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1. Application of image processing and convolutional neural networks for flood image classification and semantic segmentation

   https://doi.org/10.1016/j.envsoft.2021.105285  

   Pall, R. and ( January 2022 , Environmental modelling software)

   Deep learning algorithms are exceptionally valuable tools for collecting and analyzing the catastrophic readiness and countless actionable flood data. Convolutional neural networks (CNNs) are one form of deep learning algorithms widely used in computer vision which can be used to study flood images and assign learnable weights to various objects in the image. Here, we leveraged and discussed how connected vision systems can be used to embed cameras, image processing, CNNs, and data connectivity capabilities for flood label detection. We built a training database service of >9000 images (image annotation service) including the image geolocation information by streaming relevant images from social media platforms, Department of Transportation (DOT) 511 traffic cameras, the US Geological Survey (USGS) live river cameras, and images downloaded from search engines. We then developed a new python package called “FloodImageClassifier” to classify and detect objects within the collected flood images. “FloodImageClassifier” includes various CNNs architectures such as YOLOv3 (You look only once version 3), Fast R–CNN (Region-based CNN), Mask R–CNN, SSD MobileNet (Single Shot MultiBox Detector MobileNet), and EfficientDet (Efficient Object Detection) to perform both object detection and segmentation simultaneously. Canny Edge Detection and aspect ratio concepts are also included in the package for flood watermore »level estimation and classification. The pipeline is smartly designed to train a large number of images and calculate flood water levels and inundation areas which can be used to identify flood depth, severity, and risk. “FloodImageClassifier” can be embedded with the USGS live river cameras and 511 traffic cameras to monitor river and road flooding conditions and provide early intelligence to emergency response authorities in real-time.« less
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. Smart City Traffic Intersection: Impact of Video Quality and Scene Complexity on Precision and Inference

   https://doi.org/10.1109/HPCC-DSS-SmartCity-DependSys53884.2021.00226  

   Duan, Zhuoxu ; Yang, Zhengye ; Samoilenko, Richard ; Oza, Dwiref Snehal ; Jagadeesan, Ashvin ; Sun, Mingfei ; Ye, Hongzhe ; Xiong, Zihao ; Zussman, Gil ; Kostic, Zoran ( May 2022 , in Proc. 19th IEEE Int. Conf. on Smart City, 2021)

   Traffic intersections are prime locations for deployment of infrastructure sensors and edge computing nodes to realize the vision of a smart city. It is expected that the needs of a smart city, in regards to traffic and pedestrian traffic systems monitored by cameras/video, can be met by using stateof-the-art artificial-intelligence (AI) based object detectors and trackers. A critical component in designing an effective real-time object detection/tracking pipeline is the understanding of how object density, i.e., the number of objects in a scene, and imageresolution and frame rate influence the performance metrics. This study explores the accuracy and speed metrics with the goal of supporting pipelines that meet the precision and latency needs of a real-time environment. We examine the impact of varying image-resolution, frame rate and object-density on the object detection performance metrics. The experiments on the COSMOS testbed dataset show that varying the frame width from 416 pixels to 832 pixels, and cropping the images to a square resolution, result in the increase in average precision for all object classes. Decreasing the frame rate from 15 fps to 5 fps preserves more than 90% of the highest F1 score achieved for all object classes. The results inform the choicemore »of video preprocessing stages, modifications to established AI-based object detection/tracking methods, and suggest optimal hyper-parameter values. Index Terms—Object Detection, Smart City, Video Resolution, Deep Learning Models.« less
4. Physics-based Scene-level Reasoning for Object Pose Estimation in Clutter

   Mitash, Chaitanya ; Boularias, Abdeslam ; Bekris, Kostas ( May 2019 , The international journal of robotics research)

   This paper focuses on vision-based pose estimation for multiple rigid objects placed in clutter, especially in cases involving occlusions and objects resting on each other. Progress has been achieved recently in object recognition given advancements in deep learning. Nevertheless, such tools typically require a large amount of training data and significant manual effort to label objects. This limits their applicability in robotics, where solutions must scale to a large number of objects and variety of conditions. Moreover, the combinatorial nature of the scenes that could arise from the placement of multiple objects is hard to capture in the training dataset. Thus, the learned models might not produce the desired level of precision required for tasks, such as robotic manipulation. This work proposes an autonomous process for pose estimation that spans from data generation to scene-level reasoning and self-learning. In particular, the proposed framework first generates a labeled dataset for training a Convolutional Neural Network (CNN) for object detection in clutter. These detections are used to guide a scene-level optimization process, which considers the interactions between the different objects present in the clutter to output pose estimates of high precision. Furthermore, confident estimates are used to label online real images frommore »multiple views and re-train the process in a self-learning pipeline. Experimental results indicate that this process is quickly able to identify in cluttered scenes physically-consistent object poses that are more precise than the ones found by reasoning over individual instances of objects. Furthermore, the quality of pose estimates increases over time given the self-learning process.« less
5. Toward the Automated Detection of Light Echoes in Synoptic Surveys: Considerations on the Application of Deep Convolutional Neural Networks

   https://doi.org/10.3847/1538-3881/ac9409  

   Li, Xiaolong ; Bianco, Federica B. ; Dobler, Gregory ; Partoush, Roee ; Rest, Armin ; Acero-Cuellar, Tatiana ; Clarke, Riley ; Fortino, Willow Fox ; Khakpash, Somayeh ; Lian, Ming ( November 2022 , The Astronomical Journal)

   Light echoes (LEs) are the reflections of astrophysical transients off of interstellar dust. They are fascinating astronomical phenomena that enable studies of the scattering dust as well as of the original transients. LEs, however, are rare and extremely difficult to detect as they appear as faint, diffuse, time-evolving features. The detection of LEs still largely relies on human inspection of images, a method unfeasible in the era of large synoptic surveys. The Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) will generate an unprecedented amount of astronomical imaging data at high spatial resolution, exquisite image quality, and over tens of thousands of square degrees of sky: an ideal survey for LEs. However, the Rubin data processing pipelines are optimized for the detection of point sources and will entirely miss LEs. Over the past several years, artificial intelligence (AI) object-detection frameworks have achieved and surpassed real-time, human-level performance. In this work, we leverage a data set from the Asteroid Terrestrial-impact Last Alert System telescope to test a popular AI object-detection framework, You Only Look Once, or YOLO, developed by the computer-vision community, to demonstrate the potential of AI for the detection of LEs in astronomical images. Wemore »find that an AI framework can reach human-level performance even with a size- and quality-limited data set. We explore and highlight challenges, including class imbalance and label incompleteness, and road map the work required to build an end-to-end pipeline for the automated detection and study of LEs in high-throughput astronomical surveys.

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