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1. MoveApps: a serverless no-code analysis platform for animal tracking data

   https://doi.org/10.1186/s40462-022-00327-4  

   Kölzsch, Andrea ; Davidson, Sarah C. ; Gauggel, Dominik ; Hahn, Clemens ; Hirt, Julian ; Kays, Roland ; Lang, Ilona ; Lohr, Ashley ; Russell, Benedict ; Scharf, Anne K. ; et al ( December 2022 , Movement Ecology)

   Abstract Background Bio-logging and animal tracking datasets continuously grow in volume and complexity, documenting animal behaviour and ecology in unprecedented extent and detail, but greatly increasing the challenge of extracting knowledge from the data obtained. A large variety of analysis methods are being developed, many of which in effect are inaccessible to potential users, because they remain unpublished, depend on proprietary software or require significant coding skills. Results We developed MoveApps, an open analysis platform for animal tracking data, to make sophisticated analytical tools accessible to a global community of movement ecologists and wildlife managers. As part of the Movebank ecosystem, MoveApps allows users to design and share workflows composed of analysis modules (Apps) that access and analyse tracking data. Users browse Apps, build workflows, customise parameters, execute analyses and access results through an intuitive web-based interface. Apps, coded in R or other programming languages, have been developed by the MoveApps team and can be contributed by anyone developing analysis code. They become available to all user of the platform. To allow long-term and cross-system reproducibility, Apps have public source code and are compiled and run in Docker containers that form the basis of a serverless cloud computing system. To support reproducible science and help contributors document and benefit from their efforts, workflows of Apps can be shared, published and archived with DOIs in the Movebank Data Repository. The platform was beta launched in spring 2021 and currently contains 49 Apps that are used by 316 registered users. We illustrate its use through two workflows that (1) provide a daily report on active tag deployments and (2) segment and map migratory movements. Conclusions The MoveApps platform is meant to empower the community to supply, exchange and use analysis code in an intuitive environment that allows fast and traceable results and feedback. By bringing together analytical experts developing movement analysis methods and code with those in need of tools to explore, answer questions and inform decisions based on data they collect, we intend to increase the pace of knowledge generation and integration to match the huge growth rate in bio-logging data acquisition. 

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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. Implementing community best practice data and metadata capture into laboratory workflows using Sparrow

   Kuehn, S.C. ( January 2022 , EarthCube Annual Meeting 2022)

   An implementation of the Sparrow data system (https://sparrow-data.org) is currently being developed to support laboratory workflows for sample preparation, geochemical analysis, and SEM imaging in support of tephra research. Tephra, consisting of fragmental material ejected from volcanoes, has a multidisciplinary array of applications from volcanology to geochronology, archaeology, environmental change, and more. The international tephra research community has developed a comprehensive set of recommendations for data and metadata collection and reporting (https://doi.org/10.5281/zenodo.3866266) as part of a broader effort to adopt FAIR practices. Implementations of these recommendations now exist for field data via StraboSpot (https://strabospot.org/files/StraboSpotTephraHelp.pdf) and for samples, analytical methods, and geochemistry via SESAR and EarthChem (https://earthchem.org/communities/tephra/). Implementing these recommended practices in Sparrow helps to (1) cover laboratory workflows between field sample collection and project data archiving and (2) address a key researcher pain point. As re-emphasized by participants in the Tephra Fusion 2022 workshop earlier this year (Wallace et al., this meeting), the huge workload currently needed to capture and organize data and metadata in preparation for archiving in community data repositories is a major obstacle to achieving FAIR practices. By capturing this information on the fly during laboratory workflows and integrating it together in a single data system, this challenge may be overcome. We are implementing the tephra community recommendations as extensions to Sparrow’s core database schema. Data import pipelines and user interfaces to streamline metadata capture are also being developed. In the longer term, we aim to achieve interoperability with an ecosystem of tools and repositories like StraboSpot, SESAR, EarthChem, and Throughput. The results of these developments will be applicable not just to tephra but also to other research areas which utilize similar laboratory and analytical methods - e.g. sedimentology, mineralogy, and petrology. 

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4. BioModME for building and simulating dynamic computational models of complex biological systems

   https://doi.org/10.1093/bioadv/vbae023  

   Womack, Justin A. ; Shah, Viren ; Audi, Said H. ; Terhune, Scott S. ; Dash, Ranjan K. ; Lengauer, ed., Thomas ( February 2024 , Bioinformatics Advances)

   Molecular mechanisms of biological functions and disease processes are exceptionally complex, and our ability to interrogate and understand relationships is becoming increasingly dependent on the use of computational modeling. We have developed “BioModME,” a standalone R-based web application package, providing an intuitive and comprehensive graphical user interface to help investigators build, solve, visualize, and analyze computational models of complex biological systems. Some important features of the application package include multi-region system modeling, custom reaction rate laws and equations, unit conversion, model parameter estimation utilizing experimental data, and import and export of model information in the Systems Biology Matkup Language format. The users can also export models to MATLAB, R, and Python languages and the equations to LaTeX and Mathematical Markup Language formats. Other important features include an online model development platform, multi-modality visualization tool, and efficient numerical solvers for differential-algebraic equations and optimization.

   All relevant software information including documentation and tutorials can be found at https://mcw.marquette.edu/biomedical-engineering/computational-systems-biology-lab/biomodme.php. Deployed software can be accessed at https://biomodme.ctsi.mcw.edu/. Source code is freely available for download at https://github.com/MCWComputationalBiologyLab/BioModME.

    

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5. Surface Ocean CO2 Atlas Database Version 2022 (SOCATv2022) (NCEI Accession 0253659)

   https://doi.org/10.25921/1h9f-nb73  

   Bakker, Dorothee C. ; Alin, Simone R. ; Becker, Meike ; Bittig, Henry C. ; Castaño-Primo, Rocío ; Feely, Richard A. ; Gkritzalis, Thanos ; Kadono, Koji ; Kozyr, Alex ; Lauvset, Siv K. ; et al ( January 2022 , NOAA National Centers for Environmental Information)

   This dataset consists of the Surface Ocean CO2 Atlas Version 2022 (SOCATv2022) data product files. The ocean absorbs one quarter of the global CO2 emissions from human activity. The community-led Surface Ocean CO2 Atlas (www.socat.info) is key for the quantification of ocean CO2 uptake and its variation, now and in the future. SOCAT version 2022 has quality-controlled in situ surface ocean fCO2 (fugacity of CO2) measurements on ships, moorings, autonomous and drifting surface platforms for the global oceans and coastal seas from 1957 to 2021. The main synthesis and gridded products contain 33.7 million fCO2 values with an estimated accuracy of better than 5 μatm. A further 6.4 million fCO2 sensor data with an estimated accuracy of 5 to 10 μatm are separately available. During quality control, marine scientists assign a flag to each data set, as well as WOCE flags of 2 (good), 3 (questionable) or 4 (bad) to individual fCO2 values. Data sets are assigned flags of A and B for an estimated accuracy of better than 2 μatm, flags of C and D for an accuracy of better than 5 μatm and a flag of E for an accuracy of better than 10 μatm. Bakker et al. (2016) describe the quality control criteria used in SOCAT versions 3 to 2022. Quality control comments for individual data sets can be accessed via the SOCAT Data Set Viewer (www.socat.info). All data sets, where data quality has been deemed acceptable, have been made public. The main SOCAT synthesis files and the gridded products contain all data sets with an estimated accuracy of better than 5 µatm (data set flags of A to D) and fCO2 values with a WOCE flag of 2. Access to data sets with an estimated accuracy of 5 to 10 (flag of E) and fCO2 values with flags of 3 and 4 is via additional data products and the Data Set Viewer (Table 8 in Bakker et al., 2016). SOCAT publishes a global gridded product with a 1° longitude by 1° latitude resolution. A second product with a higher resolution of 0.25° longitude by 0.25° latitude is available for the coastal seas. The gridded products contain all data sets with an estimated accuracy of better than 5 µatm (data set flags of A to D) and fCO2 values with a WOCE flag of 2. Gridded products are available monthly, per year and per decade. Two powerful, interactive, online viewers, the Data Set Viewer and the Gridded Data Viewer (www.socat.info), enable investigation of the SOCAT synthesis and gridded data products. SOCAT data products can be downloaded. Matlab code is available for reading these files. Ocean Data View also provides access to the SOCAT data products (www.socat.info). SOCAT data products are discoverable, accessible and citable. The SOCAT Data Use Statement (www.socat.info) asks users to generously acknowledge the contribution of SOCAT scientists by invitation to co-authorship, especially for data providers in regional studies, and/or reference to relevant scientific articles. The SOCAT website (www.socat.info) provides a single access point for online viewers, downloadable data sets, the Data Use Statement, a list of contributors and an overview of scientific publications on and using SOCAT. Automation of data upload and initial data checks allows annual releases of SOCAT from version 4 onwards. SOCAT is used for quantification of ocean CO2 uptake and ocean acidification and for evaluation of climate models and sensor data. SOCAT products inform the annual Global Carbon Budget since 2013. The annual SOCAT releases by the SOCAT scientific community are a Voluntary Commitment for United Nations Sustainable Development Goal 14.3 (Reduce Ocean Acidification) (#OceanAction20464). More broadly the SOCAT releases contribute to UN SDG 13 (Climate Action) and SDG 14 (Life Below Water), and to the UN Decade of Ocean Science for Sustainable Development. Hundreds of peer-reviewed scientific publications and high-impact reports cite SOCAT. The SOCAT community-led synthesis product is a key step in the value chain based on in situ inorganic carbon measurements of the oceans, which provides policy makers with critical information on ocean CO2 uptake in climate negotiations. The need for accurate knowledge of global ocean CO2 uptake and its (future) variation makes sustained funding of in situ surface ocean CO2 observations imperative. 

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