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1. FogROS: An Adaptive Framework for Automating Fog Robotics Deployment

   https://doi.org/10.1109/case49439.2021.9551628  

   Chen, Kaiyuan Eric ; Liang, Yafei ; Jha, Nikhil ; Ichnowski, Jeffrey ; Danielczuk, Michael ; Gonzalez, Joseph ; Kubiatowicz, John ; Goldberg, Ken ( August 2021 , 2021 IEEE 17th International Conference on Automation Science and Engineering (CASE))

   As many robot automation applications increasingly rely on multi-core processing or deep-learning models, cloud computing is becoming an attractive and economically viable resource for systems that do not contain high computing power onboard. Despite its immense computing capacity, it is often underused by the robotics and automation community due to lack of expertise in cloud computing and cloud-based infrastructure. Fog Robotics balances computing and data between cloud edge devices. We propose a software framework, FogROS, as an extension of the Robot Operating System (ROS), the de-facto standard for creating robot automation applications and components. It allows researchers to deploy components of their software to the cloud with minimal effort, and correspondingly gain access to additional computing cores, GPUs, FPGAs, and TPUs, as well as predeployed software made available by other researchers. FogROS allows a researcher to specify which components of their software will be deployed to the cloud and to what type of computing hardware. We evaluate FogROS on 3 examples: (1) simultaneous localization and mapping (ORB-SLAM2), (2) Dexterity Network (Dex-Net) GPU-based grasp planning, and (3) multi-core motion planning using a 96-core cloud-based server. In all three examples, a component is deployed to the cloud and accelerated with a smallmore »change in system launch configuration, while incurring additional latency of 1.2 s, 0.6 s, and 0.5 s due to network communication, the computation speed is improved by 2.6x, 6.0x and 34.2x, respectively.« 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. FogROS 2: An Adaptive and Extensible Platform for Cloud and Fog Robotics Using ROS 2

   Ichnowski, Jeffrey ; Chen, Kaiyuan ; Dharmarajan, Karthik ; Adebola, Simeon ; Danielczuk, Michael ; Mayoral-Vilches, V ; Zhan, Hugo ; Xu, Derek ; Ghassemi, Ramtin ; Kubiatowicz, John ; et al ( May 2023 , Proceedings IEEE International Conference on Robotics and Automation)

   Mobility, power, and price points often dictate that robots do not have sufficient computing power on board to run contemporary robot algorithms at desired rates. Cloud computing providers such as AWS, GCP, and Azure offer immense computing power on demand, but tapping into that power from a robot is non-trivial. We present FogROS2, an open-source platform to facilitate cloud and fog robotics that is compatible with the emerging Robot Operating System 2 (ROS 2) standard. FogROS2 is completely redesigned and distinct from its predecessor FogROS1 in 9 ways, and has lower latency, overhead, and startup times; improved usability, and additional automa-tion, such as region and computer type selection. Additionally, FogROS2 was added to the official distribution of ROS 2, gaining performance, timing, and additional improvements associated with ROS 2. In examples, FogROS2 reduces SLAM latency by 50 %, reduces grasp planning time from 14 s to 1.2 s, and speeds up motion planning 28x. When compared to FogROS1, FogROS2 reduces network utilization by up to 3.8x, improves startup time by 63 %, and network round-trip latency by 97 %for images using video compression. The source code, examples, and documentation for FogROS2 are available at https://github.com/BerkeleyAutomation/FogROS2, and is available through themore »official ROS 2 repository at https://index.ros.org/p/fogros2/« less
4. Energy-Efficient Processing and Robust Wireless Cooperative Transmission for Edge Inference

   https://doi.org/10.1109/JIOT.2020.2979523  

   Yang, Kai ; Shi, Yuanming ; Yu, Wei ; Ding, Zhi ( July 2020 , IEEE Internet of Things Journal)

   Edge machine learning can deliver low-latency and private artificial intelligent (AI) services for mobile devices by leveraging computation and storage resources at the network edge. This paper presents an energy-efficient edge processing framework to execute deep learning inference tasks at the edge computing nodes whose wireless connections to mobile devices are prone to channel uncertainties. Aimed at minimizing the sum of computation and transmission power consumption with probabilistic quality-of-service (QoS) constraints, we formulate a joint inference tasking and downlink beamforming problem that is characterized by a group sparse objective function. We provide a statistical learning based robust optimization approach to approximate the highly intractable probabilistic-QoS constraints by nonconvex quadratic constraints, which are further reformulated as matrix inequalities with a rank-one constraint via matrix lifting. We design a reweighted power minimization approach by iteratively reweighted ℓ1 minimization with difference-of-convex-functions (DC) regularization and updating weights, where the reweighted approach is adopted for enhancing group sparsity whereas the DC regularization is designed for inducing rank-one solutions. Numerical results demonstrate that the proposed approach outperforms other state-of-the-art approaches.
5. Automating Deep Neural Network Model Selection for Edge Inference

   https://doi.org/10.1109/CogMI48466.2019.00035  

   Lu, Bingqian ; Yang, Jianyi ; Chen, Lydia Y. ; Ren, Shaolei ( December 2019 , IEEE First International Conference on Cognitive Machine Intelligence (CogMI))

   The ever increasing size of deep neural network (DNN) models once implied that they were only limited to cloud data centers for runtime inference. Nonetheless, the recent plethora of DNN model compression techniques have successfully overcome this limit, turning into a reality that DNN-based inference can be run on numerous resource-constrained edge devices including mobile phones, drones, robots, medical devices, wearables, Internet of Things devices, among many others. Naturally, edge devices are highly heterogeneous in terms of hardware specification and usage scenarios. On the other hand, compressed DNN models are so diverse that they exhibit different tradeoffs in a multi-dimension space, and not a single model can achieve optimality in terms of all important metrics such as accuracy, latency and energy consumption. Consequently, how to automatically select a compressed DNN model for an edge device to run inference with optimal quality of experience (QoE) arises as a new challenge. The state-of-the-art approaches either choose a common model for all/most devices, which is optimal for a small fraction of edge devices at best, or apply device-specific DNN model compression, which is not scalable. In this paper, by leveraging the predictive power of machine learning and keeping end users in the loop,more »we envision an automated device-level DNN model selection engine for QoE-optimal edge inference. To concretize our vision, we formulate the DNN model selection problem into a contextual multi-armed bandit framework, where features of edge devices and DNN models are contexts and pre-trained DNN models are arms selected online based on the history of actions and users' QoE feedback. We develop an efficient online learning algorithm to balance exploration and exploitation. Our preliminary simulation results validate our algorithm and highlight the potential of machine learning for automating DNN model selection to achieve QoE-optimal edge inference.« less