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1. Resource Aware Person Re-identification across Multiple Resolutions

   Wang, Yan ; Wang, Lequn ; You, Yurong ; Zou, Xu ; Chen, Vincent ; Li, Serena ; Huang, Gao ; Hariharan, Bharath ; Weinberger, Kilian ( April 2018 , CVPR 2018)

   Not all people are equally easy to identify: color statistics might be enough for some cases while others might re- quire careful reasoning about high- and low-level details. However, prevailing person re-identification(re-ID) meth- ods use one-size-fits-all high-level embeddings from deep convolutional networks for all cases. This might limit their accuracy on difficult examples or makes them needlessly ex- pensive for the easy ones. To remedy this, we present a new person re-ID model that combines effective embeddings built on multiple convolutional network layers, trained with deep-supervision. On traditional re-ID benchmarks, our method improves substantially over the previous state-of- the-art results on all five datasets that we evaluate on. We then propose two new formulations of the person re- ID problem under resource-constraints, and show how our model can be used to effectively trade off accuracy and computation in the presence of resource constraints. 

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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 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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3. Modeling and tracking Covid-19 cases using Big Data analytics on HPCC system platform

   https://doi.org/10.1186/s40537-021-00423-z  

   Villanustre, Flavio ; Chala, Arjuna ; Dev, Roger ; Xu, Lili ; LexisNexis, Jesse Shaw ; Furht, Borko ; Khoshgoftaar, Taghi ( December 2021 , Journal of Big Data)

   Abstract This project is funded by the US National Science Foundation (NSF) through their NSF RAPID program under the title “Modeling Corona Spread Using Big Data Analytics.” The project is a joint effort between the Department of Computer & Electrical Engineering and Computer Science at FAU and a research group from LexisNexis Risk Solutions. The novel coronavirus Covid-19 originated in China in early December 2019 and has rapidly spread to many countries around the globe, with the number of confirmed cases increasing every day. Covid-19 is officially a pandemic. It is a novel infection with serious clinical manifestations, including death, and it has reached at least 124 countries and territories. Although the ultimate course and impact of Covid-19 are uncertain, it is not merely possible but likely that the disease will produce enough severe illness to overwhelm the worldwide health care infrastructure. Emerging viral pandemics can place extraordinary and sustained demands on public health and health systems and on providers of essential community services. Modeling the Covid-19 pandemic spread is challenging. But there are data that can be used to project resource demands. Estimates of the reproductive number (R) of SARS-CoV-2 show that at the beginning of the epidemic, each infected person spreads the virus to at least two others, on average (Emanuel et al. in N Engl J Med. 2020, Livingston and Bucher in JAMA 323(14):1335, 2020). A conservatively low estimate is that 5 % of the population could become infected within 3 months. Preliminary data from China and Italy regarding the distribution of case severity and fatality vary widely (Wu and McGoogan in JAMA 323(13):1239–42, 2020). A recent large-scale analysis from China suggests that 80 % of those infected either are asymptomatic or have mild symptoms; a finding that implies that demand for advanced medical services might apply to only 20 % of the total infected. Of patients infected with Covid-19, about 15 % have severe illness and 5 % have critical illness (Emanuel et al. in N Engl J Med. 2020). Overall, mortality ranges from 0.25 % to as high as 3.0 % (Emanuel et al. in N Engl J Med. 2020, Wilson et al. in Emerg Infect Dis 26(6):1339, 2020). Case fatality rates are much higher for vulnerable populations, such as persons over the age of 80 years (> 14 %) and those with coexisting conditions (10 % for those with cardiovascular disease and 7 % for those with diabetes) (Emanuel et al. in N Engl J Med. 2020). Overall, Covid-19 is substantially deadlier than seasonal influenza, which has a mortality of roughly 0.1 %. Public health efforts depend heavily on predicting how diseases such as those caused by Covid-19 spread across the globe. During the early days of a new outbreak, when reliable data are still scarce, researchers turn to mathematical models that can predict where people who could be infected are going and how likely they are to bring the disease with them. These computational methods use known statistical equations that calculate the probability of individuals transmitting the illness. Modern computational power allows these models to quickly incorporate multiple inputs, such as a given disease’s ability to pass from person to person and the movement patterns of potentially infected people traveling by air and land. This process sometimes involves making assumptions about unknown factors, such as an individual’s exact travel pattern. By plugging in different possible versions of each input, however, researchers can update the models as new information becomes available and compare their results to observed patterns for the illness. In this paper we describe the development a model of Corona spread by using innovative big data analytics techniques and tools. We leveraged our experience from research in modeling Ebola spread (Shaw et al. Modeling Ebola Spread and Using HPCC/KEL System. In: Big Data Technologies and Applications 2016 (pp. 347-385). Springer, Cham) to successfully model Corona spread, we will obtain new results, and help in reducing the number of Corona patients. We closely collaborated with LexisNexis, which is a leading US data analytics company and a member of our NSF I/UCRC for Advanced Knowledge Enablement. The lack of a comprehensive view and informative analysis of the status of the pandemic can also cause panic and instability within society. Our work proposes the HPCC Systems Covid-19 tracker, which provides a multi-level view of the pandemic with the informative virus spreading indicators in a timely manner. The system embeds a classical epidemiological model known as SIR and spreading indicators based on causal model. The data solution of the tracker is built on top of the Big Data processing platform HPCC Systems, from ingesting and tracking of various data sources to fast delivery of the data to the public. The HPCC Systems Covid-19 tracker presents the Covid-19 data on a daily, weekly, and cumulative basis up to global-level and down to the county-level. It also provides statistical analysis for each level such as new cases per 100,000 population. The primary analysis such as Contagion Risk and Infection State is based on causal model with a seven-day sliding window. Our work has been released as a publicly available website to the world and attracted a great volume of traffic. The project is open-sourced and available on GitHub. The system was developed on the LexisNexis HPCC Systems, which is briefly described in the paper. 

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4. The disambiguation of people names in biological collections

   https://doi.org/10.3897/BDJ.10.e86089  

   Groom, Quentin ; Bräuchler, Christian ; Cubey, Robert ; Dillen, Mathias ; Huybrechts, Pieter ; Kearney, Nicole ; Klazenga, Niels ; Leachman, Siobhan ; Paul, Deborah L ; Rogers, Heather ; et al ( October 2022 , Biodiversity Data Journal)

   Scientific collections have been built by people. For hundreds of years, people have collected, studied, identified, preserved, documented and curated collection specimens. Understanding who those people are is of interest to historians, but much more can be made of these data by other stakeholders once they have been linked to the people’s identities and their biographies. Knowing who people are helps us attribute work correctly, validate data and understand the scientific contribution of people and institutions. We can evaluate the work they have done, the interests they have, the places they have worked and what they have created from the specimens they have collected. The problem is that all we know about most of the people associated with collections are their names written on specimens. Disambiguating these people is the challenge that this paper addresses. Disambiguation of people often proves difficult in isolation and can result in staff or researchers independently trying to determine the identity of specific individuals over and over again. By sharing biographical data and building an open, collectively maintained dataset with shared knowledge, expertise and resources, it is possible to collectively deduce the identities of individuals, aggregate biographical information for each person, reduce duplication of effort and share the information locally and globally. The authors of this paper aspire to disambiguate all person names efficiently and fully in all their variations across the entirety of the biological sciences, starting with collections. Towards that vision, this paper has three key aims: to improve the linking, validation, enhancement and valorisation of person-related information within and between collections, databases and publications; to suggest good practice for identifying people involved in biological collections; and to promote coordination amongst all stakeholders, including individuals, natural history collections, institutions, learned societies, government agencies and data aggregators. 

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5. Study on U.S. Parents' Divisions of Labor During COVID-19, Waves 1-2

   https://doi.org/10.3886/E183142V2  

   Carlson, Daniel L. ; Petts, Richard J. ( January 2022 , ICPSR - Interuniversity Consortium for Political and Social Research)

   The COVID-19 pandemic has dramatically altered family life in the United States. Over the long duration of the pandemic, parents had to adapt to shifting work conditions, virtual schooling, the closure of daycare facilities, and the stress of not only managing households without domestic and care supports but also worrying that family members may contract the novel coronavirus. Reports early in the pandemic suggest that these burdens have fallen disproportionately on mothers, creating concerns about the long-term implications of the pandemic for gender inequality and mothers’ well-being. Nevertheless, less is known about how parents’ engagement in domestic labor and paid work has changed throughout the pandemic, what factors may be driving these changes, and what the long-term consequences of the pandemic may be for the gendered division of labor and gender inequality more generally.
   
   The Study on U.S. Parents’ Divisions of Labor During COVID-19 (SPDLC) collects longitudinal survey data from partnered U.S. parents that can be used to assess changes in parents’ divisions of domestic labor, divisions of paid labor, and well-being throughout and after the COVID-19 pandemic. The goal of SPDLC is to understand both the short- and long-term impacts of the pandemic for the gendered division of labor, work-family issues, and broader patterns of gender inequality.
   
   Survey data for this study is collected using Prolifc (www.prolific.co), an opt-in online platform designed to facilitate scientific research. The sample is comprised U.S. adults who were residing with a romantic partner and at least one biological child (at the time of entry into the study). In each survey, parents answer questions about both themselves and their partners. Wave 1 of SPDLC was conducted in April 2020, and parents who participated in Wave 1 were asked about their division of labor both prior to (i.e., early March 2020) and one month after the pandemic began. Wave 2 of SPDLC was collected in November 2020. Parents who participated in Wave 1 were invited to participate again in Wave 2, and a new cohort of parents was also recruited to participate in the Wave 2 survey. Wave 3 of SPDLC was collected in October 2021. Parents who participated in either of the first two waves were invited to participate again in Wave 3, and another new cohort of parents was also recruited to participate in the Wave 3 survey. This research design (follow-up survey of panelists and new cross-section of parents at each wave) will continue through 2024, culminating in six waves of data spanning the period from March 2020 through October 2024. An estimated total of approximately 6,500 parents will be surveyed at least once throughout the duration of the study.
   
   SPDLC data will be released to the public two years after data is collected; Waves 1 and 2 are currently publicly available. Wave 3 will be publicly available in October 2023, with subsequent waves becoming available yearly. Data will be available to download in both SPSS (.sav) and Stata (.dta) formats, and the following data files will be available: (1) a data file for each individual wave, which contains responses from all participants in that wave of data collection, (2) a longitudinal panel data file, which contains longitudinal follow-up data from all available waves, and (3) a repeated cross-section data file, which contains the repeated cross-section data (from new respondents at each wave) from all available waves. Codebooks for each survey wave and a detailed user guide describing the data are also available. Response Rates: Of the 1,157 parents who participated in Wave 1, 828 (72%) also participated in the Wave 2 study. Presence of Common Scales: The following established scales are included in the survey:
   

   • Self-Efficacy, adapted from Pearlin's mastery scale (Pearlin et al., 1981) and the Rosenberg self-esteem scale (Rosenberg, 2015) and taken from the American Changing Lives Survey
   • Communication with Partner, taken from the Marriage and Relationship Survey (Lichter & Carmalt, 2009)
     
   • Gender Attitudes, taken from the National Survey of Families and Households (Sweet & Bumpass, 1996)
     
   • Depressive Symptoms (CES-D-10)
   • Stress, measured using Cohen's Perceived Stress Scale (Cohen, Kamarck, & Mermelstein, 1983)
     

   Full details about these scales and all other items included in the survey can be found in the user guide and codebook
   The second wave of the SPDLC was fielded in November 2020 in two stages. In the first stage, all parents who participated in W1 of the SPDLC and who continued to reside in the United States were re-contacted and asked to participate in a follow-up survey. The W2 survey was posted on Prolific, and messages were sent via Prolific’s messaging system to all previous participants. Multiple follow-up messages were sent in an attempt to increase response rates to the follow-up survey. Of the 1,157 respondents who completed the W1 survey, 873 at least started the W2 survey. Data quality checks were employed in line with best practices for online surveys (e.g., removing respondents who did not complete most of the survey or who did not pass the attention filters). After data quality checks, 5.2% of respondents were removed from the sample, resulting in a final sample size of 828 parents (a response rate of 72%).
   
   In the second stage, a new sample of parents was recruited. New parents had to meet the same sampling criteria as in W1 (be at least 18 years old, reside in the United States, reside with a romantic partner, and be a parent living with at least one biological child). Also similar to the W1 procedures, we oversampled men, Black individuals, individuals who did not complete college, and individuals who identified as politically conservative to increase sample diversity. A total of 1,207 parents participated in the W2 survey. Data quality checks led to the removal of 5.7% of the respondents, resulting in a final sample size of new respondents at Wave 2 of 1,138 parents.
   
   In both stages, participants were informed that the survey would take approximately 20 minutes to complete. All panelists were provided monetary compensation in line with Prolific’s compensation guidelines, which require that all participants earn above minimum wage for their time participating in studies.
   To be included in SPDLC, respondents had to meet the following sampling criteria at the time they enter the study: (a) be at least 18 years old, (b) reside in the United States, (c) reside with a romantic partner (i.e., be married or cohabiting), and (d) be a parent living with at least one biological child. Follow-up respondents must be at least 18 years old and reside in the United States, but may experience changes in relationship and resident parent statuses. Smallest Geographic Unit: U.S. State

   This work is licensed under the Creative Commons Attribution 4.0 International License. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. In accordance with this license, all users of these data must give appropriate credit to the authors in any papers, presentations, books, or other works that use the data. A suggested citation to provide attribution for these data is included below:            
   
   Carlson, Daniel L. and Richard J. Petts. 2022. Study on U.S. Parents’ Divisions of Labor During COVID-19 User Guide: Waves 1-2.  

   To help provide estimates that are more representative of U.S. partnered parents, the SPDLC includes sampling weights. Weights can be included in statistical analyses to make estimates from the SPDLC sample representative of U.S. parents who reside with a romantic partner (married or cohabiting) and a child aged 18 or younger based on age, race/ethnicity, and gender. National estimates for the age, racial/ethnic, and gender profile of U.S. partnered parents were obtained using data from the 2020 Current Population Survey (CPS). Weights were calculated using an iterative raking method, such that the full sample in each data file matches the nationally representative CPS data in regard to the gender, age, and racial/ethnic distributions within the data. This variable is labeled CPSweightW2 in the Wave 2 dataset, and CPSweightLW2 in the longitudinal dataset (which includes Waves 1 and 2). There is not a weight variable included in the W1-W2 repeated cross-section data file.
    

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