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1. Efficient Data Management for Intelligent Urban Mobility Systems

   Wilbur, Michael ; Pugliese, Philip ; Laszka, Aron ; Dubey, Abhishek ( January 2021 , Proceedings of the Workshop on AI for Urban Mobility at the 35th AAAI Conference on Artificial Intelligence (AAAI-21))

   Modern intelligent urban mobility applications are underpinned by large-scale, multivariate, spatiotemporal data streams. Working with this data presents unique challenges of data management, processing and presentation that is often overlooked by researchers. Therefore, in this work we present an integrated data management and processing framework for intelligent urban mobility systems currently in use by our partner transit agencies. We discuss the available data sources and outline our cloud-centric data management and stream processing architecture built upon open-source publish-subscribe and NoSQL data stores. We then describe our data-integrity monitoring methods. We then present a set of visualization dashboards designed for our transit agency partners. Lastly, we discuss how these tools are currently being used for AI-driven urban mobility applications that use these tools.
2. Zero to a trillion: Advancing surface process studies with open access to high resolution topography

   Crosby, C. J. ; Arrowsmith, J R. ; Nandigam, V. ( January 2020 , Developments in earth surface processes)

   Tarolli, P. ; Mudd, S. (Ed.)

   High-resolution topography (HRT) is a powerful observational tool for studying the Earth's surface, vegetation, and urban landscapes, with broad scientific, engineering, and education-based applications. Submeter resolution imaging is possible when collected with laser and photogrammetric techniques using the ground, air, and space-based platforms. Open access to these data and a cyberinfrastructure platform that enables users to discover, manage, share, and process then increases the impact of investments in data collection and catalyzes scientific discovery. Furthermore, open and online access to data enables broad interdisciplinary use of HRT across academia and in communities such as education, public agencies, and the commercial sector. OpenTopography, supported by the US National Science Foundation, aims to democratize access to Earth science-oriented, HRT data and processing tools. We utilize cyberinfrastructure, including large-scale data management, high-performance computing, and service-oriented architectures to provide efficient web-based visualization and access to large, HRT datasets. OT colocates data with processing tools to enable users to quickly access custom data and derived products for their application, with the ultimate goal of making these powerful data easier to use. OT's rapidly growing data holdings currently include 283 lidar and photogrammetric, point cloud datasets (>1.2 trillion points) covering 236,364km2. As a testament to OT'smore »success, more than 86,000 users have processed over 5 trillion lidar points. This use has resulted in more than 290 peer-reviewed publications across numerous academic domains including Earth science, geography, computer science, and ecology.« less
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 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
4. Temporal and Spatial Routing for Large Scale Safe and Connected UAS Traffic Management in Urban Areas

   https://doi.org/10.1109/RTCSA.2019.8864561  

   Zhao, Ziyi ; Jin, Zhao ; Luo, Chen ; Fang, Haowen ; Basti, Franco ; Gursoy, M. Cenk ; Caicedo, Carlos ; Qiu, Qinru ( August 2019 , IEEE 25th International Conference on Embedded and Real-Time Computing Systems and Applications (RTCSA))

   Small Unmanned Aircraft Systems (sUAS) will be an important component of the smart city and intelligent transportation environments of the near future. The demand for sUAS related applications, such as commercial delivery and land surveying, is expected to grow rapidly in next few years. In general, sUAS traffic scheduling and management functions are needed to coordinate the launching of sUAS from different launch sites and plan their trajectories to avoid conflict while considering several other constraints such as expected arrival time, minimum flight energy, and availability of communication resources. However, as the airbone sUAS density grows in a certain area, it is difficult to foresee the potential airspace and communications resource conflicts and make immediate decisions to avoid them. To address this challenge, we present a temporal and spatial routing algorithm for sUAS trajectory management in a high density urban area. It plans sUAS movements in a spatial and temporal maze with the consideration of obstacles that are either static or dynamic in time. The routing allows the sUAS to avoid static no-fly areas (i.e. static obstacles) or other in-flight sUAS and areas that have congested communication resources (i.e. dynamic obstacles). The algorithm is evaluated using an agent-based simulation platform.more »The simulation results show that the proposed algorithm outperforms reference route management algorithms in many areas, especially in processing speed and memory efficiency. Detailed comparisons are provided for the sUAS flight time, the overall throughput, the conflict rate and communication resource utilization. The results demonstrate that our proposed algorithm can be used as a solution to improve the efficiency of airspace and communication resource utilization for next generation smart city and smart transportation.« less
5. Simulation of Real-time Routing for UAS traffic Management with Communication and Airspace Safety Considerations

   https://doi.org/10.1109/DASC43569.2019.9081675  

   Jin, Zhao ; Zhao, Ziyi ; Luo, Chen ; Basti, Franco ; Solomon, Adrian ; Gursoy, M. Cenk ; Caicedo, Carlos ; Qiu, Qinru ( September 2019 , Proceedings of 38th Digital Avionics Systems Conference)

   Small Unmanned Aircraft Systems (sUAS) will be an important component of the smart city and intelligent transportation environments of the near future. The demand for sUAS related applications, such as commercial delivery and land surveying, is expected to grow rapidly in next few years. In general, sUAS traffic routing and management functions are needed to coordinate the launching of sUAS from different launch sites and determine their trajectories to avoid conflict while considering several other constraints such as expected arrival time, minimum flight energy, and availability of communication resources. However, as the airborne sUAS density grows in a certain area, it is difficult to foresee the potential airspace and communications resource conflicts and make immediate decisions to avoid them. To address this challenge, we present a temporal and spatial routing algorithm and simulation platform for sUAS trajectory management in a high density urban area that plans sUAS movements in a spatial and temporal maze taking into account obstacles that are either static or dynamic in time. The routing allows the sUAS to avoid static no-fly areas (i.e. static obstacles) or other in-flight sUAS and areas that have congested communication resources (i.e. dynamic obstacles). The algorithm is evaluated using an agent-basedmore »simulation platform. The simulation results show that the proposed algorithm outperforms other route management algorithms in many areas, especially in processing speed and memory efficiency. Detailed comparisons are provided for the sUAS flight time, the overall throughput, conflict rate and communication resource utilization. The results demonstrate that our proposed algorithm can be used to address the airspace and communication resource utilization needs for a next generation smart city and smart transportation.« less