Research internships provide students with invaluable experience conducting independent research, contributing to larger research programs, and embedding in a professional scientific setting. These experiences increase student persistence in ecology and other science, technology, engineering, and mathematics (STEM) fields and promote the inclusion of students who lack opportunities at their home institutions and/or are from groups that are underrepresented in STEM. While many ecology internship programs were canceled during the 2020 COVID‐19 pandemic, others successfully adapted to offer virtual internships for the first time. Though different from what many researchers and students envision when they think of internships, virtual ecology internship programs can create more accessible opportunities and be just as valuable as in‐person opportunities when research programs and advisors develop virtual internships with intention and planning. Here, we highlight six ways to structure a virtual intern project, spanning a spectrum from purely computer‐based opportunities (e.g., digital data gathering, data analysis, or synthesis) to fully hands‐on research (e.g., sample processing or home‐based experiments). We illustrate examples of these virtual projects through a case study of the Smithsonian Environmental Research Center's 2020 Virtual Internship Program. Next, we provide 10 recommendations for effectively developing a virtual internship program. Finally, we end with ways that virtual internships can avoid the limitations of in‐person internships, as well as possible solutions to perceived pitfalls of virtual internships. While virtual internships became a necessity in 2020 due to COVID‐19, the development and continuation of virtual internships in future can be a valuable tool to add to the suite of existing internship opportunities, possibly further promoting diversity, equity, and inclusion in ecology and STEM.
GETTING A GRIP ON GEOMETRY: DEVELOPING A TANGIBLE MANIPULATIVE FOR INCLUSIVE QUADRILATERAL LEARNING
A joint project of design-based educational researchers, mechatronic engineers, and digital accessibility experts has created a new genre of pedagogical technologies — hybrid material–digital multimodal artifacts for collaborative learning of sensorily diverse students in inclusive classrooms. Here we present the Quad, a manipulable quadrilateral hand-held object that is linked in real time to its digital screen-based simulation, whose own transformation, in turn, activates content-oriented voice description and output sonification. Pilot studies with blind and visually-impaired student-participants suggest the Quad’s potential in grounding geometric reasoning, insight, and generalization in exploratory haptic–proprioceptive investigation. In its conception and development, the Quad exemplifies the ethical, philosophical, and theoretical perspectives of its collaborating designers respecting all children’s universal right to access and participate in cultural practices, including techno–scientific activities. As researchers, we harness technological innovations to realize moral obligations and, through that, to promote the study of human perception, action, and cognition. We look forward to mutual growth of our research program along with parallel efforts advancing an Italian project to promote teachers’ pre-service training and professional development surrounding implications of the embodiment turn in the cognitive sciences for school-based instructional practice.
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- Award ID(s):
- 1814220
- NSF-PAR ID:
- 10398237
- Date Published:
- Journal Name:
- Giornale italiano di educazione alla salute sport e didattica inclusiva
- Volume:
- 6
- Issue:
- 1
- ISSN:
- 2532-3296
- Page Range / eLocation ID:
- 1-21
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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Abstract -
Background: Researcher-practitioner partnerships (RPPs) have gained increasing prominence within education, since they are crucial for identifying partners’ problems of practice and seeking solutions for improving district (or school) problems. The CS Pathways RPP project brought together researchers and practitioners, including middle school teachers and administrators from three urban school districts, to build teachers’ capacity to implement an inclusive computer science and digital literacy (CSDL) curriculum for all students in their middle schools. Objective: This study explored the teachers’ self-efficacy development in teaching a middle school CSDL curriculum under the project’s RPP framework. The ultimate goal was to gain insights into how the project’s RPP framework and its professional development (PD) program supported teachers’ self-efficacy development, in particular its challenges and success of the partnership. Method: Teacher participants attended the first-year PD program and were surveyed and/or interviewed about their self-efficacy in teaching CSDL curriculum, spanning topics ranging from digital literacy skills to app creation ability and curriculum implementation. Both survey and interview data were collected and analyzed using mixed methods 1) to examine the reach of the RPP PD program in terms of teachers’ self-efficacy; 2) to produce insightful understandings of the PD program impact on the project’s goal of building teachers’ self-efficacy. Results and Discussion: We reported the teachers’ self-efficacy profiles based on the survey data. A post-survey indicated that a majority of the teachers have high self-efficacy in teaching the CSDL curriculum addressed by the RPP PD program. Our analysis identified five critical benefits the project’s RPP PD program provided, namely collaborative efforts on resource and infrastructure building, content and pedagogical knowledge growth, collaboration and communication, and building teacher identity. All five features have shown direct impacts on teachers' self-efficacy. The study also reported teachers’ perceptions on the challenges they faced and potential areas for improvements. These findings indicate some important features of an effective PD program, informing the primary design of an RPP CS PD program.more » « less
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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.more » « less
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Broadband infrastructure in urban parks may serve crucial functions including an amenity to boost overall park use and a bridge to propagate WiFi access into contiguous neighborhoods. This project: SCC:PG Park WiFi as a BRIDGE to Community Resilience has developed a new model —Build Resilience through the Internet and Digital Greenspace Exposure, leveraging off-the-shelf WiFi technology, novel algorithms, community assets, and local partnerships to lower greenspace WiFi costs. This interdisciplinary work leverages: computer science, information studies, landscape architecture, and public health. Collaboration methodologies and relational definitions across disciplines are still nascent —especially when paired with civic-engaged, applied research. Student researchers (UG/Grad) are excellent partners in bridging disciplinary barriers and constraints. Their capacity to assimilate multiple frameworks has produced refinements to the project’s theoretical lenses and suggested novel socio-technical methodology improvements. Further, they are excellent ambassadors to community partners and stakeholders. In BRIDGE, we tested two mechanisms to augment student research participation. In both, we leveraged a classic, curriculum-based model named the Partnership for Action Learning in Sustainability program (PALS). This campus-wide, community-engaged initiative pairs faculty and students with community partners. PALS curates economic, environmental, and social sustainability challenges and scopes projects to customize appropriate coursework that addresses identified challenges. Outcomes include: literature searches, wireframes, and design plans that target solutions to civic problems. Constraints include the short semester timeframe and curriculum-learning-outcome constraints. (1) On BRIDGE, Dr. Kweon executed a semester-based Landscape Architecture PALS 400-level-studio. 18 undergraduates conducted in-class and in-field work to assess community needs and proposed design solutions for future park-wide WiFi. Research topics included: community-park history, neighborhood demographics, case-study analysis, and land-cover characteristics. The students conducted an in-Park, community engagement session —via interactive posterboard surveys, to gain input on what park amenities might be redesigned or added to promote WiFi use. The students then produced seven re-design plans; one included a café/garden, with an eco-corridor that integrated technology with nature. (2) From the classic, curriculum-based PALS model we created a summer-intensive for our five research assistants, to stimulate interdisciplinary collaboration in their research tasks and co-analysis of project data products: experimental technical WiFi-setup, community survey results, and stakeholder needs-assessments. Students met weekly with each other and team leadership, exchanged journal articles, and attended joint research events. This model shows promise for integrating students more formally into an interdisciplinary research project. An end-of-intensive focus group highlighted, from the students’ perspective, the pro/cons of this model. Results: In contrasting the two mechanisms, our results include: Model 1 is tried-and-trued and produces standardized, reliable products. However, as work is group based, student independence is limited —to explore topics/themes of interest. Civic groups are typically thrilled with the diversity of action plans produced. Model 2 provides greater independence in student-learning outcomes, fosters interdisciplinary, “dictionary-building” that can be used by the full team, deepens methodological approaches, and allows for student stipend payments. Lessons learned: intensive time frame needed more research team support and ideally should be extended, when possible, over the full project-span. UMD-IRB#1785365-4; NSF-award: 2125526.more » « less
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Sustainable provision of food, energy and clean water requires understanding of the interdependencies among systems as well as the motivations and incentives of farmers and rural policy makers. Agriculture lies at the heart of interactions among food, energy and water systems. It is an increasingly energy intensive enterprise, but is also a growing source of energy. Agriculture places large demands on water supplies while poor practices can degrade water quality. Each of these interactions creates opportunities for modeling driven by sensor-based and qualitative data collection to improve the effectiveness of system operation and control in the short term as well as investments and planning for the long term. The large volume and complexity of the data collected creates challenges for decision support and stakeholder communication. The DataFEWSion National Research Traineeship program aims to build a community of researchers that explores, develops and implements effective data-driven decision-making to efficiently produce food, transform primary energy sources into energy carriers, and enhance water quality. The initial cohort includes PhD students in agricultural and biosystems, chemical, and industrial engineering as well as statistics and crop production and physiology. The project aims to prepare trainees for multiple career paths such as research scientist, bioeconomy entrepreneur, agribusiness leader, policy maker, agriculture analytics specialist, and professor. The traineeship has four key components. First, trainees will complete a new graduate certificate to build competencies in fundamental understanding of interactions among food production, water quality and bioenergy; data acquisition, visualization, and analytics; complex systems modeling for decision support; and the economics, policy and sociology of the FEW nexus. Second, they will conduct interdisciplinary research on (a) technologies and practices to increase agriculture’s contributions to energy supply while reducing its negative impacts on water quality and human health; (b) data science to increase crop productivity within the constraints of sustainable intensification; or (c) decision sciences to manage tradeoffs and promote best practices among diverse stakeholders. Third, they will participate in a new graduate learning community to consist of a two-year series of workshops that focus in alternate years on the context of the Midwest agricultural FEW nexus and professional development; and fourth, they will have small-group experiences to promote collaboration and peer review. Each trainee will create and curate a portfolio that combines artifacts from coursework and research with reflections on the broader impacts of their work. Trainee recruitment emphasizes women and underrepresented groups.more » « less
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