Neural Metric Learning for Fast End-to-End Relation Extraction

Relation extraction (RE) is an indispensable information extraction task in several disciplines. RE models typically assume that named entity recognition (NER) is already performed in a previous step by another independent model. Several recent efforts, under the theme of end-to-end RE, seek to exploit inter-task correlations by modeling both NER and RE tasks jointly. Earlier work in this area commonly reduces the task to a table-filling problem wherein an additional expensive decoding step involving beam search is applied to obtain globally consistent cell labels. In efforts that do not employ table-filling, global optimization in the form of CRFs with Viterbi decoding for the NER component is still necessary for competitive performance. We introduce a novel neural architecture utilizing the table structure, based on repeated applications of 2D convolutions for pooling local dependency and metric-based features, that improves on the state-of-the-art without the need for global optimization. We validate our model on the ADE and CoNLL04 datasets for end-to-end RE and demonstrate $\approx 1\%$ gain (in F-score) over prior best results with training and testing times that are seven to ten times faster --- the latter highly advantageous for time-sensitive end user applications

Instance Segmentation by Deep Coloring

We propose a new and, arguably, a very simple reduction of instance segmentation to semantic segmentation. This reduction allows to train feed-forward non-recurrent deep instance segmentation systems in an end-to-end fashion using architectures that have been proposed for semantic segmentation. Our approach proceeds by introducing a fixed number of labels (colors) and then dynamically assigning object instances to those labels during training (coloring). A standard semantic segmentation objective is then used to train a network that can color previously unseen images. At test time, individual object instances can be recovered from the output of the trained convolutional network using simple connected component analysis. In the experimental validation, the coloring approach is shown to be capable of solving diverse instance segmentation tasks arising in autonomous driving (the Cityscapes benchmark), plant phenotyping (the CVPPP leaf segmentation challenge), and high-throughput microscopy image analysis. The source code is publicly available: https://github.com/kulikovv/DeepColoring.Comment: 10 pages, 6 figures, 3 table

MCODE: Multivariate Conditional Outlier Detection

Outlier detection aims to identify unusual data instances that deviate from expected patterns. The outlier detection is particularly challenging when outliers are context dependent and when they are defined by unusual combinations of multiple outcome variable values. In this paper, we develop and study a new conditional outlier detection approach for multivariate outcome spaces that works by (1) transforming the conditional detection to the outlier detection problem in a new (unconditional) space and (2) defining outlier scores by analyzing the data in the new space. Our approach relies on the classifier chain decomposition of the multi-dimensional classification problem that lets us transform the output space into a probability vector, one probability for each dimension of the output space. Outlier scores applied to these transformed vectors are then used to detect the outliers. Experiments on multiple multi-dimensional classification problems with the different outlier injection rates show that our methodology is robust and able to successfully identify outliers when outliers are either sparse (manifested in one or very few dimensions) or dense (affecting multiple dimensions)

Overview of the gene ontology task at BioCreative IV

Gene Ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation

A Disease Diagnosis and Treatment Recommendation System Based on Big Data Mining and Cloud Computing

It is crucial to provide compatible treatment schemes for a disease according to various symptoms at different stages. However, most classification methods might be ineffective in accurately classifying a disease that holds the characteristics of multiple treatment stages, various symptoms, and multi-pathogenesis. Moreover, there are limited exchanges and cooperative actions in disease diagnoses and treatments between different departments and hospitals. Thus, when new diseases occur with atypical symptoms, inexperienced doctors might have difficulty in identifying them promptly and accurately. Therefore, to maximize the utilization of the advanced medical technology of developed hospitals and the rich medical knowledge of experienced doctors, a Disease Diagnosis and Treatment Recommendation System (DDTRS) is proposed in this paper. First, to effectively identify disease symptoms more accurately, a Density-Peaked Clustering Analysis (DPCA) algorithm is introduced for disease-symptom clustering. In addition, association analyses on Disease-Diagnosis (D-D) rules and Disease-Treatment (D-T) rules are conducted by the Apriori algorithm separately. The appropriate diagnosis and treatment schemes are recommended for patients and inexperienced doctors, even if they are in a limited therapeutic environment. Moreover, to reach the goals of high performance and low latency response, we implement a parallel solution for DDTRS using the Apache Spark cloud platform. Extensive experimental results demonstrate that the proposed DDTRS realizes disease-symptom clustering effectively and derives disease treatment recommendations intelligently and accurately

Latent Dirichlet Allocation (LDA) and Topic modeling: models, applications, a survey

Topic modeling is one of the most powerful techniques in text mining for data mining, latent data discovery, and finding relationships among data, text documents. Researchers have published many articles in the field of topic modeling and applied in various fields such as software engineering, political science, medical and linguistic science, etc. There are various methods for topic modeling, which Latent Dirichlet allocation (LDA) is one of the most popular methods in this field. Researchers have proposed various models based on the LDA in topic modeling. According to previous work, this paper can be very useful and valuable for introducing LDA approaches in topic modeling. In this paper, we investigated scholarly articles highly (between 2003 to 2016) related to Topic Modeling based on LDA to discover the research development, current trends and intellectual structure of topic modeling. Also, we summarize challenges and introduce famous tools and datasets in topic modeling based on LDA.Comment: arXiv admin note: text overlap with arXiv:1505.07302 by other author

An Experience Report of Large Scale Federations

We present an experimental study of large-scale RDF federations on top of the Bio2RDF data sources, involving 29 data sets with more than four billion RDF triples deployed in a local federation. Our federation is driven by FedX, a highly optimized federation mediator for Linked Data. We discuss design decisions, technical aspects, and experiences made in setting up and optimizing the Bio2RDF federation, and present an exhaustive experimental evaluation of the federation scenario. In addition to a controlled setting with local federation members, we study implications arising in a hybrid setting, where local federation members interact with remote federation members exhibiting higher network latency. The outcome demonstrates the feasibility of federated semantic data management in general and indicates remaining bottlenecks and research opportunities that shall serve as a guideline for future work in the area of federated semantic data processing

Don't Stop Pretraining: Adapt Language Models to Domains and Tasks

Language models pretrained on text from a wide variety of sources form the foundation of today's NLP. In light of the success of these broad-coverage models, we investigate whether it is still helpful to tailor a pretrained model to the domain of a target task. We present a study across four domains (biomedical and computer science publications, news, and reviews) and eight classification tasks, showing that a second phase of pretraining in-domain (domain-adaptive pretraining) leads to performance gains, under both high- and low-resource settings. Moreover, adapting to the task's unlabeled data (task-adaptive pretraining) improves performance even after domain-adaptive pretraining. Finally, we show that adapting to a task corpus augmented using simple data selection strategies is an effective alternative, especially when resources for domain-adaptive pretraining might be unavailable. Overall, we consistently find that multi-phase adaptive pretraining offers large gains in task performance.Comment: ACL 202

Machine Intelligence Techniques for Next-Generation Context-Aware Wireless Networks

The next generation wireless networks (i.e. 5G and beyond), which would be extremely dynamic and complex due to the ultra-dense deployment of heterogeneous networks (HetNets), poses many critical challenges for network planning, operation, management and troubleshooting. At the same time, generation and consumption of wireless data are becoming increasingly distributed with ongoing paradigm shift from people-centric to machine-oriented communications, making the operation of future wireless networks even more complex. In mitigating the complexity of future network operation, new approaches of intelligently utilizing distributed computational resources with improved context-awareness becomes extremely important. In this regard, the emerging fog (edge) computing architecture aiming to distribute computing, storage, control, communication, and networking functions closer to end users, have a great potential for enabling efficient operation of future wireless networks. These promising architectures make the adoption of artificial intelligence (AI) principles which incorporate learning, reasoning and decision-making mechanism, as natural choices for designing a tightly integrated network. Towards this end, this article provides a comprehensive survey on the utilization of AI integrating machine learning, data analytics and natural language processing (NLP) techniques for enhancing the efficiency of wireless network operation. In particular, we provide comprehensive discussion on the utilization of these techniques for efficient data acquisition, knowledge discovery, network planning, operation and management of the next generation wireless networks. A brief case study utilizing the AI techniques for this network has also been provided.Comment: ITU Special Issue N.1 The impact of Artificial Intelligence (AI) on communication networks and services, (To appear

Joint-ViVo: Selecting and Weighting Visual Words Jointly for Bag-of-Features based Tissue Classification in Medical Images

Automatically classifying the tissues types of Region of Interest (ROI) in medical imaging has been an important application in Computer-Aided Diagnosis (CAD), such as classification of breast parenchymal tissue in the mammogram, classify lung disease patterns in High-Resolution Computed Tomography (HRCT) etc. Recently, bag-of-features method has shown its power in this field, treating each ROI as a set of local features. In this paper, we investigate using the bag-of-features strategy to classify the tissue types in medical imaging applications. Two important issues are considered here: the visual vocabulary learning and weighting. Although there are already plenty of algorithms to deal with them, all of them treat them independently, namely, the vocabulary learned first and then the histogram weighted. Inspired by Auto-Context who learns the features and classifier jointly, we try to develop a novel algorithm that learns the vocabulary and weights jointly. The new algorithm, called Joint-ViVo, works in an iterative way. In each iteration, we first learn the weights for each visual word by maximizing the margin of ROI triplets, and then select the most discriminate visual words based on the learned weights for the next iteration. We test our algorithm on three tissue classification tasks: identifying brain tissue type in magnetic resonance imaging (MRI), classifying lung tissue in HRCT images, and classifying breast tissue density in mammograms. The results show that Joint-ViVo can perform effectively for classifying tissues.Comment: This paper has been withdrawn by the author due to the terrible writin