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1. 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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2. Velody: Nonlinear Vibration Challenge-Response for Resilient User Authentication

   https://doi.org/10.1145/3319535.3354242  

   Li, Jingjie ; Fawaz, Kassem ; Kim, Younghyun ( November 2019 , Proceedings of the 2019 ACM SIGSAC Conference on Computer and Communications Security)

   Biometrics have been widely adopted for enhancing user authentication, benefiting usability by exploiting pervasive and collectible unique characteristics from physiological or behavioral traits of human. However, successful attacks on "static" biometrics such as fingerprints have been reported where an adversary acquires users' biometrics stealthily and compromises non-resilient biometrics. To mitigate the vulnerabilities of static biometrics, we leverage the unique and nonlinear hand-surface vibration response and design a system called Velody to defend against various attacks including replay and synthesis. The Velody system relies on two major properties in hand-surface vibration responses: uniqueness, contributed by physiological characteristics of human hands, and nonlinearity, whose complexity prevents attackers from predicting the response to an unseen challenge. Velody employs a challenge-response protocol. By changing the vibration challenge, the system elicits input-dependent nonlinear "symptoms" and unique spectrotemporal features in the vibration response, stopping both replay and synthesis attacks. Also, a large number of disposable challenge-response pairs can be collected during enrollment passively for daily authentication sessions. We build a prototype of Velody with an off-the-shelf vibration speaker and accelerometers to verify its usability and security through a comprehensive user experiment. Our results show that Velody demonstrates both strong security and long-term consistency with a low equal error rate (EER) of 5.8% against impersonation attack while correctly rejecting all other attacks including replay and synthesis attacks using a very short vibration challenge. 

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3. Use of Auxiliary Classifier Generative Adversarial Network in Touchstroke Authentication

   https://doi.org/10.1109/icmla51294.2020.00049  

   Deb, Debzani ; Guirguis, Mina M. ( December 2020 , 19th IEEE International Conference on Machine Learning and Applications (ICMLA))

   null (Ed.)

   With the growing popularity of smartphones, continuous and implicit authentication of such devices via behavioral biometrics such as touch dynamics becomes an attractive option, especially when the physical biometrics are challenging to utilize, or their frequent and continuous usage annoys the user. However, touch dynamics is vulnerable to potential security attacks such as shoulder surfing, camera attack, and smudge attack. As a result, it is challenging to rule out genuine imposters while only relying on models that learn from real touchstrokes. In this paper, a touchstroke authentication model based on Auxiliary Classifier Generative Adversarial Network (AC-GAN) is presented. Given a small subset of a legitimate user's touchstrokes data during training, the presented AC-GAN model learns to generate a vast amount of synthetic touchstrokes that closely approximate the real touchstrokes, simulating imposter behavior, and then uses both generated and real touchstrokes in discriminating real user from the imposters. The presented network is trained on the Touchanalytics dataset and the discriminability is evaluated with popular performance metrics and loss functions. The evaluation results suggest that it is possible to achieve comparable authentication accuracies with Equal Error Rate ranging from 2% to 11% even when the generative model is challenged with a vast number of synthetic data that effectively simulates an imposter behavior. The use of AC-GAN also diversifies generated samples and stabilizes training. 

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4. LivDet iris 2017 — Iris liveness detection competition 2017

   https://doi.org/10.1109/BTAS.2017.8272763  

   Yambay, David ; Becker, Benedict ; Kohli, Naman ; Yadav, Daksha ; Czajka, Adam ; Bowyer, Kevin W. ; Schuckers, Stephanie ; Singh, Richa ; Vatsa, Mayank ; Noore, Afzel ; et al ( October 2017 , International Joint Conference on Biometrics (IJCB))

   Presentation attacks such as using a contact lens with a printed pattern or printouts of an iris can be utilized to bypass a biometric security system. The first international iris liveness competition was launched in 2013 in order to assess the performance of presentation attack detection (PAD) algorithms, with a second competition in 2015. This paper presents results of the third competition, LivDet-Iris 2017. Three software-based approaches to Presentation Attack Detection were submitted. Four datasets of live and spoof images were tested with an additional cross-sensor test. New datasets and novel situations of data have resulted in this competition being of a higher difficulty than previous competitions. Anonymous received the best results with a rate of rejected live samples of 3.36% and rate of accepted spoof samples of 14.71%. The results show that even with advances, printed iris attacks as well as patterned contacts lenses are still difficult for software-based systems to detect. Printed iris images were easier to be differentiated from live images in comparison to patterned contact lenses as was also seen in previous competitions. 

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5. Late Deep Fusion of Color Spaces to Enhance Finger Photo Presentation Attack Detection in Smartphones

   https://doi.org/10.3390/app122211409  

   Marasco, Emanuela ; Vurity, Anudeep ( November 2022 , Applied Sciences)

   Finger photo recognition represents a promising touchless technology that offers portable and hygienic authentication solutions in smartphones, eliminating physical contact. Public spaces, such as banks and staff-less stores, benefit from contactless authentication considering the current public health sphere. The user captures the image of their own finger by using the camera integrated in a mobile device. Although recent research has pushed boundaries of finger photo matching, the security of this biometric methodology still represents a concern. Existing systems have been proven to be vulnerable to print attacks by presenting a color paper-printout in front of the camera and photo attacks that consist of displaying the original image in front of the capturing device. This paper aims to improve the performance of finger photo presentation attack detection (PAD) algorithms by investigating deep fusion strategies to combine deep representations obtained from different color spaces. In this work, spoofness is described by combining different color models. The proposed framework integrates multiple convolutional neural networks (CNNs), each trained using patches extracted from a specific color model and centered around minutiae points. Experiments were carried out on a publicly available database of spoofed finger photos obtained from the IIITD Smartphone Finger photo Database with spoof data, including printouts and various display attacks. The results show that deep fusion of the best color models improved the robustness of the PAD system and competed with the state-of-the-art. 

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