The web is a treasure trove for data that is increasingly used by computer scientists for building large machine learning models as well as non-computer scientists for social studies or marketing analyses. As such, web-crawling is an essential tool for both computational and non-computational scientists to conduct research. However, most of the existing web crawler frameworks and software products either require professional coding skills without an easy-to-use graphic user interface or are expensive and limited in features. They are thus not friendly to newbies and inconvenient for complicated web-crawling tasks. In this paper, we present an easy-to-use visual web crawler system, EasySpider, for designing and executing web crawling tasks without coding. The workflow of a new web crawling task can be visually programmed by following EasySpider’s visual wizard on the target webpages using an intuitive point-and-click interface. The generated crawler task can then be easily invoked locally or as a web service. Our EasySpider is cross-platform and flexible to adapt to different web-resources. It also supports advanced configuration for complicated tasks and extension. The whole system is open-sourced and transparent for free-access at GitHub, which avoids possible privacy leakage.
Federated Learning is a distributed machine learning approach that enables geographically distributed data silos to collaboratively learn a joint machine learning model without sharing data. Most of the existing work operates on unstructured data, such as images or text, or on structured data assumed to be consistent across the different sites. However, sites often have different schemata, data formats, data values, and access patterns. The field of data integration has developed many methods to address these challenges, including techniques for data exchange and query rewriting using declarative schema mappings, and for entity linkage. Therefore, we propose an architectural vision for an end-to-end Federated Learning and Integration system, incorporating the critical steps of data harmonization and data imputation, to spur further research on the intersection of data management information systems and machine learning.
Machine learning (ML) in healthcare presents numerous opportunities for enhancing patient care, population health, and healthcare providers' workflows. However, the real-world clinical and cost benefits remain limited due to challenges in data privacy, heterogeneous data sources, and the inability to fully leverage multiple data modalities. In this perspective paper, we introduce "patchwork learning" (PL), a novel paradigm that addresses these limitations by integrating information from disparate datasets composed of different data modalities (e.g., clinical free-text, medical images, omics) and distributed across separate and secure sites. PL allows the simultaneous utilization of complementary data sources while preserving data privacy, enabling the development of more holistic and generalizable ML models. We present the concept of patchwork learning and its current implementations in healthcare, exploring the potential opportunities and applicable data sources for addressing various healthcare challenges. PL leverages bridging modalities or overlapping feature spaces across sites to facilitate information sharing and impute missing data, thereby addressing related prediction tasks. We discuss the challenges associated with PL, many of which are shared by federated and multimodal learning, and provide recommendations for future research in this field. By offering a more comprehensive approach to healthcare data integration, patchwork learning has the potential to revolutionize the clinical applicability of ML models. This paradigm promises to strike a balance between personalization and generalizability, ultimately enhancing patient experiences, improving population health, and optimizing healthcare providers' workflows.
Entity Matching is the task of deciding if two entity descriptions refer to the same real-world entity. State-of-the-art entity matching methods often rely on fine-tuning Transformer models such as BERT or RoBERTa. Two major drawbacks of using these models for entity matching are that (i) the models require significant amounts of fine-tuning data for reaching a good performance and (ii) the fine-tuned models are not robust concerning out-of-distribution entities. In this paper, we investigate using ChatGPT for entity matching as a more robust, training data-efficient alternative to traditional Transformer models. We perform experiments along three dimensions: (i) general prompt design, (ii) in-context learning, and (iii) provision of higher-level matching knowledge. We show that ChatGPT is competitive with a fine-tuned RoBERTa model, reaching a zero-shot performance of 82.35% F1 on a challenging matching task on which RoBERTa requires 2000 training examples for reaching a similar performance. Adding in-context demonstrations to the prompts further improves the F1 by up to 7.85% when using similarity-based example selection. Always using the same set of 10 handpicked demonstrations leads to an improvement of 4.92% over the zero-shot performance. Finally, we show that ChatGPT can also be guided by adding higher-level matching knowledge in the form of rules to the prompts. Providing matching rules leads to similar performance gains as providing in-context demonstrations.
Effective building pattern recognition is critical for understanding urban form, automating map generalization, and visualizing 3D city models. Most existing studies use object-independent methods based on visual perception rules and proximity graph models to extract patterns. However, because human vision is a part-based system, pattern recognition may require decomposing shapes into parts or grouping them into clusters. Existing methods may not recognize all visually aware patterns, and the proximity graph model can be inefficient. To improve efficiency and effectiveness, we integrate multi-scale data using a knowledge graph, focusing on the recognition of C-shaped building patterns. First, we use a property graph to represent the relationships between buildings within and across different scales involved in C-shaped building pattern recognition. Next, we store this knowledge graph in a graph database and convert the rules for C-shaped pattern recognition and enrichment into query conditions. Finally, we recognize and enrich C-shaped building patterns using rule-based reasoning in the built knowledge graph. We verify the effectiveness of our method using multi-scale data with three levels of detail (LODs) collected from the Gaode Map. Our results show that our method achieves a higher recall rate of 26.4% for LOD1, 20.0% for LOD2, and 9.1% for LOD3 compared to existing approaches. We also achieve recognition efficiency improvements of 0.91, 1.37, and 9.35 times, respectively.
Integration of heterogeneous and high-dimensional multi-omics data is becoming increasingly important in understanding genetic data. Each omics technique only provides a limited view of the underlying biological process and integrating heterogeneous omics layers simultaneously would lead to a more comprehensive and detailed understanding of diseases and phenotypes. However, one obstacle faced when performing multi-omics data integration is the existence of unpaired multi-omics data due to instrument sensitivity and cost. Studies may fail if certain aspects of the subjects are missing or incomplete. In this paper, we propose a deep learning method for multi-omics integration with incomplete data by Cross-omics Linked unified embedding with Contrastive Learning and Self Attention (CLCLSA). Utilizing complete multi-omics data as supervision, the model employs cross-omics autoencoders to learn the feature representation across different types of biological data. The multi-omics contrastive learning, which is used to maximize the mutual information between different types of omics, is employed before latent feature concatenation. In addition, the feature-level self-attention and omics-level self-attention are employed to dynamically identify the most informative features for multi-omics data integration. Extensive experiments were conducted on four public multi-omics datasets. The experimental results indicated that the proposed CLCLSA outperformed the state-of-the-art approaches for multi-omics data classification using incomplete multi-omics data.
We develop scalable randomized kernel methods for jointly associating data from multiple sources and simultaneously predicting an outcome or classifying a unit into one of two or more classes. The proposed methods model nonlinear relationships in multiview data together with predicting a clinical outcome and are capable of identifying variables or groups of variables that best contribute to the relationships among the views. We use the idea that random Fourier bases can approximate shift-invariant kernel functions to construct nonlinear mappings of each view and we use these mappings and the outcome variable to learn view-independent low-dimensional representations. Through simulation studies, we show that the proposed methods outperform several other linear and nonlinear methods for multiview data integration. When the proposed methods were applied to gene expression, metabolomics, proteomics, and lipidomics data pertaining to COVID-19, we identified several molecular signatures forCOVID-19 status and severity. Results from our real data application and simulations with small sample sizes suggest that the proposed methods may be useful for small sample size problems. Availability: Our algorithms are implemented in Pytorch and interfaced in R and would be made available at: https://github.com/lasandrall/RandMVLearn.
One of the limitations of large language models is that they do not have access to up-to-date, proprietary or personal data. As a result, there are multiple efforts to extend language models with techniques for accessing external data. In that sense, LLMs share the vision of data integration systems whose goal is to provide seamless access to a large collection of heterogeneous data sources. While the details and the techniques of LLMs differ greatly from those of data integration, this paper shows that some of the lessons learned from research on data integration can elucidate the research path we are conducting today on language models.
Genome-Wide Association Studies (GWAS) help identify genetic variations in people with diseases such as Parkinson's disease (PD), which are less common in those without the disease. Thus, GWAS data can be used to identify genetic variations associated with the disease. Feature selection and machine learning approaches can be used to analyze GWAS data and identify potential disease biomarkers. However, GWAS studies have technical variations that affect the reproducibility of identified biomarkers, such as differences in genotyping platforms and selection criteria for individuals to be genotyped. To address this issue, we collected five GWAS datasets from the database of Genotypes and Phenotypes (dbGaP) and explored several data integration strategies. We evaluated the agreement among different strategies in terms of the Single Nucleotide Polymorphisms (SNPs) that were identified as potential PD biomarkers. Our results showed a low concordance of biomarkers discovered using different datasets or integration strategies. However, we identified fifty SNPs that were identified at least twice, which could potentially serve as novel PD biomarkers. These SNPs are indirectly linked to PD in the literature but have not been directly associated with PD before. These findings open up new potential avenues of investigation.
Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.
Integrating data from multiple parties to achieve cross-institutional machine learning is an important trend in Industry 4.0 era. However, the privacy risks from sharing data pose a significant challenge to data integration. To integrate data without sharing data and meet large-scale samples' modeling needs, we propose two vertical federation learning algorithms for ridge regression via least-squares solution for two-party and multi-party scenarios, respectively. Compared with the state-of-the-art algorithms, our algorithms only need one round of calculation for the optimization instead of iteration. Furthermore, our algorithms can effectively handle large-scale samples due to the number of cryptographic operations in our algorithms being independent of the number of samples. Through our proposed the matrix secure agent computing theory and $\delta$ -data indistinguishability theory, we provide quantitative theoretical guarantees for the security of our algorithms. Our algorithms satisfy complete data indistinguishability under the “semi-honest” assumption and the quantitative security under the “malicious” assumption. The experiments show that our proposed algorithm takes only about 400 seconds to handle up to 9.6 million large-scale samples, while the state-of-the-art algorithms take close to 1000 seconds to handle every 1000 samples, which embodies the advantage of our algorithms in handling large-scale samples.δ -data indistinguishability theory, we provide quantitative theoretical guarantees for the security of our algorithms. Our algorithms satisfy complete data indistinguishability under the “semi-honest” assumption and the quantitative security under the “malicious” assumption. The experiments show that our proposed algorithm takes only about 400 seconds to handle up to 9.6 million large-scale samples, while the state-of-the-art algorithms take close to 1000 seconds to handle every 1000 samples, which embodies the advantage of our algorithms in handling large-scale samples.
Existing methods to characterise the evolving condition of traumatic brain injury (TBI) patients in the intensive care unit (ICU) do not capture the context necessary for individualising treatment. Here, we integrate all heterogenous data stored in medical records (1,166 pre-ICU and ICU variables) to model the individualised contribution of clinical course to six-month functional outcome on the Glasgow Outcome Scale - Extended (GOSE). On a prospective cohort (n=1,550, 65 centres) of TBI patients, we train recurrent neural network models to map a token-embedded time series representation of all variables (including missing values) to an ordinal GOSE prognosis every two hours. The full range of variables explains up to 52% (95% CI: 50%-54%) of the ordinal variance in functional outcome. Up to 91% (95% CI: 90%-91%) of this explanation is derived from pre-ICU and admission information (i.e., static variables). Information collected in the ICU (i.e., dynamic variables) increases explanation (by up to 5% [95% CI: 4%-6%]), though not enough to counter poorer overall performance in longer-stay (>5.75 days) patients. Highest-contributing variables include physician-based prognoses, CT features, and markers of neurological function. Whilst static information currently accounts for the majority of functional outcome explanation after TBI, data-driven analysis highlights investigative avenues to improve dynamic characterisation of longer-stay patients. Moreover, our modelling strategy proves useful for converting large patient records into interpretable time series with missing data integration and minimal processing.
Semantic image and video segmentation stand among the most important tasks in computer vision nowadays, since they provide a complete and meaningful representation of the environment by means of a dense classification of the pixels in a given scene. Recently, Deep Learning, and more precisely Convolutional Neural Networks, have boosted semantic segmentation to a new level in terms of performance and generalization capabilities. However, designing Deep Semantic Segmentation models is a complex task, as it may involve application-dependent aspects. Particularly, when considering autonomous driving applications, the robustness-efficiency trade-off, as well as intrinsic limitations - computational/memory bounds and data-scarcity - and constraints - real-time inference - should be taken into consideration. In this respect, the use of additional data modalities, such as depth perception for reasoning on the geometry of a scene, and temporal cues from videos to explore redundancy and consistency, are promising directions yet not explored to their full potential in the literature. In this paper, we conduct a survey on the most relevant and recent advances in Deep Semantic Segmentation in the context of vision for autonomous vehicles, from three different perspectives: efficiency-oriented model development for real-time operation, RGB-Depth data integration (RGB-D semantic segmentation), and the use of temporal information from videos in temporally-aware models. Our main objective is to provide a comprehensive discussion on the main methods, advantages, limitations, results and challenges faced from each perspective, so that the reader can not only get started, but also be up to date in respect to recent advances in this exciting and challenging research field.
Name disambiguation -- a fundamental problem in online academic systems -- is now facing greater challenges with the increasing growth of research papers. For example, on AMiner, an online academic search platform, about 10% of names own more than 100 authors. Such real-world challenging cases have not been effectively addressed by existing researches due to the small-scale or low-quality datasets that they have used. The development of effective algorithms is further hampered by a variety of tasks and evaluation protocols designed on top of diverse datasets. To this end, we present WhoIsWho owning, a large-scale benchmark with over 1,000,000 papers built using an interactive annotation process, a regular leaderboard with comprehensive tasks, and an easy-to-use toolkit encapsulating the entire pipeline as well as the most powerful features and baseline models for tackling the tasks. Our developed strong baseline has already been deployed online in the AMiner system to enable daily arXiv paper assignments. The public leaderboard is available at http://whoiswho.biendata.xyz/. The toolkit is at https://github.com/THUDM/WhoIsWho. The online demo of daily arXiv paper assignments is at https://na-demo.aminer.cn/arxivpaper.
Geological modeling currently uses various computer-based applications. Data harmonization at the semantic level by means of ontologies is essential for making these applications interoperable. Since geo-modeling is currently part of multidisciplinary projects, semantic harmonization is required to model not only geological knowledge but also to integrate other domain knowledge at a general level. For this reason, the domain ontologies used for describing geological knowledge must be based on a sound ontology background to ensure the described geological knowledge is integratable. This paper presents a domain ontology: GeoFault, resting on the Basic Formal Ontology BFO (Arp et al., 2015) and the GeoCore ontology (Garcia et al., 2020). It models the knowledge related to geological faults. Faults are essential to various industries but are complex to model. They can be described as thin deformed rock volumes or as spatial arrangements resulting from the different displacements of geological blocks. At a broader scale, faults are currently described as mere surfaces, which are the components of complex fault arrays. The reference to the BFO and GeoCore package allows assigning these various fault elements to define ontology classes and their logical linkage within a consistent ontology framework. The GeoFault ontology covers the core knowledge of faults 'strico sensu,' excluding ductile shear deformations. This considered vocabulary is essentially descriptive and related to regional to outcrop scales, excluding microscopic, orogenic, and tectonic plate structures. The ontology is molded in OWL 2, validated by competency questions with two use cases, and tested using an in-house ontology-driven data entry application. The work of GeoFault provides a solid framework for disambiguating fault knowledge and a foundation of fault data integration for the applications and the users.
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 domain-specific knowledge graph~(KG) is an explicit conceptualization of a specific subject-matter domain represented w.r.t semantically interrelated entities and relations. A 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. Such a KG will not only allow deducing new knowledge and question answering(QA) but also allows domain experts to explore. Since cross-disciplinary explanations are important for accurate diagnosis, it is important to query the KG to provide interactive explanations about learned biomarkers. Inspired by these, we construct a domain-specific KG, particularly for cancer-specific biomarker discovery. The KG is constructed by integrating cancer-related knowledge and facts from multiple sources. First, we construct a domain-specific ontology, which we call OncoNet Ontology (ONO). The ONO ontology is developed to enable semantic reasoning for verification of the predictions for relations between diseases and genes. The KG is then developed and enriched by harmonizing the ONO, additional metadata schemas, ontologies, controlled vocabularies, and additional concepts from external sources using a BERT-based information extraction method. BioBERT and SciBERT are finetuned with the selected articles crawled from PubMed. We listed down some queries and some examples of QA and deducing knowledge based on the KG.
Entity alignment (EA) is a fundamental data integration task that identifies equivalent entities between different knowledge graphs (KGs). Temporal Knowledge graphs (TKGs) extend traditional knowledge graphs by introducing timestamps, which have received increasing attention. State-of-the-art time-aware EA studies have suggested that the temporal information of TKGs facilitates the performance of EA. However, existing studies have not thoroughly exploited the advantages of temporal information in TKGs. Also, they perform EA by pre-aligning entity pairs, which can be labor-intensive and thus inefficient. In this paper, we present DualMatch which effectively fuses the relational and temporal information for EA. DualMatch transfers EA on TKGs into a weighted graph matching problem. More specifically, DualMatch is equipped with an unsupervised method, which achieves EA without necessitating seed alignment. DualMatch has two steps: (i) encoding temporal and relational information into embeddings separately using a novel label-free encoder, Dual-Encoder; and (ii) fusing both information and transforming it into alignment using a novel graph-matching-based decoder, GM-Decoder. DualMatch is able to perform EA on TKGs with or without supervision, due to its capability of effectively capturing temporal information. Extensive experiments on three real-world TKG datasets offer the insight that DualMatch outperforms the state-of-the-art methods in terms of H@1 by 2.4% - 10.7% and MRR by 1.7% - 7.6%, respectively.
The difficulty of an entity matching task depends on a combination of multiple factors such as the amount of corner-case pairs, the fraction of entities in the test set that have not been seen during training, and the size of the development set. Current entity matching benchmarks usually represent single points in the space along such dimensions or they provide for the evaluation of matching methods along a single dimension, for instance the amount of training data. This paper presents WDC Products, an entity matching benchmark which provides for the systematic evaluation of matching systems along combinations of three dimensions while relying on real-world data. The three dimensions are (i) amount of corner-cases (ii) generalization to unseen entities, and (iii) development set size (training set plus validation set). Generalization to unseen entities is a dimension not covered by any of the existing English-language benchmarks yet but is crucial for evaluating the robustness of entity matching systems. Instead of learning how to match entity pairs, entity matching can also be formulated as a multi-class classification task that requires the matcher to recognize individual entities. WDC Products is the first benchmark that provides a pair-wise and a multi-class formulation of the same tasks. We evaluate WDC Products using several state-of-the-art matching systems, including Ditto, HierGAT, and R-SupCon. The evaluation shows that all matching systems struggle with unseen entities to varying degrees. It also shows that for entity matching contrastive learning is more training data efficient compared to cross-encoders.
We propose a new method for combining in situ buoy measurements with Earth system models (ESMs) to improve the accuracy of temperature predictions in the ocean. The technique utilizes the dynamics \textit{and} modes identified in ESMs alongside buoy measurements to improve accuracy while preserving features such as seasonality. We use this technique, which we call Dynamic Basis Function Interpolation, to correct errors in localized temperature predictions made by the Model for Prediction Across Scales Ocean component (MPAS-O) with the Global Drifter Program's in situ ocean buoy dataset.
Rapid advancements in collection and dissemination of multi-platform molecular and genomics data has resulted in enormous opportunities to aggregate such data in order to understand, prevent, and treat human diseases. While significant improvements have been made in multi-omic data integration methods to discover biological markers and mechanisms underlying both prognosis and treatment, the precise cellular functions governing these complex mechanisms still need detailed and data-driven de-novo evaluations. We propose a framework called Functional Integrative Bayesian Analysis of High-dimensional Multiplatform Genomic Data (fiBAG), that allows simultaneous identification of upstream functional evidence of proteogenomic biomarkers and the incorporation of such knowledge in Bayesian variable selection models to improve signal detection. fiBAG employs a conflation of Gaussian process models to quantify (possibly non-linear) functional evidence via Bayes factors, which are then mapped to a novel calibrated spike-and-slab prior, thus guiding selection and providing functional relevance to the associations with patient outcomes. Using simulations, we illustrate how integrative methods with functional calibration have higher power to detect disease related markers than non-integrative approaches. We demonstrate the profitability of fiBAG via a pan-cancer analysis of 14 cancer types to identify and assess the cellular mechanisms of proteogenomic markers associated with cancer stemness and patient survival.