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1. Efficient unsupervised drift detector for fast and high-dimensional data streams

   https://doi.org/10.1007/s10115-021-01564-6  

   Souza, Vinicius M. ; Parmezan, Antonio R. ; Chowdhury, Farhan A. ; Mueen, Abdullah ( April 2021 , Knowledge and Information Systems)

   Stream mining considers the online arrival of examples at high speed and the possibility of changes in its descriptive features or class definitions compared with past knowledge (i.e., concept drifts). The fast detection of drifts is essential to keep the predictive model updated and stable in changing environments. For many applications, such as those related to smart sensors, the high number of features is an additional challenge in terms of memory and time for stream processing. This paper presents an unsupervised and model-independent concept drift detector suitable for high-speed and high-dimensional data streams. We propose a straightforward two-dimensional data representation that allows the faster processing of datasets with a large number of examples and dimensions. We developed an adaptive drift detector on this visual representation that is efficient for fast streams with thousands of features and is accurate as existing costly methods that perform various statistical tests considering each feature individually. Our method achieves better performance measured by execution time and accuracy in classification problems for different types of drifts. The experimental evaluation considering synthetic and real data demonstrates the method’s versatility in several domains, including entomology, medicine, and transportation systems.
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. Adaptive Sampling and Quick Anomaly Detection in Large Networks

   Xian, X. ; Semenov, A. ; Hu, Y. ; Wang, A. ; Jin, Y. ( October 2022 , IEEE transactions on automation science and engineering)

   The monitoring of data streams with a network structure have drawn increasing attention due to its wide applications in modern process control. In these applications, high-dimensional sensor nodes are interconnected with an underlying network topology. In such a case, abnormalities occurring to any node may propagate dynamically across the network and cause changes of other nodes over time. Furthermore, high dimensionality of such data significantly increased the cost of resources for data transmission and computation, such that only partial observations can be transmitted or processed in practice. Overall, how to quickly detect abnormalities in such large networks with resource constraints remains a challenge, especially due to the sampling uncertainty under the dynamic anomaly occurrences and network-based patterns. In this paper, we incorporate network structure information into the monitoring and adaptive sampling methodologies for quick anomaly detection in large networks where only partial observations are available. We develop a general monitoring and adaptive sampling method and further extend it to the case with memory constraints, both of which exploit network distance and centrality information for better process monitoring and identification of abnormalities. Theoretical investigations of the proposed methods demonstrate their sampling efficiency on balancing between exploration and exploitation, as well asmore »the detection performance guarantee. Numerical simulations and a case study on power network have demonstrated the superiority of the proposed methods in detecting various types of shifts. Note to Practitioners —Continuous monitoring of networks for anomalous events is critical for a large number of applications involving power networks, computer networks, epidemiological surveillance, social networks, etc. This paper aims at addressing the challenges in monitoring large networks in cases where monitoring resources are limited such that only a subset of nodes in the network is observable. Specifically, we integrate network structure information of nodes for constructing sequential detection methods via effective data augmentation, and for designing adaptive sampling algorithms to observe suspicious nodes that are likely to be abnormal. Then, the method is further generalized to the case that the memory of the computation is also constrained due to the network size. The developed method is greatly beneficial and effective for various anomaly patterns, especially when the initial anomaly randomly occurs to nodes in the network. The proposed methods are demonstrated to be capable of quickly detecting changes in the network and dynamically changes the sampling priority based on online observations in various cases, as shown in the theoretical investigation, simulations and case studies.« less
4. DriftSurf: Stable-State / Reactive-State Learning under Concept Drift

   Tahmasbi, Ashraf ; Jothimurugesan, Ellango ; Tirthapura, Srikanta ; Gibbons, Phillip B. ( July 2021 , Proceedings of the 38th International Conference on Machine Learning, {ICML} 2021, 18-24 July 2021, Virtual Even)

   When learning from streaming data, a change in the data distribution, also known as concept drift, can render a previously-learned model inaccurate and require training a new model. We present an adaptive learning algorithm that extends previous drift-detection-based methods by incorporating drift detection into a broader stable-state/reactive-state process. The advantage of our approach is that we can use aggressive drift detection in the stable state to achieve a high detection rate, but mitigate the false positive rate of standalone drift detection via a reactive state that reacts quickly to true drifts while eliminating most false positives. The algorithm is generic in its base learner and can be applied across a variety of supervised learning problems. Our theoretical analysis shows that the risk of the algorithm is (i) statistically better than standalone drift detection and (ii) competitive to an algorithm with oracle knowledge of when (abrupt) drifts occur. Experiments on synthetic and real datasets with concept drifts confirm our theoretical analysis.
5. DriftSurf: A Risk-competitive Learning Algorithm under Concept Drift

   Tahmasbi, Ashraf ; Jothimurugesan, Ellango ; Tirthapura, Srikanta ; Gibbons, Phillip B. ( January 2020 , ArXivorg)

   When learning from streaming data, a change in the data distribution, also known as concept drift, can render a previously-learned model inaccurate and require training a new model. We present an adaptive learning algorithm that extends previous drift-detection-based methods by incorporating drift detection into a broader stable-state/reactive-state process. The advantage of our approach is that we can use aggressive drift detection in the stable state to achieve a high detection rate, but mitigate the false positive rate of standalone drift detection via a reactive state that reacts quickly to true drifts while eliminating most false positives. The algorithm is generic in its base learner and can be applied across a variety of supervised learning problems. Our theoretical analysis shows that the risk of the algorithm is competitive to an algorithm with oracle knowledge of when (abrupt) drifts occur. Experiments on synthetic and real datasets with concept drifts confirm our theoretical analysis.