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1. Simulation integration platforms for cyber-physical systems

   https://doi.org/10.1145/3313151.3313169  

   Neema, Himanshu ; Sztipanovits, Janos ; Steinbrink, Cornelius ; Raub, Thomas ; Cornelsen, Bastian ; Lehnhoff, Sebastian ( January 2019 , Proceedings of the Workshop on Design Automation for CPS and IoT)

   Simulation-based analysis is essential in the model-based design process of Cyber-Physical Systems (CPS). Since heterogeneity is inherent to CPS, virtual prototyping of CPS designs and the simulation of their behavior in various environments typically involve a number of physical and computation/communication domains interacting with each other. Affordability of the model-based design process makes the use of existing domain-specific modeling and simulation tools all but mandatory. However, this pressure establishes the requirement for integrating the domain-specific models and simulators into a semantically consistent and efficient system-of-system simulation. The focus of the paper is the interoperability of popular integration platforms supporting heterogeneous multi-model simulations. We examine the relationship among three existing platforms: the High-Level Architecture (HLA)-based CPS Wind Tunnel (CPSWT), MOSAIK, and the Functional Mockup Unit (FMU). We discuss approaches to establish interoperability and present results of ongoing work in the context of an example.
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 Survey on Silicon Photonics for Deep Learning

   https://doi.org/10.1145/3459009  

   Sunny, Febin P. ; Taheri, Ebadollah ; Nikdast, Mahdi ; Pasricha, Sudeep ( June 2021 , ACM Journal on Emerging Technologies in Computing Systems)

   Deep learning has led to unprecedented successes in solving some very difficult problems in domains such as computer vision, natural language processing, and general pattern recognition. These achievements are the culmination of decades-long research into better training techniques and deeper neural network models, as well as improvements in hardware platforms that are used to train and execute the deep neural network models. Many application-specific integrated circuit (ASIC) hardware accelerators for deep learning have garnered interest in recent years due to their improved performance and energy-efficiency over conventional CPU and GPU architectures. However, these accelerators are constrained by fundamental bottlenecks due to (1) the slowdown in CMOS scaling, which has limited computational and performance-per-watt capabilities of emerging electronic processors; and (2) the use of metallic interconnects for data movement, which do not scale well and are a major cause of bandwidth, latency, and energy inefficiencies in almost every contemporary processor. Silicon photonics has emerged as a promising CMOS-compatible alternative to realize a new generation of deep learning accelerators that can use light for both communication and computation. This article surveys the landscape of silicon photonics to accelerate deep learning, with a coverage of developments across design abstractions in a bottom-up manner,more »to convey both the capabilities and limitations of the silicon photonics paradigm in the context of deep learning acceleration.« less
4. A Novel ROS2 QoS Policy-enabled Synchronizing Middleware for Co-simulation of Heterogeneous Multi-Robot Systems

   Dey, E ; Walczak, M ; Anwar, M ; Roy, N ; Freeman, J ; Gregory, T ; Suri, N ; Busart, C ( July 2023 , 32nd IEEE International Conference on Computer Communications and Networks (ICCCN), Honolulu, HI, USA, July 2023)

   Recent Internet-of-Things (IoT) networks span across a multitude of stationary and robotic devices, namely unmanned ground vehicles, surface vessels, and aerial drones, to carry out mission-critical services such as search and rescue operations, wildfire monitoring, and flood/hurricane impact assessment. Achieving communication synchrony, reliability, and minimal communication jitter among these devices is a key challenge both at the simulation and system levels of implementation due to the underpinning differences between a physics-based robot operating system (ROS) simulator that is time-based and a network-based wireless simulator that is event-based, in addition to the complex dynamics of mobile and heterogeneous IoT devices deployed in a real environment. Nevertheless, synchronization between physics (robotics) and network simulators is one of the most difficult issues to address in simulating a heterogeneous multi-robot system before transitioning it into practice. The existing TCP/IP communication protocol-based synchronizing middleware mostly relied on Robot Operating System 1 (ROS1), which expends a significant portion of communication bandwidth and time due to its master-based architecture. To address these issues, we design a novel synchronizing middleware between robotics and traditional wireless network simulators, relying on the newly released real-time ROS2 architecture with a master-less packet discovery mechanism. Additionally, we propose a ground and aerialmore »agents’ velocity-aware customized QoS policy for Data Distribution Service (DDS) to minimize the packet loss and transmission latency between a diverse set of robotic agents, and we offer the theoretical guarantee of our proposed QoS policy. We performed extensive network performance evaluations both at the simulation and system levels in terms of packet loss probability and average latency with line-of-sight (LOS) and non-line-of-sight (NLOS) and TCP/UDP communication protocols over our proposed ROS2-based synchronization middleware. Moreover, for a comparative study, we presented a detailed ablation study replacing NS-3 with a real-time wireless network simulator, EMANE, and masterless ROS2 with master-based ROS1. Our proposed middleware attests to the promise of building a largescale IoT infrastructure with a diverse set of stationary and robotic devices that achieve low-latency communications (12% and 11% reduction in simulation and reality, respectively) while satisfying the reliability (10% and 15% packet loss reduction in simulation and reality, respectively) and high-fidelity requirements of mission-critical applications.« less
5. Managing code transformations for better performance portability

   https://doi.org/10.1177/1094342019865606  

   Teixeira, Thiago SFX ; Gropp, William ; Padua, David ( May 2019 , The International Journal of High Performance Computing Applications)

   Code optimization is an intricate task that is getting more complex as computing systems evolve. Managing the program optimization process, including the implementation and evaluation of code variants, is tedious, inefficient, and errors are likely to be introduced in the process. Moreover, because each platform typically requires a different sequence of transformations to fully harness its computing power, the optimization process complexity grows as new platforms are adopted. To address these issues, systems and frameworks have been proposed to automate the code optimization process. They, however, have not been widely adopted and are primarily used by experts with deep knowledge about underlying architecture and compiler intricacies. This article describes the requirements that we believe necessary for making automatic performance tuning more broadly used, especially in complex, long-lived high-performance computing applications. Besides discussing limitations of current systems and strategies to overcome these, we describe the design of a system that is able to semi-automatically generate efficient platform-specific code. In the proposed system, the code optimization is programmer-guided, separately from application code, on an external file in what we call optimization programming. The language to program the optimization process is able to represent complex collections of transformations and, as a result, generatemore »efficient platform-specific code. A database manages different optimized versions of code regions, providing a pragmatic approach to performance portability, and the framework itself has separate components, allowing the optimized code to be used on systems without installing all of the modules required for the code generation. We present experiments on two different platforms to illustrate the generation of efficient platform-specific code that performs comparable to hand-optimized, vendor-provided code.« less