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1. Learning Integrated Holism-Landmark Representations for Long-Term Loop Closure Detection

   Fei Han, Hua Wang ( January 2018 , The Proceedings of the 32nd AAAI Conference on Artificial Intelligence (AAAI 2018))

   Loop closure detection is a critical component of large-scale simultaneous localization and mapping (SLAM) in loopy environments. This capability is challenging to achieve in long-term SLAM, when the environment appearance exhibits significant long-term variations across various time of the day, months, and even seasons. In this paper, we introduce a novel formulation to learn an integrated long-term representation based upon both holistic and landmark information, which integrates two previous insights under a unified framework: (1) holistic representations outperform keypoint-based representations, and (2) landmarks as an intermediate representation provide informative cues to detect challenging locations. Our new approach learns the representation by projecting input visual data into a low-dimensional space, which preserves both the global consistency (to minimize representation error) and the local consistency (to preserve landmarks’ pairwise relationship) of the input data. To solve the formulated optimization problem, a new algorithm is developed with theoretically guaranteed convergence. Extensive experiments have been conducted using two large-scale public benchmark data sets, in which the promising performances have demonstrated the effectiveness of the proposed approach. 

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2. A Fast and Robust Place Recognition Approach for Stereo Visual Odometry Using LiDAR Descriptors

   https://doi.org/10.1109/IROS45743.2020.9341733  

   Mo, Jiawei ; Sattar, Junaed ( October 2020 , 2020 IEEE/RSJ International Conference on Intelligent Robots and Systems (IROS))

   null (Ed.)

   Place recognition is a core component of Simultaneous Localization and Mapping (SLAM) algorithms. Particularly in visual SLAM systems, previously-visited places are recognized by measuring the appearance similarity between images representing these locations. However, such approaches are sensitive to visual appearance change and also can be computationally expensive. In this paper, we propose an alternative approach adapting LiDAR descriptors for 3D points obtained from stereo-visual odometry for place recognition. 3D points are potentially more reliable than 2D visual cues (e.g., 2D features) against environmental changes (e.g., variable illumination) and this may benefit visual SLAM systems in long-term deployment scenarios. Stereo-visual odometry generates 3D points with an absolute scale, which enables us to use LiDAR descriptors for place recognition with high computational efficiency. Through extensive evaluations on standard benchmark datasets, we demonstrate the accuracy, efficiency, and robustness of using 3D points for place recognition over 2D methods. 

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3. 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 not 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. 

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4. Dynamic Motion Representation for Human Action Recognition

   https://doi.org/10.1109/WACV45572.2020.9093500  

   Asghari-Esfeden, Sadjad ; Sznaier, Mario ; Camps, Octavia ( March 2020 , 2020 IEEE Winter Conference on Applications of Computer Vision (WACV))

   Despite the advances in Human Activity Recognition, the ability to exploit the dynamics of human body motion in videos has yet to be achieved. In numerous recent works, re- searchers have used appearance and motion as independent inputs to infer the action that is taking place in a specific video. In this paper, we highlight that while using a novel representation of human body motion, we can benefit from appearance and motion simultaneously. As a result, bet- ter performance of action recognition can be achieved. We start with a pose estimator to extract the location and heat- map of body joints in each frame. We use a dynamic encoder to generate a fixed size representation from these body joint heat-maps. Our experimental results show that training a convolutional neural network with the dynamic motion representation outperforms state-of-the-art action recognition models. By modeling distinguishable activities as distinct dynamical systems and with the help of two stream net- works, we obtain the best performance on HMDB, JHMDB, UCF-101, and AVA datasets. 

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5. Integrating Place and Sense of Place into Geovisualizations of Hurricane Storm Surge Risk

   https://doi.org/10.1175/WCAS-D-23-0044.1  

   Wilhelmi, O. V. ; Chamberlain, B. C. ; Morss, R. E. ; Demuth, J. L. ; Walpole, H. D. ; Boehnert, J. ; Gambill, J. M. ; Lazrus, H. ; Dobson, J. G. ( October 2023 , Weather, Climate, and Society)

   Geovisualizations play a central role in communicating hurricane storm surge risks to the public by connecting information about the hazard to a place. Meanwhile, people connect to places through meaning, functions, and emotional bond, known as a sense of place. The mixed-method approach presented in this paper focuses on the intersection of sense of place, geovisualization, and risk communication. We explored place meaning, scale of place, and place attachment in the coastal communities in Georgia and South Carolina. We conducted cognitive mapping focus groups and developed a series of geovisualizations of storm surge risk with varying representations of place. We then investigated people’s ability to connect visual storm surge information to a place and understand their risk by testing these geovisualizations in a large population survey (n= 1442). We found that a 2D regional-scale map displayed together with a 3D abstract representation of a neighborhood was the most helpful in enabling people to relate to a place, quickly make sense of the information, and understand the risk. Our results showed that while the geovisualizations of storm surge risk can be effective generally, they were less effective in several important and vulnerable groups. We found substantial impacts of race, income, map-reading ability, place attachment, and scale of place on how people connected the storm surge risk shown in the visual to a place. These findings have implications for future research and for considering the way weather forecasters and emergency managers communicate storm surge information with diverse audiences using geovisualizations.

   Weather forecasters and emergency managers often use geovisualizations to communicate hurricane storm surge risks and threats to the public. Despite the important role that geovisualizations play, few studies have empirically investigated their effectiveness in hazardous weather risk communication. With the overarching goal of understanding how geovisualizations enable coastal residents to understand and respond to risk, we use an interdisciplinary approach to create new knowledge about the effectiveness of geovisualizations in storm surge risk communication. Our results show substantial impacts of sociodemographic factors across many of the measures that enable people to connect to a place through visualizations. These findings have implications for communicating geospatially varying risk to diverse audiences.

    

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