Automatic categorization of diverse experimental information in the bioscience literature

Background: Curation of information from bioscience literature into biological knowledge databases is a crucial way of capturing experimental information in a computable form. During the biocuration process, a critical first step is to identify from all published literature the papers that contain results for a specific data type the curator is interested in annotating. This step normally requires curators to manually examine many papers to ascertain which few contain information of interest and thus, is usually time consuming. We developed an automatic method for identifying papers containing these curation data types among a large pool of published scientific papers based on the machine learning method Support Vector Machine (SVM). This classification system is completely automatic and can be readily applied to diverse experimental data types. It has been in use in production for automatic categorization of 10 different experimental datatypes in the biocuration process at WormBase for the past two years and it is in the process of being adopted in the biocuration process at FlyBase and the Saccharomyces Genome Database (SGD). We anticipate that this method can be readily adopted by various databases in the biocuration community and thereby greatly reducing time spent on an otherwise laborious and demanding task. We also developed a simple, readily automated procedure to utilize training papers of similar data types from different bodies of literature such as C. elegans and D. melanogaster to identify papers with any of these data types for a single database. This approach has great significance because for some data types, especially those of low occurrence, a single corpus often does not have enough training papers to achieve satisfactory performance. Results: We successfully tested the method on ten data types from WormBase, fifteen data types from FlyBase and three data types from Mouse Genomics Informatics (MGI). It is being used in the curation work flow at WormBase for automatic association of newly published papers with ten data types including RNAi, antibody, phenotype, gene regulation, mutant allele sequence, gene expression, gene product interaction, overexpression phenotype, gene interaction, and gene structure correction. Conclusions: Our methods are applicable to a variety of data types with training set containing several hundreds to a few thousand documents. It is completely automatic and, thus can be readily incorporated to different workflow at different literature-based databases. We believe that the work presented here can contribute greatly to the tremendous task of automating the important yet labor-intensive biocuration effort

Enhanced spatial pyramid matching using log-polar-based image subdivision and representation

This paper presents a new model for capturing spatial information for object categorization with bag-of-words (BOW). BOW models have recently become popular for the task of object recognition, owing to their good performance and simplicity. Much work has been proposed over the years to improve the BOW model, where the Spatial Pyramid Matching (SPM) technique is the most notable. We propose a new method to exploit spatial relationships between image features, based on binned log-polar grids. Our model works by partitioning the image into grids of different scales and orientations and computing histogram of local features within each grid. Experimental results show that our approach improves the results on three diverse datasets over the SPM technique

Social relation recognition in egocentric photostreams

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.This paper proposes an approach to automatically categorize the social interactions of a user wearing a photo-camera (2fpm), by relying solely on what the camera is seeing. The problem is challenging due to the overwhelming complexity of social life and the extreme intra-class variability of social interactions captured under unconstrained conditions. We adopt the formalization proposed in Bugental’s social theory, that groups human relations into five social domains with related categories. Our method is a new deep learning architecture that exploits the hierarchical structure of the label space and relies on a set of social attributes estimated at frame level to provide a semantic representation of social interactions. Experimental results on the new EgoSocialRelation dataset demonstrate the effectiveness of our proposal.Peer ReviewedPostprint (author's final draft

Social Relation Recognition in Egocentric Photostreams

This paper proposes an approach to automatically categorize the social interactions of a user wearing a photo-camera 2fpm, by relying solely on what the camera is seeing. The problem is challenging due to the overwhelming complexity of social life and the extreme intra-class variability of social interactions captured under unconstrained conditions. We adopt the formalization proposed in Bugental's social theory, that groups human relations into five social domains with related categories. Our method is a new deep learning architecture that exploits the hierarchical structure of the label space and relies on a set of social attributes estimated at frame level to provide a semantic representation of social interactions. Experimental results on the new EgoSocialRelation dataset demonstrate the effectiveness of our proposal.Comment: Accepted at ICIP 201