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1. Estimating asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan: a mathematical modeling study

   https://doi.org/10.1186/s12879-021-06078-8  

   Huo, Xi ; Chen, Jing ; Ruan, Shigui ( December 2021 , BMC Infectious Diseases)

   Abstract Background The COVID-19 outbreak in Wuhan started in December 2019 and was under control by the end of March 2020 with a total of 50,006 confirmed cases by the implementation of a series of nonpharmaceutical interventions (NPIs) including unprecedented lockdown of the city. This study analyzes the complete outbreak data from Wuhan, assesses the impact of these public health interventions, and estimates the asymptomatic, undetected and total cases for the COVID-19 outbreak in Wuhan. Methods By taking different stages of the outbreak into account, we developed a time-dependent compartmental model to describe the dynamics of disease transmission and case detection and reporting. Model coefficients were parameterized by using the reported cases and following key events and escalated control strategies. Then the model was used to calibrate the complete outbreak data by using the Monte Carlo Markov Chain (MCMC) method. Finally we used the model to estimate asymptomatic and undetected cases and approximate the overall antibody prevalence level. Results We found that the transmission rate between Jan 24 and Feb 1, 2020, was twice as large as that before the lockdown on Jan 23 and 67.6 % (95% CI [0.584,0.759]) of detectable infections occurred during this period. Based on the reported estimates that around 20% of infections were asymptomatic and their transmission ability was about 70% of symptomatic ones, we estimated that there were about 14,448 asymptomatic and undetected cases (95% CI [12,364,23,254]), which yields an estimate of a total of 64,454 infected cases (95% CI [62,370,73,260]), and the overall antibody prevalence level in the population of Wuhan was 0.745% (95% CI [0.693 % ,0.814 % ]) by March 31, 2020. Conclusions We conclude that the control of the COVID-19 outbreak in Wuhan was achieved via the enforcement of a combination of multiple NPIs: the lockdown on Jan 23, the stay-at-home order on Feb 2, the massive isolation of all symptomatic individuals via newly constructed special shelter hospitals on Feb 6, and the large scale screening process on Feb 18. Our results indicate that the population in Wuhan is far away from establishing herd immunity and provide insights for other affected countries and regions in designing control strategies and planing vaccination programs. 

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2. Predictive performance of multi-model ensemble forecasts of COVID-19 across European nations

   https://doi.org/10.7554/eLife.81916  

   Sherratt, Katharine ; Gruson, Hugo ; Grah, Rok ; Johnson, Helen ; Niehus, Rene ; Prasse, Bastian ; Sandmann, Frank ; Deuschel, Jannik ; Wolffram, Daniel ; Abbott, Sam ; et al ( April 2023 , eLife)

   Short-term forecasts of infectious disease burden can contribute to situational awareness and aid capacity planning. Based on best practice in other fields and recent insights in infectious disease epidemiology, one can maximise the predictive performance of such forecasts if multiple models are combined into an ensemble. Here, we report on the performance of ensembles in predicting COVID-19 cases and deaths across Europe between 08 March 2021 and 07 March 2022.

   We used open-source tools to develop a public European COVID-19 Forecast Hub. We invited groups globally to contribute weekly forecasts for COVID-19 cases and deaths reported by a standardised source for 32 countries over the next 1–4 weeks. Teams submitted forecasts from March 2021 using standardised quantiles of the predictive distribution. Each week we created an ensemble forecast, where each predictive quantile was calculated as the equally-weighted average (initially the mean and then from 26th July the median) of all individual models’ predictive quantiles. We measured the performance of each model using the relative Weighted Interval Score (WIS), comparing models’ forecast accuracy relative to all other models. We retrospectively explored alternative methods for ensemble forecasts, including weighted averages based on models’ past predictive performance.

   Over 52 weeks, we collected forecasts from 48 unique models. We evaluated 29 models’ forecast scores in comparison to the ensemble model. We found a weekly ensemble had a consistently strong performance across countries over time. Across all horizons and locations, the ensemble performed better on relative WIS than 83% of participating models’ forecasts of incident cases (with a total N=886 predictions from 23 unique models), and 91% of participating models’ forecasts of deaths (N=763 predictions from 20 models). Across a 1–4 week time horizon, ensemble performance declined with longer forecast periods when forecasting cases, but remained stable over 4 weeks for incident death forecasts. In every forecast across 32 countries, the ensemble outperformed most contributing models when forecasting either cases or deaths, frequently outperforming all of its individual component models. Among several choices of ensemble methods we found that the most influential and best choice was to use a median average of models instead of using the mean, regardless of methods of weighting component forecast models.

   Our results support the use of combining forecasts from individual models into an ensemble in order to improve predictive performance across epidemiological targets and populations during infectious disease epidemics. Our findings further suggest that median ensemble methods yield better predictive performance more than ones based on means. Our findings also highlight that forecast consumers should place more weight on incident death forecasts than incident case forecasts at forecast horizons greater than 2 weeks.

   AA, BH, BL, LWa, MMa, PP, SV funded by National Institutes of Health (NIH) Grant 1R01GM109718, NSF BIG DATA Grant IIS-1633028, NSF Grant No.: OAC-1916805, NSF Expeditions in Computing Grant CCF-1918656, CCF-1917819, NSF RAPID CNS-2028004, NSF RAPID OAC-2027541, US Centers for Disease Control and Prevention 75D30119C05935, a grant from Google, University of Virginia Strategic Investment Fund award number SIF160, Defense Threat Reduction Agency (DTRA) under Contract No. HDTRA1-19-D-0007, and respectively Virginia Dept of Health Grant VDH-21-501-0141, VDH-21-501-0143, VDH-21-501-0147, VDH-21-501-0145, VDH-21-501-0146, VDH-21-501-0142, VDH-21-501-0148. AF, AMa, GL funded by SMIGE - Modelli statistici inferenziali per governare l'epidemia, FISR 2020-Covid-19 I Fase, FISR2020IP-00156, Codice Progetto: PRJ-0695. AM, BK, FD, FR, JK, JN, JZ, KN, MG, MR, MS, RB funded by Ministry of Science and Higher Education of Poland with grant 28/WFSN/2021 to the University of Warsaw. BRe, CPe, JLAz funded by Ministerio de Sanidad/ISCIII. BT, PG funded by PERISCOPE European H2020 project, contract number 101016233. CP, DL, EA, MC, SA funded by European Commission - Directorate-General for Communications Networks, Content and Technology through the contract LC-01485746, and Ministerio de Ciencia, Innovacion y Universidades and FEDER, with the project PGC2018-095456-B-I00. DE., MGu funded by Spanish Ministry of Health / REACT-UE (FEDER). DO, GF, IMi, LC funded by Laboratory Directed Research and Development program of Los Alamos National Laboratory (LANL) under project number 20200700ER. DS, ELR, GG, NGR, NW, YW funded by National Institutes of General Medical Sciences (R35GM119582; the content is solely the responsibility of the authors and does not necessarily represent the official views of NIGMS or the National Institutes of Health). FB, FP funded by InPresa, Lombardy Region, Italy. HG, KS funded by European Centre for Disease Prevention and Control. IV funded by Agencia de Qualitat i Avaluacio Sanitaries de Catalunya (AQuAS) through contract 2021-021OE. JDe, SMo, VP funded by Netzwerk Universitatsmedizin (NUM) project egePan (01KX2021). JPB, SH, TH funded by Federal Ministry of Education and Research (BMBF; grant 05M18SIA). KH, MSc, YKh funded by Project SaxoCOV, funded by the German Free State of Saxony. Presentation of data, model results and simulations also funded by the NFDI4Health Task Force COVID-19 (https://www.nfdi4health.de/task-force-covid-19-2) within the framework of a DFG-project (LO-342/17-1). LP, VE funded by Mathematical and Statistical modelling project (MUNI/A/1615/2020), Online platform for real-time monitoring, analysis and management of epidemic situations (MUNI/11/02202001/2020); VE also supported by RECETOX research infrastructure (Ministry of Education, Youth and Sports of the Czech Republic: LM2018121), the CETOCOEN EXCELLENCE (CZ.02.1.01/0.0/0.0/17-043/0009632), RECETOX RI project (CZ.02.1.01/0.0/0.0/16-013/0001761). NIB funded by Health Protection Research Unit (grant code NIHR200908). SAb, SF funded by Wellcome Trust (210758/Z/18/Z).

    

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3. Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2000-2010)

   https://doi.org/10.5281/zenodo.7406675  

   Porter, Nicholas ; Silver, Adrienne ; Gangopadhyay, Avijit ( January 2022 , Zenodo)

   This dataset consists of weekly trajectory information of Gulf Stream Warm Core Rings from 2000-2010. This work builds upon Silver et al. (2022a) ( https://doi.org/10.5281/zenodo.6436380) which contained Warm Core Ring trajectory information from 2011 to 2020. Combining the two datasets a total of 21 years of weekly Warm Core Ring trajectories can be obtained. An example of how to use such a dataset can be found in Silver et al. (2022b).

   The format of the dataset is similar to that of  Silver et al. (2022a), and the following description is adapted from their dataset. This dataset is comprised of individual files containing each ring’s weekly center location and its area for 374 WCRs present between January 1, 2000 and December 31, 2010. Each Warm Core Ring is identified by a unique alphanumeric code 'WEyyyymmddA', where 'WE' represents a Warm Eddy (as identified in the analysis charts); 'yyyymmdd' is the year, month and day of formation; and the last character 'A' represents the sequential sighting of the eddies in a particular year. Continuity of a ring which passes from one year to the next is maintained by the same character in the first sighting.  For example, the first ring in 2002 having a trailing alphabet of 'F' indicates that five rings were carried over from 2001 which were still observed on January 1, 2002. Each ring has its own netCDF (.nc) filename following its alphanumeric code. Each file contains 4 variables, “Lon”- the ring center’s weekly longitude, “Lat”- the ring center’s weekly latitude, “Area” - the rings weekly size in km², and “Date” in days - representing the days since Jan 01, 0000. 

   The process of creating the WCR tracking dataset follows the same methodology of the previously generated WCR census (Gangopadhyay et al., 2019, 2020). The Jenifer Clark’s Gulf Stream Charts used to create this dataset are 2-3 times a week from 2000-2010. Thus, we used approximately 1560 Charts for the 10 years of analysis. All of these charts were reanalyzed between 75° and 55°W using QGIS 2.18.16 (2016) and geo-referenced on a WGS84 coordinate system (Decker, 1986). 

    

   Silver, A., Gangopadhyay, A, & Gawarkiewicz, G. (2022a). Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2011-2020) (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6436380

   Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Andres, M., Flierl, G., & Clark, J. (2022b). Spatial Variability of Movement, Structure, and Formation of Warm Core Rings in the Northwest Atlantic Slope Sea. Journal of Geophysical Research: Oceans, 127(8), e2022JC018737. https://doi.org/10.1029/2022JC018737 

   Gangopadhyay, A., G. Gawarkiewicz, N. Etige, M. Monim and J. Clark, 2019. An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream, Nature - Scientific Reports, https://doi.org/10.1038/s41598-019-48661-9. www.nature.com/articles/s41598-019-48661-9.

   Gangopadhyay, A., N. Etige, G. Gawarkiewicz, A. M. Silver, M. Monim and J. Clark, 2020.  A Census of the Warm Core Rings of the Gulf Stream (1980-2017). Journal of Geophysical Research, Oceans, 125, e2019JC016033. https://doi.org/10.1029/2019JC016033.

   QGIS Development Team. QGIS Geographic Information System (2016).

   Decker, B. L. World Geodetic System 1984. World geodetic system 1984 (1986).

    

   Funded by two NSF US grants OCE-1851242, OCE-212328 {"references": ["Silver, A., Gangopadhyay, A, & Gawarkiewicz, G. (2022). Warm Core Ring Trajectories in the Northwest Atlantic Slope Sea (2011-2020) (1.0.0) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.6436380", "Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Andres, M., Flierl, G., & Clark, J. (2022b). Spatial Variability of Movement, Structure, and Formation of Warm Core Rings in the Northwest Atlantic Slope Sea.\u00a0Journal of Geophysical Research: Oceans,\u00a0127(8), e2022JC018737.\u00a0https://doi.org/10.1029/2022JC018737", "Gangopadhyay, A., G. Gawarkiewicz, N. Etige, M. Monim and J. Clark, 2019. An Observed Regime Shift in the Formation of Warm Core Rings from the Gulf Stream, Nature - Scientific Reports, https://doi.org/10.1038/s41598-019-48661-9. www.nature.com/articles/s41598-019-48661-9.", "Gangopadhyay, A., N. Etige, G. Gawarkiewicz, A. M. Silver, M. Monim and J. Clark, 2020. A Census of the Warm Core Rings of the Gulf Stream (1980-2017). Journal of Geophysical Research, Oceans, 125, e2019JC016033. https://doi.org/10.1029/2019JC016033.", "QGIS Development Team. QGIS Geographic Information System (2016).", "Decker, B. L. World Geodetic System 1984. World geodetic system 1984 (1986)."]} 

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4. The Centrality of Black Identity for Black Students in Engineering

   Mobley, Catherine ; Brawner, Catherine E. ; Brent, Rebecca ; Orr, Marisa K. ( January 2021 , Collaborative Network for Engineering and Computing Diversity (CoNECD) Conference)

   Introduction and Theoretical Frameworks Our study draws upon several theoretical foundations to investigate and explain the educational experiences of Black students majoring in ME, CpE, and EE: intersectionality, critical race theory, and community cultural wealth theory. Intersectionality explains how gender operates together with race, not independently, to produce multiple, overlapping forms of discrimination and social inequality (Crenshaw, 1989; Collins, 2013). Critical race theory recognizes the unique experiences of marginalized groups and strives to identify the micro- and macro-institutional sources of discrimination and prejudice (Delgado & Stefancic, 2001). Community cultural wealth integrates an asset-based perspective to our analysis of engineering education to assist in the identification of factors that contribute to the success of engineering students (Yosso, 2005). These three theoretical frameworks are buttressed by our use of Racial Identity Theory, which expands understanding about the significance and meaning associated with students’ sense of group membership. Sellers and colleagues (1997) introduced the Multidimensional Model of Racial Identity (MMRI), in which they indicated that racial identity refers to the “significance and meaning that African Americans place on race in defining themselves” (p. 19). The development of this model was based on the reality that individuals vary greatly in the extent to which they attach meaning to being a member of the Black racial group. Sellers et al. (1997) posited that there are four components of racial identity: 1. Racial salience: “the extent to which one’s race is a relevant part of one’s self-concept at a particular moment or in a particular situation” (p. 24). 2. Racial centrality: “the extent to which a person normatively defines himself or herself with regard to race” (p. 25). 3. Racial regard: “a person’s affective or evaluative judgment of his or her race in terms of positive-negative valence” (p. 26). This element consists of public regard and private regard. 4. Racial ideology: “composed of the individual’s beliefs, opinions and attitudes with respect to the way he or she feels that the members of the race should act” (p. 27). The resulting 56-item inventory, the Multidimensional Inventory of Black Identity (MIBI), provides a robust measure of Black identity that can be used across multiple contexts. Research Questions Our 3-year, mixed-method study of Black students in computer (CpE), electrical (EE) and mechanical engineering (ME) aims to identify institutional policies and practices that contribute to the retention and attrition of Black students in electrical, computer, and mechanical engineering. Our four study institutions include historically Black institutions as well as predominantly white institutions, all of which are in the top 15 nationally in the number of Black engineering graduates. We are using a transformative mixed-methods design to answer the following overarching research questions: 1. Why do Black men and women choose and persist in, or leave, EE, CpE, and ME? 2. What are the academic trajectories of Black men and women in EE, CpE, and ME? 3. In what way do these pathways vary by gender or institution? 4. What institutional policies and practices promote greater retention of Black engineering students? Methods This study of Black students in CpE, EE, and ME reports initial results from in-depth interviews at one HBCU and one PWI. We asked students about a variety of topics, including their sense of belonging on campus and in the major, experiences with discrimination, the impact of race on their experiences, and experiences with microaggressions. For this paper, we draw on two methodological approaches that allowed us to move beyond a traditional, linear approach to in-depth interviews, allowing for more diverse experiences and narratives to emerge. First, we used an identity circle to gain a better understanding of the relative importance to the participants of racial identity, as compared to other identities. The identity circle is a series of three concentric circles, surrounding an “inner core” representing one’s “core self.” Participants were asked to place various identities from a provided list that included demographic, family-related, and school-related identities on the identity circle to reflect the relative importance of the different identities to participants’ current engineering education experiences. Second, participants were asked to complete an 8-item survey which measured the “centrality” of racial identity as defined by Sellers et al. (1997). Following Enders’ (2018) reflection on the MMRI and Nigrescence Theory, we chose to use the measure of racial centrality as it is generally more stable across situations and best “describes the place race holds in the hierarchy of identities an individual possesses and answers the question ‘How important is race to me in my life?’” (p. 518). Participants completed the MIBI items at the end of the interview to allow us to learn more about the participants’ identification with their racial group, to avoid biasing their responses to the Identity Circle, and to avoid potentially creating a stereotype threat at the beginning of the interview. This paper focuses on the results of the MIBI survey and the identity circles to investigate whether these measures were correlated. Recognizing that Blackness (race) is not monolithic, we were interested in knowing the extent to which the participants considered their Black identity as central to their engineering education experiences. Combined with discussion about the identity circles, this approach allowed us to learn more about how other elements of identity may shape the participants’ educational experiences and outcomes and revealed possible differences in how participants may enact various points of their identity. Findings For this paper, we focus on the results for five HBCU students and 27 PWI students who completed the MIBI and identity circle. The overall MIBI average for HBCU students was 43 (out of a possible 56) and the overall MIBI scores ranged from 36-51; the overall MIBI average for the PWI students was 40; the overall MIBI scores for the PWI students ranged from 24-51. Twenty-one students placed race in the inner circle, indicating that race was central to their identity. Five placed race on the second, middle circle; three placed race on the third, outer circle. Three students did not place race on their identity circle. For our cross-case qualitative analysis, we will choose cases across the two institutions that represent low, medium and high MIBI scores and different ranges of centrality of race to identity, as expressed in the identity circles. Our final analysis will include descriptive quotes from these in-depth interviews to further elucidate the significance of race to the participants’ identities and engineering education experiences. The results will provide context for our larger study of a total of 60 Black students in engineering at our four study institutions. Theoretically, our study represents a new application of Racial Identity Theory and will provide a unique opportunity to apply the theories of intersectionality, critical race theory, and community cultural wealth theory. Methodologically, our findings provide insights into the utility of combining our two qualitative research tools, the MIBI centrality scale and the identity circle, to better understand the influence of race on the education experiences of Black students in engineering. 

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5. 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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