need for ontology design patterns for observational data, and leave the remaining patterns to future work. Our paper thus describes interoperability issues along with modeling challenges as a starting point for developing a set of extensible and reusable design patterns.
ICLP is the premier international event for presenting research in logic programming. Contributions to ICLP 2022 were sought in all areas of logic programming, including but not limited to: Foundations: Semantics, Formalisms, Nonmonotonic reasoning, Knowledge representation. Languages issues: Concurrency, Objects, Coordination, Mobility, Higher order, Types, Modes, Assertions, Modules, Meta-programming, Logic-based domain-specific languages, Programming techniques. Programming support: Program analysis, Transformation, Validation, Verification, Debugging, Profiling, Testing, Execution visualization. Implementation: Compilation, Virtual machines, Memory management, Parallel and Distributed execution, Constraint handling rules, Tabling, Foreign interfaces, User interfaces. Related Paradigms and Synergies: Inductive and coinductive logic programming, Constraint logic programming, Answer set programming, Interaction with SAT, SMT and CSP solvers, Theorem proving, Argumentation, Probabilistic programming, Machine learning. Applications: Databases, Big data, Data integration and federation, Software engineering, Natural language processing, Web and semantic web, Agents, Artificial intelligence, Computational life sciences, Cyber-security, Robotics, Education.
The management of people with long-term or chronic illness is one of the biggest challenges for national health systems. In fact, these diseases are among the leading causes of hospitalization, especially for the elderly, and huge amount of resources required to monitor them leads to problems with sustainability of the healthcare systems. The increasing diffusion of portable devices and new connectivity technologies allows the implementation of telemonitoring system capable of providing support to health care providers and lighten the burden on hospitals and clinics. In this paper, we present the implementation of a telemonitoring platform for healthcare, designed to capture several types of physiological health parameters from different consumer mobile and custom devices. Consumer medical devices can be integrated into the platform via the Google Fit ecosystem that supports hundreds of devices, while custom devices can directly interact with the platform with standard communication protocols. The platform is designed to process the acquired data using machine learning algorithms, and to provide patients and physicians the physiological health parameters with a user-friendly, comprehensive, and easy to understand dashboard which monitors the parameters through time. Preliminary usability tests show a good user satisfaction in terms of functionality and usefulness.
Cancer survival prediction is important for developing personalized treatments and inducing disease-causing mechanisms. Multi-omics data integration is attracting widespread interest in cancer research for providing information for understanding cancer progression at multiple genetic levels. Many works, however, are limited because of the high dimensionality and heterogeneity of multi-omics data. In this paper, we propose a novel method to integrate multi-omics data for cancer survival prediction, called Stacked AutoEncoder-based Survival Prediction Neural Network (SAEsurv-net). In the cancer survival prediction for TCGA cases, SAEsurv-net addresses the curse of dimensionality with a two-stage dimensionality reduction strategy and handles multi-omics heterogeneity with a stacked autoencoder model. The two-stage dimensionality reduction strategy achieves a balance between computation complexity and information exploiting. The stacked autoencoder model removes most heterogeneities such as data's type and size in the first group of autoencoders, and integrates multiple omics data in the second autoencoder. The experiments show that SAEsurv-net outperforms models based on a single type of data as well as other state-of-the-art methods.
Machine learning (ML) is playing an increasingly important role in data management tasks, particularly in Data Integration and Preparation (DI&P). The success of ML-based approaches, however, heavily relies on the availability of large-scale, high-quality labeled datasets for different tasks. Moreover, the wide variety of DI&P tasks and pipelines oftentimes requires customizing ML solutions which can incur a significant cost for model engineering and experimentation. These factors inevitably hold back the adoption of ML-based approaches to new domains and tasks. In this paper, we propose Sudowoodo, a multi-purpose DI&P framework based on contrastive representation learning. Sudowoodo features a unified, matching-based problem definition capturing a wide range of DI&P tasks including Entity Matching (EM) in data integration, error correction in data cleaning, semantic type detection in data discovery, and more. Contrastive learning enables Sudowoodo to learn similarity-aware data representations from a large corpus of data items (e.g., entity entries, table columns) without using any labels. The learned representations can later be either directly used or facilitate fine-tuning with only a few labels to support different DI&P tasks. Our experiment results show that Sudowoodo achieves multiple state-of-the-art results on different levels of supervision and outperforms previous best specialized blocking or matching solutions for EM. Sudowoodo also achieves promising results in data cleaning and semantic type detection tasks showing its versatility in DI&P applications.
Human life expectancy has dramatically improved over the course of the last century. Although this reflects a global improvement in sanitation and medical care, this also implies that more people suffer from diseases that typically manifest later in life, like Alzheimer and atherosclerosis. Increasing healthspan by delaying or reverting the development of these age-related diseases has therefore become an urgent challenge in biomedical research. Research in this field is complicated by the multi-factorial nature of age-related diseases. They are rooted in complex physiological mechanisms impacted by heritable, environment and life-style factors that can be unique to each individual. Although technological advances in high-throughput biomolecular assays have enabled researchers to investigate individual physiology at the molecular level, integrating information about its different components, and accounting for individual variations remains a challenge. We are using a large collection of omics and phenotype data derived from the BXD mouse genetic diversity panel to explore how good data management practices, as fostered by the FAIR principles, paired with an explainable artificial intelligence framework, can provide solutions to decipher the complex roots of age-related diseases. These developments will help to propose innovative approaches to extend healthspan in the aging global population.