title: A framework for biomedical figure segmentation towards image-based document retrieval.
abstract: The figures included in many of the biomedical publications play an important role in understanding the biological experiments and facts described within. Recent studies have shown that it is possible to integrate the information that is extracted from figures in classical document classification and retrieval tasks in order to improve their accuracy. One important observation about the figures included in biomedical publications is that they are often composed of multiple subfigures or panels, each describing different methodologies or results. The use of these multimodal figures is a common practice in bioscience, as experimental results are graphically validated via multiple methodologies or procedures. Thus, for a better use of multimodal figures in document classification or retrieval tasks, as well as for providing the evidence source for derived assertions, it is important to automatically segment multimodal figures into subfigures and panels. This is a challenging task, however, as different panels can contain similar objects (i.e., barcharts and linecharts) with multiple layouts. Also, certain types of biomedical figures are text-heavy (e.g., DNA sequences and protein sequences images) and they differ from traditional images. As a result, classical image segmentation techniques based on low-level image features, such as edges or color, are not directly applicable to robustly partition multimodal figures into single modal panels. In this paper, we describe a robust solution for automatically identifying and segmenting unimodal panels from a multimodal figure. Our framework starts by robustly harvesting figure-caption pairs from biomedical articles. We base our approach on the observation that the document layout can be used to identify encoded figures and figure boundaries within PDF files. Taking into consideration the document layout allows us to correctly extract figures from the PDF document and associate their corresponding caption. We combine pixel-level representations of the extracted images with information gathered from their corresponding captions to estimate the number of panels in the figure. Thus, our approach simultaneously identifies the number of panels and the layout of figures. In order to evaluate the approach described here, we applied our system on documents containing protein-protein interactions (PPIs) and compared the results against a gold standard that was annotated by biologists. Experimental results showed that our automatic figure segmentation approach surpasses pure caption-based and image-based approaches, achieving a 96.64% accuracy. To allow for efficient retrieval of information, as well as to provide the basis for integration into document classification and retrieval systems among other, we further developed a web-based interface that lets users easily retrieve panels containing the terms specified in the user queries.
authors.forename: Luis D
authors.initials: LD
authors.lastname: Lopez
authors.forename: Jingyi
authors.initials: J
authors.lastname: Yu
authors.forename: Cecilia
authors.initials: C
authors.lastname: Arighi
authors.forename: Catalina O
authors.initials: CO
authors.lastname: Tudor
authors.forename: Manabu
authors.initials: M
authors.lastname: Torii
authors.forename: Hongzhan
authors.initials: H
authors.lastname: Huang
authors.forename: K
authors.initials: K
authors.lastname: Vijay-Shanker
authors.forename: Cathy
authors.initials: C
authors.lastname: Wu
mesh_terms: D035843:Biomedical Research; D019295:Computational Biology / Q000379:methods*; D003196:Computer Graphics; D007091:Image Processing, Computer-Assisted; D016247:Information Storage and Retrieval / Q000379:methods*