Cancer is a complex disease with significant social and economic impact. Advancements in high-throughput molecular assays and the reduced cost for performing high-quality multi-omics measurements have fuelled insights through machine learning . Previous studies have shown promise on using multiple omic layers to predict survival and stratify cancer patients. In this paper, we developed a Supervised Autoencoder (SAE) model for survival-based multi-omic integration which improves upon previous work, and report a Concrete Supervised Autoencoder model (CSAE), which uses feature selection to jointly reconstruct the input features as well as predict survival. Our experiments show that our models outperform or are on par with some of the most commonly used baselines, while either providing a better survival separation (SAE) or being more interpretable (CSAE). We also perform a feature selection stability analysis on our models and notice that there is a power-law relationship with features which are commonly associated with survival. The code for this project is available at: https://github.com/phcavelar/coxae
Engineered solutions are becoming more complex and multi-disciplinary in nature. This evolution requires new techniques to enhance design and analysis tasks that incorporate data integration and interoperability across various engineering tool suites spanning multiple domains at different abstraction levels. Semantic Web Technologies (SWT) offer data integration and interoperability benefits as well as other opportunities to enhance reasoning across knowledge represented in multiple disparate models. This paper introduces the Digital Engineering Framework for Integration and Interoperability (DEFII) for incorporating SWT into engineering design and analysis tasks. The framework includes three notional interfaces for interacting with ontology-aligned data. It also introduces a novel Model Interface Specification Diagram (MISD) that provides a tool-agnostic model representation enabled by SWT that exposes data stored for use by external users through standards-based interfaces. Use of the framework results in a tool-agnostic authoritative source of truth spanning the entire project, system, or mission.
Entity Resolution (ER) links entities that refer to the same real-world entity from different sources. Existing work usually takes pairs of entities as input and judges those pairs independently. However, there is often interdependence between different pairs of ER decisions, e.g., the entities from the same data source are usually semantically related to each other. Furthermore, current ER approaches are mainly based on attribute similarity comparison, but ignore interdependence between attributes. To address the limits of existing methods, we propose HierGAT, a new method for ER based on a Hierarchical Graph Attention Transformer Network, which can model and exploit the interdependence between different ER decisions. The benefit of our method comes from: 1) The graph attention network model for joint ER decisions; 2) The graph-attention capability to identify the discriminative words from attributes and find the most discriminative attributes. Furthermore, we propose to learn contextual embeddings to enrich word embeddings for better performance. The experimental results on publicly available benchmark datasets show that HierGAT outperforms DeepMatcher by up to 32.5% of F1 score and up to 8.7% of F1 score compared with Ditto.
The integration of multimodal data presents a challenge in cases when the study of a given phenomena by different instruments or conditions generates distinct but related domains. Many existing data integration methods assume a known one-to-one correspondence between domains of the entire dataset, which may be unrealistic. Furthermore, existing manifold alignment methods are not suited for cases where the data contains domain-specific regions, i.e., there is not a counterpart for a certain portion of the data in the other domain. We propose Diffusion Transport Alignment (DTA), a semi-supervised manifold alignment method that exploits prior correspondence knowledge between only a few points to align the domains. By building a diffusion process, DTA finds a transportation plan between data measured from two heterogeneous domains with different feature spaces, which by assumption, share a similar geometrical structure coming from the same underlying data generating process. DTA can also compute a partial alignment in a data-driven fashion, resulting in accurate alignments when some data are measured in only one domain. We empirically demonstrate that DTA outperforms other methods in aligning multimodal data in this semisupervised setting. We also empirically show that the alignment obtained by DTA can improve the performance of machine learning tasks, such as domain adaptation, inter-domain feature mapping, and exploratory data analysis, while outperforming competing methods.
Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which can no longer completely be labeled manually. In recent years, deep learning algorithms achieved impressive results in both pixel-level labeling (semantic segmentation) and the labeling of separate instances of the same class (instance segmentation). In this review, we examine how these algorithms were adapted to the task of segmenting cellular and sub-cellular structures in EM images. The special challenges posed by such images and the network architectures that overcame some of them are described. Moreover, a thorough overview is also provided on the notable datasets that contributed to the proliferation of deep learning in EM. Finally, an outlook of current trends and future prospects of EM segmentation is given, especially in the area of label-free learning.
Computational pathology is part of precision oncology medicine. The integration of high-throughput data including genomics, transcriptomics, proteomics, metabolomics, pathomics, and radiomics into clinical practice improves cancer treatment plans, treatment cycles, and cure rates, and helps doctors open up innovative approaches to patient prognosis. In the past decade, rapid advances in artificial intelligence, chip design and manufacturing, and mobile computing have facilitated research in computational pathology and have the potential to provide better-integrated solutions for whole-slide images, multi-omics data, and clinical informatics. However, tumor computational pathology now brings some challenges to the application of tumour screening, diagnosis and prognosis in terms of data integration, hardware processing, network sharing bandwidth and machine learning technology. This review investigates image preprocessing methods in computational pathology from a pathological and technical perspective, machine learning-based methods, and applications of computational pathology in breast, colon, prostate, lung, and various tumour disease scenarios. Finally, the challenges and prospects of machine learning in computational pathology applications are discussed.
Anomaly subgraph detection has been widely used in various applications, ranging from cyber attack in computer networks to malicious activities in social networks. Despite an increasing need for federated anomaly detection across multiple attributed networks, only a limited number of approaches are available for this problem. Federated anomaly detection faces two major challenges. One is that isolated data in most industries are restricted share with others for data privacy and security. The other is most of the centralized approaches training based on data integration. The main idea of federated anomaly detection is aligning private anomalies from local data owners on the public anomalies from the attributed network in the server through public anomalies to federate local anomalies. In each private attributed network, the detected anomaly subgraph is aligned with an anomaly subgraph in the public attributed network. The significant public anomaly subgraphs are selected for federated private anomalies while preventing local private data leakage. The proposed algorithm FadMan is a vertical federated learning framework for public node aligned with many private nodes of different features, and is validated on two tasks correlated anomaly detection on multiple attributed networks and anomaly detection on an attributeless network using five real-world datasets. In the first scenario, FadMan outperforms competitive methods by at least 12% accuracy at 10% noise level. In the second scenario, by analyzing the distribution of abnormal nodes, we find that the nodes of traffic anomalies are associated with the event of postgraduate entrance examination on the same day.
Identification of human genes involved in the aging process is critical due to the incidence of many diseases with age. A state-of-the-art approach for this purpose infers a weighted dynamic aging-specific subnetwork by mapping gene expression (GE) levels at different ages onto the protein-protein interaction network (PPIN). Then, it analyzes this subnetwork in a supervised manner by training a predictive model to learn how network topologies of known aging- vs. non-aging-related genes change across ages. Finally, it uses the trained model to predict novel aging-related genes. However, the best current subnetwork resulting from this approach still yields suboptimal prediction accuracy. This could be because it was inferred using outdated GE and PPIN data. Here, we evaluate whether analyzing a weighted dynamic aging-specific subnetwork inferred from newer GE and PPIN data improves prediction accuracy upon analyzing the best current subnetwork inferred from outdated data. Unexpectedly, we find that not to be the case. To understand this, we perform aging-related pathway and Gene Ontology (GO) term enrichment analyses. We find that the suboptimal prediction accuracy, regardless of which GE or PPIN data is used, may be caused by the current knowledge about which genes are aging-related being incomplete, or by the current methods for inferring or analyzing an aging-specific subnetwork being unable to capture all of the aging-related knowledge. These findings can potentially guide future directions towards improving supervised prediction of aging-related genes via -omics data integration.
Modern high-throughput sequencing technologies have enabled us to profile multiple molecular modalities from the same single cell, providing unprecedented opportunities to assay celluar heterogeneity from multiple biological layers. However, the datasets generated from these technologies tend to have high level of noise and are highly sparse, bringing challenges to data analysis. In this paper, we develop a novel information-theoretic co-clustering-based multi-view learning (scICML) method for multi-omics single-cell data integration. scICML utilizes co-clusterings to aggregate similar features for each view of data and uncover the common clustering pattern for cells. In addition, scICML automatically matches the clusters of the linked features across different data types for considering the biological dependency structure across different types of genomic features. Our experiments on four real-world datasets demonstrate that scICML improves the overall clustering performance and provides biological insights into the data analysis of peripheral blood mononuclear cells.
Semiconductor supply chains are described by significant demand fluctuation that increases as one moves up the supply chain, the so-called bullwhip effect. To counteract, semiconductor manufacturers aim to optimize capacity utilization, to deliver with shorter lead times and exploit this to generate revenue. Additionally, in a competitive market, firms seek to maintain customer relationships while applying revenue management strategies such as dynamic pricing. Price change potentially generates conflicts with customers. In this paper, we present KnowGraph-PM, a knowledge graph-based dynamic pricing model. The semantic model uses the potential of faster delivery and shorter lead times to define premium prices, thus entail increased profits based on the customer profile. The knowledge graph enables the integration of customer-related information, e.g., customer class and location to customer order data. The pricing algorithm is realized as a SPARQL query that relies on customer profile and order behavior to determine the corresponding price premium. We evaluate the approach by calculating the revenue generated after applying the pricing algorithm. Based on competency questions that translate to SPARQL queries, we validate the created knowledge graph. We demonstrate that semantic data integration enables customer-tailored revenue management.
Recently, industrial recommendation services have been boosted by the continual upgrade of deep learning methods. However, they still face de-biasing challenges such as exposure bias and cold-start problem, where circulations of machine learning training on human interaction history leads algorithms to repeatedly suggest exposed items while ignoring less-active ones. Additional problems exist in multi-scenario platforms, e.g. appropriate data fusion from subsidiary scenarios, which we observe could be alleviated through graph structured data integration via message passing. In this paper, we present a multi-graph structured multi-scenario recommendation solution, which encapsulates interaction data across scenarios with multi-graph and obtains representation via graph learning. Extensive offline and online experiments on real-world datasets are conducted where the proposed method demonstrates an increase of 0.63% and 0.71% in CTR and Video Views per capita on new users over deployed set of baselines and outperforms regular method in increasing the number of outer-scenario videos by 25% and video watches by 116%, validating its superiority in activating cold videos and enriching target recommendation.
Data integration has been recently challenged by the need to handle large volumes of data, arriving at high velocity from a variety of sources, which demonstrate varying levels of veracity. This challenging setting, often referred to as big data, renders many of the existing techniques, especially those that are human-intensive, obsolete. Big data also produces technological advancements such as Internet of things, cloud computing, and deep learning, and accordingly, provides a new, exciting, and challenging research agenda. Given the availability of data and the improvement of machine learning techniques, this blog discusses the respective roles of humans and machines in achieving cognitive tasks in matching, aiming to determine whether traditional roles of humans and machines are subject to change. Such investigation, we believe, will pave a way to better utilize both human and machine resources in new and innovative manners. We shall discuss two possible modes of change, namely humans out and humans in. Humans out aim at exploring out-of-the-box latent matching reasoning using machine learning algorithms when attempting to overpower human matcher performance. Pursuing out-of-the-box thinking, machine and deep learning can be involved in matching. Humans in explores how to better involve humans in the matching loop by assigning human matchers with a symmetric role to algorithmic matcher in the matching process.
The current cancer treatment practice collects multimodal data, such as radiology images, histopathology slides, genomics and clinical data. The importance of these data sources taken individually has fostered the recent raise of radiomics and pathomics, i.e. the extraction of quantitative features from radiology and histopathology images routinely collected to predict clinical outcomes or to guide clinical decisions using artificial intelligence algorithms. Nevertheless, how to combine them into a single multimodal framework is still an open issue. In this work we therefore develop a multimodal late fusion approach that combines hand-crafted features computed from radiomics, pathomics and clinical data to predict radiation therapy treatment outcomes for non-small-cell lung cancer patients. Within this context, we investigate eight different late fusion rules (i.e. product, maximum, minimum, mean, decision template, Dempster-Shafer, majority voting, and confidence rule) and two patient-wise aggregation rules leveraging the richness of information given by computer tomography images and whole-slide scans. The experiments in leave-one-patient-out cross-validation on an in-house cohort of 33 patients show that the proposed multimodal paradigm with an AUC equal to $90.9\%$ outperforms each unimodal approach, suggesting that data integration can advance precision medicine. As a further contribution, we also compare the hand-crafted representations with features automatically computed by deep networks, and the late fusion paradigm with early fusion, another popular multimodal approach. In both cases, the experiments show that the proposed multimodal approach provides the best results.
Since data is often stored in different sources, it needs to be integrated to gather a global view that is required in order to create value and derive knowledge from it. A critical step in data integration is schema matching which aims to find semantic correspondences between elements of two schemata. In order to reduce the manual effort involved in schema matching, many solutions for the automatic determination of schema correspondences have already been developed. In this paper, we propose a novel end-to-end approach for schema matching based on neural embeddings. The main idea is to use a two-step approach consisting of a table matching step followed by an attribute matching step. In both steps we use embeddings on different levels either representing the whole table or single attributes. Our results show that our approach is able to determine correspondences in a robust and reliable way and compared to traditional schema matching approaches can find non-trivial correspondences.
Recent advances in multimodal single-cell technologies have enabled simultaneous acquisitions of multiple omics data from the same cell, providing deeper insights into cellular states and dynamics. However, it is challenging to learn the joint representations from the multimodal data, model the relationship between modalities, and, more importantly, incorporate the vast amount of single-modality datasets into the downstream analyses. To address these challenges and correspondingly facilitate multimodal single-cell data analyses, three key tasks have been introduced: $\textit{modality prediction}$, $\textit{modality matching}$ and $\textit{joint embedding}$. In this work, we present a general Graph Neural Network framework $\textit{scMoGNN}$ to tackle these three tasks and show that $\textit{scMoGNN}$ demonstrates superior results in all three tasks compared with the state-of-the-art and conventional approaches. Our method is an official winner in the overall ranking of $\textit{Modality prediction}$ from NeurIPS 2021 Competition, and all implementations of our methods have been integrated into DANCE package~\url{https://github.com/OmicsML/dance}.
Many statistical machine approaches could ultimately highlight novel features of the etiology of complex diseases by analyzing multi-omics data. However, they are sensitive to some deviations in distribution when the observed samples are potentially contaminated with adversarial corrupted outliers (e.g., a fictional data distribution). Likewise, statistical advances lag in supporting comprehensive data-driven analyses of complex multi-omics data integration. We propose a novel non-linear M-estimator-based approach, "robust kernel machine regression (RobKMR)," to improve the robustness of statistical machine regression and the diversity of fictional data to examine the higher-order composite effect of multi-omics datasets. We address a robust kernel-centered Gram matrix to estimate the model parameters accurately. We also propose a robust score test to assess the marginal and joint Hadamard product of features from multi-omics data. We apply our proposed approach to a multi-omics dataset of osteoporosis (OP) from Caucasian females. Experiments demonstrate that the proposed approach effectively identifies the inter-related risk factors of OP. With solid evidence (p-value = 0.00001), biological validations, network-based analysis, causal inference, and drug repurposing, the selected three triplets ((DKK1, SMTN, DRGX), (MTND5, FASTKD2, CSMD3), (MTND5, COG3, CSMD3)) are significant biomarkers and directly relate to BMD. Overall, the top three selected genes (DKK1, MTND5, FASTKD2) and one gene (SIDT1 at p-value= 0.001) significantly bond with four drugs- Tacrolimus, Ibandronate, Alendronate, and Bazedoxifene out of 30 candidates for drug repurposing in OP. Further, the proposed approach can be applied to any disease model where multi-omics datasets are available.
Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. We propose a solution for automatically semantifying biological assays. Our solution contrasts the problem of automated semantification as labeling versus clustering where the two methods are on opposite ends of the method complexity spectrum. Characteristically modeling our problem, we find the clustering solution significantly outperforms a deep neural network state-of-the-art labeling approach. This novel contribution is based on two factors: 1) a learning objective closely modeled after the data outperforms an alternative approach with sophisticated semantic modeling; 2) automatically semantifying biological assays achieves a high performance F1 of nearly 83%, which to our knowledge is the first reported standardized evaluation of the task offering a strong benchmark model.
In the era of big data, standard analysis tools may be inadequate for making inference and there is a growing need for more efficient and innovative ways to collect, process, analyze and interpret the massive and complex data. We provide an overview of challenges in big data problems and describe how innovative analytical methods, machine learning tools and metaheuristics can tackle general healthcare problems with a focus on the current pandemic. In particular, we give applications of modern digital technology, statistical methods, data platforms and data integration systems to improve diagnosis and treatment of diseases in clinical research and novel epidemiologic tools to tackle infection source problems, such as finding Patient Zero in the spread of epidemics. We make the case that analyzing and interpreting big data is a very challenging task that requires a multi-disciplinary effort to continuously create more effective methodologies and powerful tools to transfer data information into knowledge that enables informed decision making.
Entity matching is a central task in data integration which has been researched for decades. Over this time, a wide range of benchmark tasks for evaluating entity matching methods has been developed. This resource paper systematically complements, profiles, and compares 21 entity matching benchmark tasks. In order to better understand the specific challenges associated with different tasks, we define a set of profiling dimensions which capture central aspects of the matching tasks. Using these dimensions, we create groups of benchmark tasks having similar characteristics. Afterwards, we assess the difficulty of the tasks in each group by computing baseline evaluation results using standard feature engineering together with two common classification methods. In order to enable the exact reproducibility of evaluation results, matching tasks need to contain exactly defined sets of matching and non-matching record pairs, as well as a fixed development and test split. As this is not the case for some widely-used benchmark tasks, we complement these tasks with fixed sets of non-matching pairs, as well as fixed splits, and provide the resulting development and test sets for public download. By profiling and complementing the benchmark tasks, we support researchers to select challenging as well as diverse tasks and to compare matching systems on clearly defined grounds.
An increasing number of data providers have adopted shared numbering schemes such as GTIN, ISBN, DUNS, or ORCID numbers for identifying entities in the respective domain. This means for data integration that shared identifiers are often available for a subset of the entity descriptions to be integrated while such identifiers are not available for others. The challenge in these settings is to learn a matcher for entity descriptions without identifiers using the entity descriptions containing identifiers as training data. The task can be approached by learning a binary classifier which distinguishes pairs of entity descriptions for the same real-world entity from descriptions of different entities. The task can also be modeled as a multi-class classification problem by learning classifiers for identifying descriptions of individual entities. We present a dual-objective training method for BERT, called JointBERT, which combines binary matching and multi-class classification, forcing the model to predict the entity identifier for each entity description in a training pair in addition to the match/non-match decision. Our evaluation across five entity matching benchmark datasets shows that dual-objective training can increase the matching performance for seen products by 1% to 5% F1 compared to single-objective Transformer-based methods, given that enough training data is available for both objectives. In order to gain a deeper understanding of the strengths and weaknesses of the proposed method, we compare JointBERT to several other BERT-based matching methods as well as baseline systems along a set of specific matching challenges. This evaluation shows that JointBERT, given enough training data for both objectives, outperforms the other methods on tasks involving seen products, while it underperforms for unseen products. Using a combination of LIME explanations and domain-specific word classes, we analyze the matching decisions of the different deep learning models and conclude that BERT-based models are better at focusing on relevant word classes compared to RNN-based models.