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1. Extracting text from scanned Arabic books: a large-scale benchmark dataset and a fine-tuned Faster-R-CNN model

   https://doi.org/10.1007/s10032-021-00382-4  

   Elanwar, Randa ; Qin, Wenda ; Betke, Margrit ; Wijaya, Derry ( June 2021 , International Journal on Document Analysis and Recognition (IJDAR))

   Datasets of documents in Arabic are urgently needed to promote computer vision and natural language processing research that addresses the specifics of the language. Unfortunately, publicly available Arabic datasets are limited in size and restricted to certain document domains. This paper presents the release of BE-Arabic-9K, a dataset of more than 9000 high-quality scanned images from over 700 Arabic books. Among these, 1500 images have been manually segmented into regions and labeled by their functionality. BE-Arabic-9K includes book pages with a wide variety of complex layouts and page contents, making it suitable for various document layout analysis and text recognition research tasks. The paper also presents a page layout segmentation and text extraction baseline model based on fine-tuned Faster R-CNN structure (FFRA). This baseline model yields cross-validation results with an average accuracy of 99.4% and F1 score of 99.1% for text versus non-text block classification on 1500 annotated images of BE-Arabic-9K. These results are remarkably better than those of the state-of-the-art Arabic book page segmentation system ECDP. FFRA also outperforms three other prior systems when tested on a competition benchmark dataset, making it an outstanding baseline model to challenge.
2. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do notmore »have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA.« less
3. A Large Dataset of Historical Japanese Documents with Complex Layouts

   Shen, Zejiang ; Zhang, Kaixuan ; Dell, Melissa ( January 2020 , IEEE/CVF Conference on Computer Vision and Pattern Recognition)

   Deep learning-based approaches for automatic document layout analysis and content extraction have the potential to unlock rich information trapped in historical documents on a large scale. One major hurdle is the lack of large datasets for training robust models. In particular, little training data exist for Asian languages. To this end, we present HJDataset, a Large Dataset of Historical Japanese Documents with Complex Layouts. It contains over 250,000 layout element annotations of seven types. In addition to bounding boxes and masks of the content regions, it also includes the hierarchical structures and reading orders for layout elements. The dataset is constructed using a combination of human and machine efforts. A semi-rule based method is developed to extract the layout elements, and the results are checked by human inspectors. The resulting large-scale dataset is used to provide baseline performance analyses for text region detection using state-of-the-art deep learning models. And we demonstrate the usefulness of the dataset on real-world document digitization tasks.
4. Visual Segmentation for Information Extraction from Heterogeneous Visually Rich Documents

   https://doi.org/10.1145/3299869.3319867  

   Sarkhel, Ritesh ; Nandi, Arnab ( June 2019 , International Conference on Management of Data (SIGMOD), 2019)

   Physical and digital documents often contain visually rich information. With such information, there is no strict order- ing or positioning in the document where the data values must appear. Along with textual cues, these documents often also rely on salient visual features to define distinct semantic boundaries and augment the information they disseminate. When performing information extraction (IE), traditional techniques fall short, as they use a text-only representation and do not consider the visual cues inherent to the layout of these documents. We propose VS2, a generalized approach for information extraction from heterogeneous visually rich documents. There are two major contributions of this work. First, we propose a robust segmentation algorithm that de- composes a visually rich document into a bag of visually iso- lated but semantically coherent areas, called logical blocks. Document type agnostic low-level visual and semantic fea- tures are used in this process. Our second contribution is a distantly supervised search-and-select method for identify- ing the named entities within these documents by utilizing the context boundaries defined by these logical blocks. Ex- perimental results on three heterogeneous datasets suggest that the proposed approach significantly outperforms its text-only counterparts on all datasets. Comparing it against the state-of-the-art methodsmore »also reveal that VS2 performs comparably or better on all datasets.« less
5. Deep Neural Network for Semantic-based Text Recognition in Images

   Zheng, Yi ; Wang, Qitong ; Betke, Margrit ( December 2019 , ArXivorg)

   State-of-the-art text spotting systems typically aim to detect isolated words or word-by-word text in images of natural scenes and ignore the semantic coherence within a region of text. However, when interpreted together, seemingly isolated words may be easier to recognize. On this basis, we propose a novel "semantic-based text recognition" (STR) deep learning model that reads text in images with the help of understanding context. STR consists of several modules. We introduce the Text Grouping and Arranging (TGA) algorithm to connect and order isolated text regions. A text-recognition network interprets isolated words. Benefiting from semantic information, a sequence-to-sequence network model efficiently corrects inaccurate and uncertain phrases produced earlier in the STR pipeline. We present experiments on two new distinct datasets that contain scanned catalog images of interior designs and photographs of protesters with hand-written signs, respectively. Our results show that our STR model outperforms a baseline method that uses state-of-the-art single-word recognition techniques on both datasets. STR yields a high accuracy rate of 90% on the catalog images and 71% on the more difficult protest images, suggesting its generality in recognizing text.