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1. ARRU Phase Picker: Attention Recurrent-Residual U-Net for Picking Seismic P - and S -Phase Arrivals

   https://doi.org/10.1785/0220200382  

   Liao, Wu-Yu ; Lee, En-Jui ; Mu, Dawei ; Chen, Po ; Rau, Ruey-Juin ( March 2021 , Seismological Research Letters)

   null (Ed.)

   Abstract Seismograms are convolution results between seismic sources and the media that seismic waves propagate through, and, therefore, the primary observations for studying seismic source parameters and the Earth interior. The routine earthquake location and travel-time tomography rely on accurate seismic phase picks (e.g., P and S arrivals). As data increase, reliable automated seismic phase-picking methods are needed to analyze data and provide timely earthquake information. However, most traditional autopickers suffer from low signal-to-noise ratio and usually require additional efforts to tune hyperparameters for each case. In this study, we proposed a deep-learning approach that adapted soft attention gates (AGs) and recurrent-residual convolution units (RRCUs) into the backbone U-Net for seismic phase picking. The attention mechanism was implemented to suppress responses from waveforms irrelevant to seismic phases, and the cooperating RRCUs further enhanced temporal connections of seismograms at multiple scales. We used numerous earthquake recordings in Taiwan with diverse focal mechanisms, wide depth, and magnitude distributions, to train and test our model. Setting the picking errors within 0.1 s and predicted probability over 0.5, the AG with recurrent-residual convolution unit (ARRU) phase picker achieved the F1 score of 98.62% for P arrivals and 95.16% for S arrivals, and picking rates were 96.72% for P waves and 90.07% for S waves. The ARRU phase picker also shown a great generalization capability, when handling unseen data. When applied the model trained with Taiwan data to the southern California data, the ARRU phase picker shown no cognitive downgrade. Comparing with manual picks, the arrival times determined by the ARRU phase picker shown a higher consistency, which had been evaluated by a set of repeating earthquakes. The arrival picks with less human error could benefit studies, such as earthquake location and seismic tomography. 

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2. PhaseLink: A Deep Learning Approach to Seismic Phase Association

   https://doi.org/10.1029/2018JB016674  

   Ross, Zachary E. ; Yue, Yisong ; Meier, Men‐Andrin ; Hauksson, Egill ; Heaton, Thomas H. ( January 2019 , Journal of Geophysical Research: Solid Earth)

   Seismic phase association is a fundamental task in seismology that pertains to linking together phase detections on different sensors that originate from a common earthquake. It is widely employed to detect earthquakes on permanent and temporary seismic networks and underlies most seismicity catalogs produced around the world. This task can be challenging because the number of sources is unknown, events frequently overlap in time, or can occur simultaneously in different parts of a network. We present PhaseLink, a framework based on recent advances in deep learning for grid‐free earthquake phase association. Our approach learns to link phases together that share a common origin and is trained entirely on millions of synthetic sequences ofPandSwave arrival times generated using a 1‐D velocity model. Our approach is simple to implement for any tectonic regime, suitable for real‐time processing, and can naturally incorporate errors in arrival time picks. Rather than tuning a set of ad hoc hyperparameters to improve performance, PhaseLink can be improved by simply adding examples of problematic cases to the training data set. We demonstrate the state‐of‐the‐art performance of PhaseLink on a challenging sequence from southern California and synthesized sequences from Japan designed to test the point at which the method fails. For the examined data sets, PhaseLink can precisely associate phases to events that occur only ∼12 s apart in origin time. This approach is expected to improve the resolution of seismicity catalogs, add stability to real‐time seismic monitoring, and streamline automated processing of large seismic data sets.

    

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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. Receiver Function Investigations of Seismic Anisotropy Layering Beneath Southern California

   https://doi.org/10.1029/2018JB015830  

   Kong, Fansheng ; Gao, Stephen S. ; Liu, Kelly H. ; Song, Jianguo ; Ding, Weiwei ; Fang, Yinxia ; Ruan, Aiguo ; Li, Jiabiao ( December 2018 , Journal of Geophysical Research: Solid Earth)

   Seismic azimuthal anisotropy characterized by shear wave splitting analyses using teleseismicXKSphases (includingSKS,SKKS, andPKS) is widely employed to constrain the deformation field in the Earth's crust and mantle. Due to the near‐vertical incidence of theXKSarrivals, the resulting splitting parameters (fast polarization orientations and splitting times) have an excellent horizontal but poor vertical resolution, resulting in considerable ambiguities in the geodynamic interpretation of the measurements. Here we useP‐to‐Sconverted phases from the Moho and the 410‐ (d410) and 660‐km (d660) discontinuities to investigate anisotropy layering beneath Southern California. Similarities between the resulting splitting parameters from theXKSandP‐to‐Sconverted phases from thed660 suggest that the lower mantle beneath the study area is azimuthally isotropic. Similarly, significant azimuthal anisotropy is not present in the mantle transition zone on the basis of the consistency between the splitting parameters obtained usingP‐to‐Sconverted phases from thed410 andd660. Crustal anisotropy measurements exhibit a mean splitting time of 0.2 ± 0.1 s and mostly NW‐SE fast orientations, which are significantly different from the dominantly E‐W fast orientations revealed usingXKSandP‐to‐Sconversions from thed410 andd660. Anisotropy measurements using shear waves with different depths of origin suggest that the Earth's upper mantle is the major anisotropic layer beneath Southern California. Additionally, this study demonstrates the effectiveness of applying a set of azimuthal anisotropy analysis techniques to reduce ambiguities in the depth of the source of the observed anisotropy.

    

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5. Unsupervised Deep Clustering of Seismic Data: Monitoring the Ross Ice Shelf, Antarctica

   https://doi.org/10.1029/2021JB021716  

   Jenkins, II, William F. ; Gerstoft, Peter ; Bianco, Michael J. ; Bromirski, Peter D. ( September 2021 , Journal of Geophysical Research: Solid Earth)

   Advances in machine learning (ML) techniques and computational capacity have yielded state‐of‐the‐art methodologies for processing, sorting, and analyzing large seismic data sets. In this study, we consider an application of ML for automatically identifying dominant types of impulsive seismicity contained in observations from a 34‐station broadband seismic array deployed on the Ross Ice Shelf (RIS), Antarctica from 2014 to 2017. The RIS seismic data contain signals and noise generated by many glaciological processes that are useful for monitoring the integrity and dynamics of ice shelves. Deep clustering was employed to efficiently investigate these signals. Deep clustering automatically groups signals into hypothetical classes without the need for manual labeling, allowing for the comparison of their signal characteristics and spatial and temporal distribution with potential source mechanisms. The method uses spectrograms as input and encodes their salient features into a lower‐dimensional latent representation using an autoencoder, a type of deep neural network. For comparison, two clustering methods are applied to the latent data: a Gaussian mixture model (GMM) and deep embedded clustering (DEC). Eight classes of dominant seismic signals were identified and compared with environmental data such as temperature, wind speed, tides, and sea ice concentration. The greatest seismicity levels occurred at the RIS front during the 2016 El Niño summer, and near grounding zones near the front throughout the deployment. We demonstrate the spatial and temporal association of certain classes of seismicity with seasonal changes at the RIS front, and with tidally driven seismicity at Roosevelt Island.

    

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