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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. Toward Real-Time, Robust Wearable Sensor Fall Detection Using Deep Learning Methods: A Feasibility Study

   https://doi.org/10.3390/app13084988  

   Yhdego, Haben ; Paolini, Christopher ; Audette, Michel ( April 2023 , Applied Sciences)

   Real-time fall detection using a wearable sensor remains a challenging problem due to high gait variability. Furthermore, finding the type of sensor to use and the optimal location of the sensors are also essential factors for real-time fall-detection systems. This work presents real-time fall-detection methods using deep learning models. Early detection of falls, followed by pneumatic protection, is one of the most effective means of ensuring the safety of the elderly. First, we developed and compared different data-segmentation techniques for sliding windows. Next, we implemented various techniques to balance the datasets because collecting fall datasets in the real-time setting has an imbalanced nature. Moreover, we designed a deep learning model that combines a convolution-based feature extractor and deep neural network blocks, the LSTM block, and the transformer encoder block, followed by a position-wise feedforward layer. We found that combining the input sequence with the convolution-learned features of different kernels tends to increase the performance of the fall-detection model. Last, we analyzed that the sensor signals collected by both accelerometer and gyroscope sensors can be leveraged to develop an effective classifier that can accurately detect falls, especially differentiating falls from near-falls. Furthermore, we also used data from sixteen different body parts and compared them to determine the better sensor position for fall-detection methods. We found that the shank is the optimal position for placing our sensors, with an F1 score of 0.97, and this could help other researchers collect high-quality fall datasets.

    

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3. Auto-ASD-Network: A Technique Based on Deep Learning and Support Vector Machines for Diagnosing Autism Spectrum Disorder using fMRI Data

   https://doi.org/10.1145/3307339.3343482  

   Eslami, Taban ; Saeed, Fahad ( January 2019 , Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics)

   Quantitative analysis of brain disorders such as Autism Spectrum Disorder (ASD) is an ongoing field of research. Machine learning and deep learning techniques have been playing an important role in automating the diagnosis of brain disorders by extracting discriminative features from the brain data. In this study, we propose a model called Auto-ASD-Network in order to classify subjects with Autism disorder from healthy subjects using only fMRI data. Our model consists of a multilayer perceptron (MLP) with two hidden layers. We use an algorithm called SMOTE for performing data augmentation in order to generate artificial data and avoid overfitting, which helps increase the classification accuracy. We further investigate the discriminative power of features extracted using MLP by feeding them to an SVM classifier. In order to optimize the hyperparameters of SVM, we use a technique called Auto Tune Models (ATM) which searches over the hyperparameter space to find the best values of SVM hyperparameters. Our model achieves more than 70% classification accuracy for 4 fMRI datasets with the highest accuracy of 80%. It improves the performance of SVM by 26%, the stand-alone MLP by 16% and the state of the art method in ASD classification by 14%. The implemented code will be available as GPL license on GitHub portal of our lab (https://github.com/PCDS). 

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4. Driver Maneuver Interaction Identification with Anomaly-Aware Federated Learning on Heterogeneous Feature Representations

   https://doi.org/10.1145/3631421  

   Tabatabaie, Mahan ; He, Suining ( December 2023 , Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies)

   Driver maneuver interaction learning (DMIL) refers to the classification task with the goal of identifying different driver-vehicle maneuver interactions (e.g., left/right turns). Existing conventional studies largely focused on the centralized collection of sensor data from the drivers' smartphones (say, inertial measurement units or IMUs, like accelerometer and gyroscope). Such a centralized mechanism might be precluded by data regulatory constraints. Furthermore, how to enable an adaptive and accurate DMIL framework remains challenging due to (i) complexity in heterogeneous driver maneuver patterns, and (ii) impacts of anomalous driver maneuvers due to, for instance, aggressive driving styles and behaviors.

   To overcome the above challenges, we propose AF-DMIL, an Anomaly-aware Federated Driver Maneuver Interaction Learning system. We focus on the real-world IMU sensor datasets (e.g., collected by smartphones) for our pilot case study. In particular, we have designed three heterogeneous representations for AF-DMIL regarding spectral, time series, and statistical features that are derived from the IMU sensor readings. We have designed a novel heterogeneous representation attention network (HetRANet) based on spectral channel attention, temporal sequence attention, and statistical feature learning mechanisms, jointly capturing and identifying the complex patterns within driver maneuver behaviors. Furthermore, we have designed a densely-connected convolutional neural network in HetRANet to enable the complex feature extraction and enhance the computational efficiency of HetRANet. In addition, we have designed within AF-DMIL a novel anomaly-aware federated learning approach for decentralized DMIL in response to anomalous maneuver data. To ease extraction of the maneuver patterns and evaluation of their mutual differences, we have designed an embedding projection network that projects the high-dimensional driver maneuver features into low-dimensional space, and further derives the exemplars that represent the driver maneuver patterns for mutual comparison. Then, AF-DMIL further leverages the mutual differences of the exemplars to identify those that exhibit anomalous patterns and deviate from others, and mitigates their impacts upon the federated DMIL. We have conducted extensive driver data analytics and experimental studies on three real-world datasets (one is harvested on our own) to evaluate the prototype of AF-DMIL, demonstrating AF-DMIL's accuracy and effectiveness compared to the state-of-the-art DMIL baselines (on average by more than 13% improvement in terms of DMIL accuracy), as well as fewer communication rounds (on average 29.20% fewer than existing distributed learning mechanisms).

    

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5. Metamorphic Detection of Repackaged Malware

   https://doi.org/10.1109/MET52542.2021.00009  

   Singh, Shirish ; Kaiser, Gail ( June 2021 , 6th International Workshop on Metamorphic Testing (MET))

   null (Ed.)

   Machine learning-based malware detection systems are often vulnerable to evasion attacks, in which a malware developer manipulates their malicious software such that it is misclassified as benign. Such software hides some properties of the real class or adopts some properties of a different class by applying small perturbations. A special case of evasive malware hides by repackaging a bonafide benign mobile app to contain malware in addition to the original functionality of the app, thus retaining most of the benign properties of the original app. We present a novel malware detection system based on metamorphic testing principles that can detect such benign-seeming malware apps. We apply metamorphic testing to the feature representation of the mobile app, rather than to the app itself. That is, the source input is the original feature vector for the app and the derived input is that vector with selected features removed. If the app was originally classified benign, and is indeed benign, the output for the source and derived inputs should be the same class, i.e., benign, but if they differ, then the app is exposed as (likely) malware. Malware apps originally classified as malware should retain that classification, since only features prevalent in benign apps are removed. This approach enables the machine learning model to classify repackaged malware with reasonably few false negatives and false positives. Our training pipeline is simpler than many existing ML-based malware detection methods, as the network is trained end-to-end to jointly learn appropriate features and to perform classification. We pre-trained our classifier model on 3 million apps collected from the widely-used AndroZoo dataset. 1 We perform an extensive study on other publicly available datasets to show our approach’s effectiveness in detecting repackaged malware with more than 94% accuracy, 0.98 precision, 0.95 recall, and 0.96 F1 score. 

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