Record linkage is aimed at the accurate and efficient identification of records that represent the same entity within or across disparate databases. It is a fundamental task in data integration and increasingly required for accurate decision making in application domains ranging from health analytics to national security. Traditional record linkage techniques calculate string similarities between quasi-identifying (QID) values, such as the names and addresses of people. Errors, variations, and missing QID values can however lead to low linkage quality because the similarities between records cannot be calculated accurately. To overcome this challenge, we propose a novel technique that can accurately link records even when QID values contain errors or variations, or are missing. We first generate attribute signatures (concatenated QID values) using an Apriori based selection of suitable QID attributes, and then relational signatures that encapsulate relationship information between records. Combined, these signatures can uniquely identify individual records and facilitate fast and high quality linking of very large databases through accurate similarity calculations between records. We evaluate the linkage quality and scalability of our approach using large real-world databases, showing that it can achieve high linkage quality even when the databases being linked contain substantial amounts of missing values and errors.
Corynebacterium glutamicum is a Gram-positive bacterium found in soil where the condition changes demand plasticity of the regulatory machinery. The study of such machinery at the global scale has been challenged by the lack of data integration. Here, we report three regulatory network models for C. glutamicum: strong (3040 interactions) constructed solely with regulations previously supported by directed experiments; all evidence (4665 interactions) containing the strong network, regulations previously supported by non-directed experiments, and protein-protein interactions with a direct effect on gene transcription; and sRNA (5222 interactions) containing the all evidence network and sRNA-mediated regulations. Compared to the previous version (2018), the strong and all evidence networks increased by 75 and 1225 interactions, respectively. We analyzed the system-level components of the three networks to identify how they differ and compared their structures against those for the networks of more than 40 species. The inclusion of the sRNAs regulations changed the proportions of the system-level components and increased the number of modules but decreased their size. The C. glutamicum regulatory structure contrasted with other bacterial regulatory networks. Finally, we used the strong networks of three model organisms to provide insights and future directions of the C. glutamicum regulatory network characterization.
Identifying potential drug targets using metabolic modeling requires integrating multiple modeling methods and heterogenous biological datasets, which can be challenging without sophisticated tools. We developed COMO, a user-friendly pipeline that integrates multi-omics data processing, context-specific metabolic model development, simulations, drug databases, and disease data to aid drug discovery. COMO can be installed as a Docker image and includes intuitive instructions within a Jupyter Lab environment. It provides a comprehensive solution for multi-omics integration of bulk and single-cell RNA-seq, microarrays, and proteomics to develop context-specific metabolic models. Using public databases, open-source solutions for model construction, and a streamlined approach for predicting repurposable drugs, COMO empowers researchers to investigate low-cost alternatives and novel disease treatments. As a case study, we used the pipeline to construct metabolic models of B cells, which simulate and analyze them to predict 25 and 23 metabolic drug targets for rheumatoid arthritis and systemic lupus erythematosus, respectively. COMO can be used to construct models for any cell or tissue type and identify drugs for any human disease. The pipeline has the potential to improve the health of the global community cost-effectively by providing high-confidence targets to pursue in preclinical and clinical studies.
Multimodal imaging has transformed neuroscience research. While it presents unprecedented opportunities, it also imposes serious challenges. Particularly, it is difficult to combine the merits of the interpretability attributed to a simple association model with the flexibility achieved by a highly adaptive nonlinear model. In this article, we propose an orthogonalized kernel debiased machine learning approach, which is built upon the Neyman orthogonality and a form of decomposition orthogonality, for multimodal data analysis. We target the setting that naturally arises in almost all multimodal studies, where there is a primary modality of interest, plus additional auxiliary modalities. We establish the root-$N$-consistency and asymptotic normality of the estimated primary parameter, the semi-parametric estimation efficiency, and the asymptotic validity of the confidence band of the predicted primary modality effect. Our proposal enjoys, to a good extent, both model interpretability and model flexibility. It is also considerably different from the existing statistical methods for multimodal data integration, as well as the orthogonality-based methods for high-dimensional inferences. We demonstrate the efficacy of our method through both simulations and an application to a multimodal neuroimaging study of Alzheimer's disease.
AI application developers typically begin with a dataset of interest and a vision of the end analytic or insight they wish to gain from the data at hand. Although these are two very important components of an AI workflow, one often spends the first few weeks (sometimes months) in the phase we refer to as data conditioning. This step typically includes tasks such as figuring out how to prepare data for analytics, dealing with inconsistencies in the dataset, and determining which algorithm (or set of algorithms) will be best suited for the application. Larger, faster, and messier datasets such as those from Internet of Things sensors, medical devices or autonomous vehicles only amplify these issues. These challenges, often referred to as the three Vs (volume, velocity, variety) of Big Data, require low-level tools for data management, preparation and integration. In most applications, data can come from structured and/or unstructured sources and often includes inconsistencies, formatting differences, and a lack of ground-truth labels. In this report, we highlight a number of tools that can be used to simplify data integration and preparation steps. Specifically, we focus on data integration tools and techniques, a deep dive into an exemplar data integration tool, and a deep-dive in the evolving field of knowledge graphs. Finally, we provide readers with a list of practical steps and considerations that they can use to simplify the data integration challenge. The goal of this report is to provide readers with a view of state-of-the-art as well as practical tips that can be used by data creators that make data integration more seamless.
Social media are digitalising massive amounts of users' cognitions in terms of timelines and emotional content. Such Big Data opens unprecedented opportunities for investigating cognitive phenomena like perception, personality and information diffusion but requires suitable interpretable frameworks. Since social media data come from users' minds, worthy candidates for this challenge are cognitive networks, models of cognition giving structure to mental conceptual associations. This work outlines how cognitive network science can open new, quantitative ways for understanding cognition through online media, like: (i) reconstructing how users semantically and emotionally frame events with contextual knowledge unavailable to machine learning, (ii) investigating conceptual salience/prominence through knowledge structure in social discourse; (iii) studying users' personality traits like openness-to-experience, curiosity, and creativity through language in posts; (iv) bridging cognitive/emotional content and social dynamics via multilayer networks comparing the mindsets of influencers and followers. These advancements combine cognitive-, network- and computer science to understand cognitive mechanisms in both digital and real-world settings but come with limitations concerning representativeness, individual variability and data integration. Such aspects are discussed along the ethical implications of manipulating socio-cognitive data. In the future, reading cognitions through networks and social media can expose cognitive biases amplified by online platforms and relevantly inform policy making, education and markets about massive, complex cognitive trends.
Semantic web technologies have shown their effectiveness, especially when it comes to knowledge representation, reasoning, and data integration. However, the original semantic web vision, whereby machine readable web data could be automatically actioned upon by intelligent software web agents, has yet to be realised. In order to better understand the existing technological opportunities and challenges, in this paper we examine the status quo in terms of intelligent software web agents, guided by research with respect to requirements and architectural components, coming from the agents community. We use the identified requirements to both further elaborate on the semantic web agent motivating use case scenario, and to summarise different perspectives on the requirements from the semantic web agent literature. We subsequently propose a hybrid semantic web agent architecture, and use the various components and subcomponents in order to provide a focused discussion in relation to existing semantic web standards and community activities. Finally, we highlight open research opportunities and challenges and take a broader perspective of the research by discussing the potential for intelligent software web agents as an enabling technology for emerging domains, such as digital assistants, cloud computing, and the internet of things.
Ontology Alignment is an important research problem applied to various fields such as data integration, data transfer, data preparation, etc. State-of-the-art (SOTA) Ontology Alignment systems typically use naive domain-dependent approaches with handcrafted rules or domain-specific architectures, making them unscalable and inefficient. In this work, we propose VeeAlign, a Deep Learning based model that uses a novel dual-attention mechanism to compute the contextualized representation of a concept which, in turn, is used to discover alignments. By doing this, not only is our approach able to exploit both syntactic and semantic information encoded in ontologies, it is also, by design, flexible and scalable to different domains with minimal effort. We evaluate our model on four different datasets from different domains and languages, and establish its superiority through these results as well as detailed ablation studies. The code and datasets used are available at https://github.com/Remorax/VeeAlign.
Integration of data from multiple omics techniques is becoming increasingly important in biomedical research. Due to non-uniformity and technical limitations in omics platforms, such integrative analyses on multiple omics, which we refer to as views, involve learning from incomplete observations with various view-missing patterns. This is challenging because i) complex interactions within and across observed views need to be properly addressed for optimal predictive power and ii) observations with various view-missing patterns need to be flexibly integrated. To address such challenges, we propose a deep variational information bottleneck (IB) approach for incomplete multi-view observations. Our method applies the IB framework on marginal and joint representations of the observed views to focus on intra-view and inter-view interactions that are relevant for the target. Most importantly, by modeling the joint representations as a product of marginal representations, we can efficiently learn from observed views with various view-missing patterns. Experiments on real-world datasets show that our method consistently achieves gain from data integration and outperforms state-of-the-art benchmarks.
Objective: Surgical activity recognition is a fundamental step in computer-assisted interventions. This paper reviews the state-of-the-art in methods for automatic recognition of fine-grained gestures in robotic surgery focusing on recent data-driven approaches and outlines the open questions and future research directions. Methods: An article search was performed on 5 bibliographic databases with the following search terms: robotic, robot-assisted, JIGSAWS, surgery, surgical, gesture, fine-grained, surgeme, action, trajectory, segmentation, recognition, parsing. Selected articles were classified based on the level of supervision required for training and divided into different groups representing major frameworks for time series analysis and data modelling. Results: A total of 52 articles were reviewed. The research field is showing rapid expansion, with the majority of articles published in the last 4 years. Deep-learning-based temporal models with discriminative feature extraction and multi-modal data integration have demonstrated promising results on small surgical datasets. Currently, unsupervised methods perform significantly less well than the supervised approaches. Conclusion: The development of large and diverse open-source datasets of annotated demonstrations is essential for development and validation of robust solutions for surgical gesture recognition. While new strategies for discriminative feature extraction and knowledge transfer, or unsupervised and semi-supervised approaches, can mitigate the need for data and labels, they have not yet been demonstrated to achieve comparable performance. Important future research directions include detection and forecast of gesture-specific errors and anomalies. Significance: This paper is a comprehensive and structured analysis of surgical gesture recognition methods aiming to summarize the status of this rapidly evolving field.
Behavioural symptoms and urinary tract infections (UTI) are among the most common problems faced by people with dementia. One of the key challenges in the management of these conditions is early detection and timely intervention in order to reduce distress and avoid unplanned hospital admissions. Using in-home sensing technologies and machine learning models for sensor data integration and analysis provides opportunities to detect and predict clinically significant events and changes in health status. We have developed an integrated platform to collect in-home sensor data and performed an observational study to apply machine learning models for agitation and UTI risk analysis. We collected a large dataset from 88 participants with a mean age of 82 and a standard deviation of 6.5 (47 females and 41 males) to evaluate a new deep learning model that utilises attention and rational mechanism. The proposed solution can process a large volume of data over a period of time and extract significant patterns in a time-series data (i.e. attention) and use the extracted features and patterns to train risk analysis models (i.e. rational). The proposed model can explain the predictions by indicating which time-steps and features are used in a long series of time-series data. The model provides a recall of 91\% and precision of 83\% in detecting the risk of agitation and UTIs. This model can be used for early detection of conditions such as UTIs and managing of neuropsychiatric symptoms such as agitation in association with initial treatment and early intervention approaches. In our study we have developed a set of clinical pathways for early interventions using the alerts generated by the proposed model and a clinical monitoring team has been set up to use the platform and respond to the alerts according to the created intervention plans.
Detecting semantic concept of columns in tabular data is of particular interest to many applications ranging from data integration, cleaning, search to feature engineering and model building in machine learning. Recently, several works have proposed supervised learning-based or heuristic pattern-based approaches to semantic type annotation. Both have shortcomings that prevent them from generalizing over a large number of concepts or examples. Many neural network based methods also present scalability issues. Additionally, none of the known methods works well for numerical data. We propose $C^2$, a column to concept mapper that is based on a maximum likelihood estimation approach through ensembles. It is able to effectively utilize vast amounts of, albeit somewhat noisy, openly available table corpora in addition to two popular knowledge graphs to perform effective and efficient concept prediction for structured data. We demonstrate the effectiveness of $C^2$ over available techniques on 9 datasets, the most comprehensive comparison on this topic so far.
Deep neural networks excel at comprehending complex visual signals, delivering on par or even superior performance to that of human experts. However, ad-hoc visual explanations of model decisions often reveal an alarming level of reliance on exploiting non-causal visual cues that strongly correlate with the target label in training data. As such, deep neural nets suffer compromised generalization to novel inputs collected from different sources, and the reverse engineering of their decision rules offers limited interpretability. To overcome these limitations, we present a novel contrastive learning strategy called {\it Proactive Pseudo-Intervention} (PPI) that leverages proactive interventions to guard against image features with no causal relevance. We also devise a novel causally informed salience mapping module to identify key image pixels to intervene, and show it greatly facilitates model interpretability. To demonstrate the utility of our proposals, we benchmark on both standard natural images and challenging medical image datasets. PPI-enhanced models consistently deliver superior performance relative to competing solutions, especially on out-of-domain predictions and data integration from heterogeneous sources. Further, our causally trained saliency maps are more succinct and meaningful relative to their non-causal counterparts.
The automatic search performance of search engines has become an essential part of measuring the difference in user experience. An efficient automatic search system can significantly improve the performance of search engines and increase user traffic. Hadoop has strong data integration and analysis capabilities, while R has excellent statistical capabilities in linear regression. This article will propose a linear regression based on Hadoop and R to quantify the efficiency of the automatic retrieval system. We use R's functional properties to transform the user's search results upon linear correlations. In this way, the final output results have multiple display forms instead of web page preview interfaces. This article provides feasible solutions to the drawbacks of current search engine algorithms lacking once or twice search accuracies and multiple types of search results. We can conduct personalized regression analysis for user's needs with public datasets and optimize resources integration for most relevant information.
Patient similarity analysis is important in health care applications. It takes patient information such as their electronic medical records and genetic data as input and computes the pairwise similarity between patients. Procedures of typical a patient similarity study can be divided into several steps including data integration, similarity measurement, and neighborhood identification. And according to an analysis of patient similarity, doctors can easily find the most suitable treatments. There are many methods to analyze the similarity such as cluster analysis. And during machine learning become more and more popular, Using neural networks such as CNN is a new hot topic. This review summarizes representative methods used in each step and discusses applications of patient similarity networks especially in the context of precision medicine.
Background. Human aging is linked to many prevalent diseases. The aging process is highly influenced by genetic factors. Hence, it is important to identify human aging-related genes. We focus on supervised prediction of such genes. Gene expression-based methods for this purpose study genes in isolation from each other. While protein-protein interaction (PPI) network-based methods for this purpose account for interactions between genes' protein products, current PPI network data are context-unspecific, spanning different biological conditions. Instead, here, we focus on an aging-specific subnetwork of the entire PPI network, obtained by integrating aging-specific gene expression data and PPI network data. The potential of such data integration has been recognized but mostly in the context of cancer. So, we are the first to propose a supervised learning framework for predicting aging-related genes from an aging-specific PPI subnetwork. Results. In a systematic and comprehensive evaluation, we find that in many of the evaluation tests: (i) using an aging-specific subnetwork indeed yields more accurate aging-related gene predictions than using the entire network, and (ii) predictive methods from our framework that have not previously been used for supervised prediction of aging-related genes outperform existing prominent methods for the same purpose. Conclusion. These results justify the need for our framework.
In this review we make the statement that hybrid models in oncology are required as a mean for enhanced data integration. In the context of systems oncology, experimental and clinical data need to be at the heart of the models developments from conception to validation to ensure a relevant use of the models in the clinical context. The main applications pursued are to improve diagnosis and to optimize therapies.We first present the Successes achieved thanks to hybrid modelling approaches to advance knowledge, treatments or drug discovery. Then we present the Challenges than need to be addressed to allow for a better integration of the model parts and of the data into the models. And Finally, the Hopes with a focus towards making personalised medicine a reality. Mathematics Subject Classification. 35Q92, 68U20, 68T05, 92-08, 92B05.
Publicly available social media archives facilitate research in a variety of fields, such as data science, sociology or the digital humanities, where Twitter has emerged as one of the most prominent sources. However, obtaining, archiving and annotating large amounts of tweets is costly. In this paper, we describe TweetsKB, a publicly available corpus of currently more than 1.5 billion tweets, spanning almost 5 years (Jan'13-Nov'17). Metadata information about the tweets as well as extracted entities, hashtags, user mentions and sentiment information are exposed using established RDF/S vocabularies. Next to a description of the extraction and annotation process, we present use cases to illustrate scenarios for entity-centric information exploration, data integration and knowledge discovery facilitated by TweetsKB.
In recent years numerous attempts to understand the human brain were undertaken from a network point of view. A network framework takes into account the relationships between the different parts of the system and enables to examine how global and complex functions might emerge from network topology. Previous work revealed that the human brain features 'small world' characteristics and that cortical hubs tend to interconnect among themselves. However, in order to fully understand the topological structure of hubs one needs to go beyond the properties of a specific hub and examine the various structural layers of the network. To address this topic further, we applied an analysis known in statistical physics and network theory as k-shell decomposition analysis. The analysis was applied on a human cortical network, derived from MRI\DSI data of six participants. Such analysis enables us to portray a detailed account of cortical connectivity focusing on different neighborhoods of interconnected layers across the cortex. Our findings reveal that the human cortex is highly connected and efficient, and unlike the internet network contains no isolated nodes. The cortical network is comprised of a nucleus alongside shells of increasing connectivity that formed one connected giant component. All these components were further categorized into three hierarchies in accordance with their connectivity profile, with each hierarchy reflecting different functional roles. Such a model may explain an efficient flow of information from the lowest hierarchy to the highest one, with each step enabling increased data integration. At the top, the highest hierarchy (the nucleus) serves as a global interconnected collective and demonstrates high correlation with consciousness related regions, suggesting that the nucleus might serve as a platform for consciousness to emerge.
The goals of the Triple Aim of health care and the goals of P4 medicine outline objectives that require a significant health informatics component. However, the goals do not provide specifications about how all of the new individual patient data will be combined in meaningful ways and with data from other sources, like epidemiological data, to promote the health of individuals and society. We seem to have more data than ever before but few resources and means to use it efficiently. We need a general, extensible solution that integrates and homogenizes data of disparate origin, incompatible formats, and multiple spatial and temporal scales. To address this problem, we introduce the Scientific Knowledge Extraction from Data (SKED) architecture, as a technology-agnostic framework to minimize the overhead of data integration, permit reuse of analytical pipelines, and guarantee reproducible quantitative results. The SKED architecture consists of a Resource Allocation Service to locate resources, and the definition of data primitives to simplify and harmonize data. SKED allows automated knowledge discovery and provides a platform for the realization of the major goals of modern health care.