A brief network analysis of Artificial Intelligence publication

In this paper, we present an illustration to the history of Artificial Intelligence(AI) with a statistical analysis of publish since 1940. We collected and mined through the IEEE publish data base to analysis the geological and chronological variance of the activeness of research in AI. The connections between different institutes are showed. The result shows that the leading community of AI research are mainly in the USA, China, the Europe and Japan. The key institutes, authors and the research hotspots are revealed. It is found that the research institutes in the fields like Data Mining, Computer Vision, Pattern Recognition and some other fields of Machine Learning are quite consistent, implying a strong interaction between the community of each field. It is also showed that the research of Electronic Engineering and Industrial or Commercial applications are very active in California. Japan is also publishing a lot of papers in robotics. Due to the limitation of data source, the result might be overly influenced by the number of published articles, which is to our best improved by applying network keynode analysis on the research community instead of merely count the number of publish.Comment: 18 pages, 7 figure

DeepOpht: Medical Report Generation for Retinal Images via Deep Models and Visual Explanation

In this work, we propose an AI-based method that intends to improve the conventional retinal disease treatment procedure and help ophthalmologists increase diagnosis efficiency and accuracy. The proposed method is composed of a deep neural networks-based (DNN-based) module, including a retinal disease identifier and clinical description generator, and a DNN visual explanation module. To train and validate the effectiveness of our DNN-based module, we propose a large-scale retinal disease image dataset. Also, as ground truth, we provide a retinal image dataset manually labeled by ophthalmologists to qualitatively show, the proposed AI-based method is effective. With our experimental results, we show that the proposed method is quantitatively and qualitatively effective. Our method is capable of creating meaningful retinal image descriptions and visual explanations that are clinically relevant.Comment: Accepted to IEEE WACV 202

Literature Retrieval for Precision Medicine with Neural Matching and Faceted Summarization

Information retrieval (IR) for precision medicine (PM) often involves looking for multiple pieces of evidence that characterize a patient case. This typically includes at least the name of a condition and a genetic variation that applies to the patient. Other factors such as demographic attributes, comorbidities, and social determinants may also be pertinent. As such, the retrieval problem is often formulated as ad hoc search but with multiple facets (e.g., disease, mutation) that may need to be incorporated. In this paper, we present a document reranking approach that combines neural query-document matching and text summarization toward such retrieval scenarios. Our architecture builds on the basic BERT model with three specific components for reranking: (a). document-query matching (b). keyword extraction and (c). facet-conditioned abstractive summarization. The outcomes of (b) and (c) are used to essentially transform a candidate document into a concise summary that can be compared with the query at hand to compute a relevance score. Component (a) directly generates a matching score of a candidate document for a query. The full architecture benefits from the complementary potential of document-query matching and the novel document transformation approach based on summarization along PM facets. Evaluations using NIST's TREC-PM track datasets (2017--2019) show that our model achieves state-of-the-art performance. To foster reproducibility, our code is made available here: https://github.com/bionlproc/text-summ-for-doc-retrieval.Comment: Accepted to EMNLP 2020 Findings as Long Paper (11 page, 4 figures

Deep Learning -- A first Meta-Survey of selected Reviews across Scientific Disciplines, their Commonalities, Challenges and Research Impact

Deep learning belongs to the field of artificial intelligence, where machines perform tasks that typically require some kind of human intelligence. Similar to the basic structure of a brain, a deep learning algorithm consists of an artificial neural network, which resembles the biological brain structure. Mimicking the learning process of humans with their senses, deep learning networks are fed with (sensory) data, like texts, images, videos or sounds. These networks outperform the state-of-the-art methods in different tasks and, because of this, the whole field saw an exponential growth during the last years. This growth resulted in way over 10,000 publications per year in the last years. For example, the search engine PubMed alone, which covers only a sub-set of all publications in the medical field, provides already over 11,000 results in Q3 2020 for the search term 'deep learning', and around 90% of these results are from the last three years. Consequently, a complete overview over the field of deep learning is already impossible to obtain and, in the near future, it will potentially become difficult to obtain an overview over a subfield. However, there are several review articles about deep learning, which are focused on specific scientific fields or applications, for example deep learning advances in computer vision or in specific tasks like object detection. With these surveys as a foundation, the aim of this contribution is to provide a first high-level, categorized meta-survey of selected reviews on deep learning across different scientific disciplines. The categories (computer vision, language processing, medical informatics and additional works) have been chosen according to the underlying data sources (image, language, medical, mixed). In addition, we review the common architectures, methods, pros, cons, evaluations, challenges and future directions for every sub-category.Comment: 83 pages, 22 figures, 9 tables, 100 reference

Overview of ImageCLEFcaption 2017 – Image Caption Prediction and Concept Detection for Biomedical Images

This paper presents an overview of the ImageCLEF 2017 caption tasks on the analysis of images from the biomedical literature. Two subtasks were proposed to the participants: a concept detectiontask and caption prediction task, both using only images as input. Thetwo subtasks tackle the problem of providing image interpretation by extracting concepts and predicting a caption based on the visual information of an image alone. A dataset of 184,000 figure-caption pairs from the biomedical open access literature (PubMed Central) are provided asa testbed with the majority of them as training data and then 10,000 as validation and 10,000 as test data. Across two tasks, 11 participating groups submitted 71 runs. While the domain remains challenging and the data highly heterogeneous, we can note some surprisingly good results of the difficult task with a quality that could be beneficial for health applications by better exploiting the visual content of biomedical figures

Semantics-driven Abstractive Document Summarization

The evolution of the Web over the last three decades has led to a deluge of scientific and news articles on the Internet. Harnessing these publications in different fields of study is critical to effective end user information consumption. Similarly, in the domain of healthcare, one of the key challenges with the adoption of Electronic Health Records (EHRs) for clinical practice has been the tremendous amount of clinical notes generated that can be summarized without which clinical decision making and communication will be inefficient and costly. In spite of the rapid advances in information retrieval and deep learning techniques towards abstractive document summarization, the results of these efforts continue to resemble extractive summaries, achieving promising results predominantly on lexical metrics but performing poorly on semantic metrics. Thus, abstractive summarization that is driven by intrinsic and extrinsic semantics of documents is not adequately explored. Resources that can be used for generating semantics-driven abstractive summaries include: • Abstracts of multiple scientific articles published in a given technical field of study to generate an abstractive summary for topically-related abstracts within the field, thus reducing the load of having to read semantically duplicate abstracts on a given topic. • Citation contexts from different authoritative papers citing a reference paper can be used to generate utility-oriented abstractive summary for a scientific article. • Biomedical articles and the named entities characterizing the biomedical articles along with background knowledge bases to generate entity and fact-aware abstractive summaries. • Clinical notes of patients and clinical knowledge bases for abstractive clinical text summarization using knowledge-driven multi-objective optimization. In this dissertation, we develop semantics-driven abstractive models based on intra- document and inter-document semantic analyses along with facts of named entities retrieved from domain-specific knowledge bases to produce summaries. Concretely, we propose a sequence of frameworks leveraging semantics at various granularity (e.g., word, sentence, document, topic, citations, and named entities) levels, by utilizing external resources. The proposed frameworks have been applied to a range of tasks including 1. Abstractive summarization of topic-centric multi-document scientific articles and news articles. 2. Abstractive summarization of scientific articles using crowd-sourced citation contexts. 3. Abstractive summarization of biomedical articles clustered based on entity-relatedness. 4. Abstractive summarization of clinical notes of patients with heart failure and Chest X-Rays recordings. The proposed approaches achieve impressive performance in terms of preserving semantics in abstractive summarization while paraphrasing. For summarization of topic-centric multiple scientific/news articles, we propose a three-stage approach where abstracts of scientific articles or news articles are clustered based on their topical similarity determined from topics generated using Latent Dirichlet Allocation (LDA), followed by extractive phase and abstractive phase. Then, in the next stage, we focus on abstractive summarization of biomedical literature where we leverage named entities in biomedical articles to 1) cluster related articles; and 2) leverage the named entities towards guiding abstractive summarization. Finally, in the last stage, we turn to external resources such as citation contexts pointing to a scientific article to generate a comprehensive and utility-centric abstractive summary of a scientific article, domain-specific knowledge bases to fill gaps in information about entities in a biomedical article to summarize and clinical notes to guide abstractive summarization of clinical text. Thus, the bottom-up progression of exploring semantics towards abstractive summarization in this dissertation starts with (i) Semantic Analysis of Latent Topics; builds on (ii) Internal and External Knowledge-I (gleaned from abstracts and Citation Contexts); and extends it to make it comprehensive using (iii) Internal and External Knowledge-II (Named Entities and Knowledge Bases)