PadChest: A large chest x-ray image dataset with multi-label annotated reports

We present a labeled large-scale, high resolution chest x-ray dataset for the automated exploration of medical images along with their associated reports. This dataset includes more than 160,000 images obtained from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan Hospital (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography. The reports were labeled with 174 different radiographic findings, 19 differential diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and mapped onto standard Unified Medical Language System (UMLS) terminology. Of these reports, 27% were manually annotated by trained physicians and the remaining set was labeled using a supervised method based on a recurrent neural network with attention mechanisms. The labels generated were then validated in an independent test set achieving a 0.93 Micro-F1 score. To the best of our knowledge, this is one of the largest public chest x-ray database suitable for training supervised models concerning radiographs, and the first to contain radiographic reports in Spanish. The PadChest dataset can be downloaded from http://bimcv.cipf.es/bimcv-projects/padchest/

Isolating contour information from arbitrary images

Aspects of natural vision (physiological and perceptual) serve as a basis for attempting the development of a general processing scheme for contour extraction. Contour information is assumed to be central to visual recognition skills. While the scheme must be regarded as highly preliminary, initial results do compare favorably with the visual perception of structure. The scheme pays special attention to the construction of a smallest scale circular difference-of-Gaussian (DOG) convolution, calibration of multiscale edge detection thresholds with the visual perception of grayscale boundaries, and contour/texture discrimination methods derived from fundamental assumptions of connectivity and the characteristics of printed text. Contour information is required to fall between a minimum connectivity limit and maximum regional spatial density limit at each scale. Results support the idea that contour information, in images possessing good image quality, is (centered at about 10 cyc/deg and 30 cyc/deg). Further, lower spatial frequency channels appear to play a major role only in contour extraction from images with serious global image defects

Localized anomaly detection via hierarchical integrated activity discovery

2014 Spring.Includes bibliographical references.With the increasing number and variety of camera installations, unsupervised methods that learn typical activities have become popular for anomaly detection. In this thesis, we consider recent methods based on temporal probabilistic models and improve them in multiple ways. Our contributions are the following: (i) we integrate the low level processing and the temporal activity modeling, showing how this feedback improves the overall quality of the captured information, (ii) we show how the same approach can be taken to do hierarchical multi-camera processing, (iii) we use spatial analysis of the anomalies both to perform local anomaly detection and to frame automatically the detected anomalies. We illustrate the approach on both traffic data and videos coming from a metro station. We also investigate the application of topic models in Brain Computing Interfaces for Mental Task classification. We observe a classification accuracy of up to 68% for four Mental Tasks on individual subjects

Extraction of Transcript Diversity from Scientific Literature

Transcript diversity generated by alternative splicing and associated mechanisms contributes heavily to the functional complexity of biological systems. The numerous examples of the mechanisms and functional implications of these events are scattered throughout the scientific literature. Thus, it is crucial to have a tool that can automatically extract the relevant facts and collect them in a knowledge base that can aid the interpretation of data from high-throughput methods. We have developed and applied a composite text-mining method for extracting information on transcript diversity from the entire MEDLINE database in order to create a database of genes with alternative transcripts. It contains information on tissue specificity, number of isoforms, causative mechanisms, functional implications, and experimental methods used for detection. We have mined this resource to identify 959 instances of tissue-specific splicing. Our results in combination with those from EST-based methods suggest that alternative splicing is the preferred mechanism for generating transcript diversity in the nervous system. We provide new annotations for 1,860 genes with the potential for generating transcript diversity. We assign the MeSH term “alternative splicing” to 1,536 additional abstracts in the MEDLINE database and suggest new MeSH terms for other events. We have successfully extracted information about transcript diversity and semiautomatically generated a database, LSAT, that can provide a quantitative understanding of the mechanisms behind tissue-specific gene expression. LSAT (Literature Support for Alternative Transcripts) is publicly available at http://www.bork.embl.de/LSAT/

Exploiting Sparse Representations for Robust Analysis of Noisy Complex Video Scenes

Abstract. Recent works have shown that, even with simple low level visual cues, complex behaviors can be extracted automatically from crowded scenes, e.g. those depicting public spaces recorded from video surveillance cameras. However, low level features as optical flow or fore-ground pixels are inherently noisy. In this paper we propose a novel unsupervised learning approach for the analysis of complex scenes which is specifically tailored to cope directly with features ’ noise and uncer-tainty. We formalize the task of extracting activity patterns as a matrix factorization problem, considering as reconstruction function the robust Earth Mover’s Distance. A constraint of sparsity on the computed basis matrix is imposed, filtering out noise and leading to the identification of the most relevant elementary activities in a typical high level behavior. We further derive an alternate optimization approach to solve the pro-posed problem efficiently and we show that it is reduced to a sequence of linear programs. Finally, we propose to use short trajectory snippets to account for object motion information, in alternative to the noisy optical flow vectors used in previous works. Experimental results demonstrate that our method yields similar or superior performance to state-of-the arts approaches.