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1. ARCH-COMP20 Category Report: Artificial Intelligence and Neural Network Control Systems (AINNCS) for Continuous and Hybrid Systems Plants

   https://doi.org/10.29007/9xgv  

   Johnson, Taylor T ; Manzanas Lopez, Diego ; Musau, Patrick ; Tran, Hoang-Dung ; Botoeva, Elena ; Leofante, Francesco ; Maleki, Amir ; Sidrane, Chelsea ; Fan, Jiameng ; Huang, Chao ( September 2020 , EPiC Series in Computing)

   This report presents the results of a friendly competition for formal verification of continuous and hybrid systems with artificial intelligence (AI) components. Specifically, machine learning (ML) components in cyber-physical systems (CPS), such as feedforward neural networks used as feedback controllers in closed-loop systems are considered, which is a class of systems classically known as intelligent control systems, or in more modern and specific terms, neural network control systems (NNCS). We more broadly refer to this category as AI and NNCS (AINNCS). The friendly competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020. In the second edition of this AINNCS category at ARCH-COMP, four tools have been applied to solve seven different benchmark problems, (in alphabetical order): NNV, OVERT, ReachNN*, and VenMAS. This report is a snapshot of the current landscape of tools and the types of benchmarks for which these tools are suited. Due to the diversity of problems, lack of a shared hardware platform, and the early stage of the competition, we are not ranking tools in terms of performance, yet the presented results probably provide the most complete assessment of current tools for safety verification of NNCS. 

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2. ARCH-COMP20 Repeatability Evaluation Report

   https://doi.org/10.29007/8dp4  

   Johnson, Taylor T ( September 2020 , EPiC Series in Computing)

   This report presents the results of the repeatability evaluation for the 4th International Competition on Verifying Continuous and Hybrid Systems (ARCH-COMP’20). The competition took place as part of the workshop Applied Verification for Continuous and Hybrid Systems (ARCH) in 2020, affiliated with the IFAC World Congress. In its fourth edition, twenty-eight tools submitted artifacts through a Git repository for the repeatability evaluation, applied to solve benchmark problems for seven competition categories. The majority of participants adhered to the requirements for this year’s repeatability evaluation, namely to submit scripts to automatically install and execute tools in containerized virtual environments (specifically Dockerfiles to execute within Docker), and several categories used performance evaluation information from a common execution platform. The repeatability results represent a snapshot of the current landscape of tools and the types of benchmarks for which they are particularly suited and for which others may repeat their analyses. Due to the diversity of problems in verification of continuous and hybrid systems, as well as basing on standard practice in repeatability evaluations, we evaluate the tools with pass and/or failing being repeatable. 

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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. NNV2.0: The neural network verification tool

   Diego Manzanas Lopez ; Sung Woo Choi ; Hoang-Dung Tran ; Taylor T. Johnson ( July 2023 , The 35th International Conference on Computer-Aided Verification)

   This manuscript presents the updated version of the Neural Network Verification (NNV) tool. NNV is a formal verification software tool for deep learning models and cyber-physical systems with neural network components. NNV was first introduced as a verification framework for feedforward and convolutional neural networks, as well as for neural network control systems. Since then, numerous works have made significant improvements in the verification of new deep learning models, as well as tackling some of the scalability issues that may arise when verifying complex models. In this new version of NNV, we introduce verification support for multiple deep learning models, including neural ordinary differential equations, semantic segmentation networks and recurrent neural networks, as well as a collection of reachability methods that aim to reduce the computation cost of reachability analysis of complex neural networks. We have also added direct support for standard input verification formats in the community such as VNNLIB (verification properties), and ONNX (neural networks) formats. We present a collection of experiments in which NNV verifies safety and robustness properties of feedforward, convolutional, semantic segmentation and recurrent neural networks, as well as neural ordinary differential equations and neural network control systems. Furthermore, we demonstrate the capabilities of NNV against a commercially available product in a collection of benchmarks from control systems, semantic segmentation, image classification, and time-series data. 

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5. Verifying Binary Neural Networks on Continuous Input Space using Star Reachability

   https://doi.org/10.1109/FormaliSE58978.2023.00009  

   Ivashchenko, Mykhailo ; Choi, Sung Woo ; Nguyen, Luan Viet ; Tran, Hoang-Dung ( May 2023 , 2023 IEEE/ACM 11th International Conference on Formal Methods in Software Engineering (FormaliSE))

   Deep Neural Networks (DNNs) have become a popular instrument for solving various real-world problems. DNNs’ sophisticated structure allows them to learn complex representations and features. For this reason, Binary Neural Networks (BNNs) are widely used on edge devices, such as microcomputers. However, architecture specifics and floating-point number usage result in an increased computational operations complexity. Like other DNNs, BNNs are vulnerable to adversarial attacks; even a small perturbation to the input set may lead to an errant output. Unfortunately, only a few approaches have been proposed for verifying BNNs.This paper proposes an approach to verify BNNs on continuous input space using star reachability analysis. Our approach can compute both exact and overapproximate reachable sets of BNNs with Sign activation functions and use them for verification. The proposed approach is also efficient in constructing a complete set of counterexamples in case a network is unsafe. We implemented our approach in NNV, a neural network verification tool for DNNs and learning-enabled Cyber-Physical Systems. The experimental results show that our star-based approach is less conservative, more efficient, and scalable than the recent SMT-based method implemented in Marabou. We also provide a comparison with a quantization-based tool EEVBNN. 

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