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1. WIP: Using Machine Learning to Automate Coding of Student Explanations to Challenging Mechanics Concept Questions

   Harpreet Auby ; Namrata Shivagunde ; Anna Rumshisky ; Milo Koretsky ( June 2022 , ASEE Annual Conference proceedings)

   This work-in-progress paper describes a collaborative effort between engineering education and machine learning researchers to automate analysis of written responses to conceptually challenging questions in mechanics. These qualitative questions are often used in large STEM classes to support active learning pedagogies; they require minimum calculations and focus on the application of underlying physical phenomena to various situations. Active learning pedagogies using this type of questions has been demonstrated to increase student achievement (Freeman et al., 2014; Hake, 1998) and engagement (Deslauriers, et al., 2011) of all students (Haak et al., 2011). To emphasize reasoning and sense-making, we use the Concept Warehouse (Koretsky et al., 2014), an audience response system where students provide written justifications to concept questions. Written justifications better prepare students for discussions with peers and in the whole class and can also improve students’ answer choices (Koretsky et al., 2016a, 2016b). In addition to their use as a tool to foster learning, written explanations can also provide valuable information to concurrently assess that learning (Koretsky and Magana, 2019). However, in practice, there has been limited deployment of written justifications with concept questions, in part, because they provide a daunting amount of information for instructors to process and for researchers to analyze. In this study, we describe the initial evaluation of large pre-trained generative sequence-to-sequence language models (Raffel et al., 2019; Brown et al., 2020) to automate the laborious coding process of student written responses. Adaptation of machine learning algorithms in this context is challenging since each question targets specific concepts which elicit their own unique reasoning processes. This exploratory project seeks to utilize responses collected through the Concept Warehouse to identify viable strategies for adapting machine learning to support instructors and researchers in identifying salient aspects of student thinking and understanding with these conceptually challenging questions. 

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2. Best 2019 PIC III Paper: Do They Understand Your Language? Access Their Fluency with Vector Representation

   https://doi.org/10.18260/1-2--34205  

   Davishahl, Eric ; Haskell, Todd ; Davishahl, Jill ; Singleton, Lee ; Goodridge, Wade ( June 2020 , 2020 ASEE Virtual Annual Conference Content Access)

   In teaching mechanics, we use multiple representations of vectors to develop concepts and analysis techniques. These representations include pictorials, diagrams, symbols, numbers and narrative language. Through years of study as students, researchers, and teachers, we develop a fluency rooted in a deep conceptual understanding of what each representation communicates. Many novice learners, however, struggle to gain such understanding and rely on superficial mimicry of the problem solving procedures we demonstrate in examples. The term representational competence refers to the ability to interpret, switch between, and use multiple representations of a concept as appropriate for learning, communication and analysis. In engineering statics, an understanding of what each vector representation communicates and how to use different representations in problem solving is important to the development of both conceptual and procedural knowledge. Science education literature identifies representational competence as a marker of true conceptual understanding. This paper presents development work for a new assessment instrument designed to measure representational competence with vectors in an engineering mechanics context. We developed the assessment over two successive terms in statics courses at a community college, a medium-sized regional university, and a large state university. We started with twelve multiple-choice questions that survey the vector representations commonly employed in statics. Each question requires the student to interpret and/or use two or more different representations of vectors and requires no calculation beyond single digit integer arithmetic. Distractor answer choices include common student mistakes and misconceptions drawn from the literature and from our teaching experience. We piloted these twelve questions as a timed section of the first exam in fall 2018 statics courses at both Whatcom Community College (WCC) and Western Washington University. Analysis of students’ unprompted use of vector representations on the open-ended problem-solving section of the same exam provides evidence of the assessment’s validity as a measurement instrument for representational competence. We found a positive correlation between students’ accurate and effective use of representations and their score on the multiple choice test. We gathered additional validity evidence by reviewing student responses on an exam wrapper reflection. We used item difficulty and item discrimination scores (point-biserial correlation) to eliminate two questions and revised the remaining questions to improve clarity and discriminatory power. We administered the revised version in two contexts: (1) again as part of the first exam in the winter 2019 Statics course at WCC, and (2) as an extra credit opportunity for statics students at Utah State University. This paper includes sample questions from the assessment to illustrate the approach. The full assessment is available to interested instructors and researchers through an online tool. 

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3. Do They Understand Your Language? Assess Their Fluency with Vector Representations

   Davishahl, E. ; Haskell, T. R. ; Davishahl, J. ; Singleton, L. ; Goodridge, W. H. ( June 2019 , ASEE Annual Conference proceedings)

   In teaching mechanics, we use multiple representations of vectors to develop concepts and analysis techniques. These representations include pictorials, diagrams, symbols, numbers and narrative language. Through years of study as students, researchers, and teachers, we develop a fluency rooted in a deep conceptual understanding of what each representation communicates. Many novice learners, however, struggle to gain such understanding and rely on superficial mimicry of the problem solving procedures we demonstrate in examples. The term representational competence refers to the ability to interpret, switch between, and use multiple representations of a concept as appropriate for learning, communication and analysis. In engineering statics, an understanding of what each vector representation communicates and how to use different representations in problem solving is important to the development of both conceptual and procedural knowledge. Science education literature identifies representational competence as a marker of true conceptual understanding. This paper presents development work for a new assessment instrument designed to measure representational competence with vectors in an engineering mechanics context. We developed the assessment over two successive terms in statics courses at a community college, a medium-sized regional university, and a large state university. We started with twelve multiple-choice questions that survey the vector representations commonly employed in statics. Each question requires the student to interpret and/or use two or more different representations of vectors and requires no calculation beyond single digit integer arithmetic. Distractor answer choices include common student mistakes and misconceptions drawn from the literature and from our teaching experience. We piloted these twelve questions as a timed section of the first exam in fall 2018 statics courses at both Whatcom Community College (WCC) and Western Washington University. Analysis of students’ unprompted use of vector representations on the open-ended problem-solving section of the same exam provides evidence of the assessment’s validity as a measurement instrument for representational competence. We found a positive correlation between students’ accurate and effective use of representations and their score on the multiple choice test. We gathered additional validity evidence by reviewing student responses on an exam wrapper reflection. We used item difficulty and item discrimination scores (point-biserial correlation) to eliminate two questions and revised the remaining questions to improve clarity and discriminatory power. We administered the revised version in two contexts: (1) again as part of the first exam in the winter 2019 Statics course at WCC, and (2) as an extra credit opportunity for statics students at Utah State University. This paper includes sample questions from the assessment to illustrate the approach. The full assessment is available to interested instructors and researchers through an online tool. 

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4. WIP: Instances of Dynamic Pedagogical Decision Making in the Uptake of a Technology Tool

   Harpreet Auby ; John Galisky ; Susan Nolen ; Milo Koretsky ( June 2022 , ASEE Annual Conference proceedings)

   In this work-in-progress paper, we continue investigation into the propagation of the Concept Warehouse within mechanical engineering (Friedrichsen et al., 2017; Koretsky et al., 2019a). Even before the pandemic forced most instruction online, educational technology was a growing element in classroom culture (Koretsky & Magana, 2019b). However, adoption of technology tools for widespread use is often conceived from a turn-key lens, with professional development focused on procedural competencies and fidelity of implementation as the goal (Mills & Ragan, 2000; O’Donnell, 2008). Educators are given the tool with initial operating instructions, then left on their own to implement it in particular instructional contexts. There is little emphasis on the inevitable instructional decisions around incorporating the tool (Hodge, 2019) or on sustainable incorporation of technologies into existing instructional practice (Forkosh-Baruch et al., 2021). We consider the take-up of a technology tool as an emergent, rather than a prescribed process (Henderson et al., 2011). In this WIP paper, we examine how two instructors who we call Al and Joe reason through their adoption of a technology tool, focusing on interactions among instructors, tool, and students within and across contexts. The Concept Warehouse (CW) is a widely-available, web-based, open educational technology tool used to facilitate concept-based active learning in different contexts (Friedrichsen et al., 2017; Koretsky et al., 2014). Development of the CW is ongoing and collaboration-driven, where user-instructors from different institutions and disciplines can develop conceptual questions (called ConcepTests) and other learning and assessment tools that can be shared with other users. Currently there are around 3,500 ConcepTests, 1,500 faculty users, and 36,000 student users. About 700 ConcepTests have been developed for mechanics (statics and dynamics). The tool’s spectrum of affordances allows different entry points for instructor engagement, but also allows their use to grow and change as they become familiar with the tool and take up ideas from the contexts around them. Part of a larger study of propagation and use across five diverse institutions (Nolen & Koretsky, 2020), instructors were introduced to the tool, offered an introductory workshop and opportunity to participate in a community of practice (CoP), then interviewed early and later in their adoption. For this paper, we explore a bounded case study of the two instructors, Al and Joe, who took up the CW to teach Introductory Statics. Al and Joe were experienced instructors, committed to active learning, who presented examples from their ongoing adaptation of the tool for discussion in the community of practice. However, their decisions about how to integrate the tool fundamentally differed, including the aspects of the tool they took up and the ways they made sense of their use. In analyzing these two cases, we begin to uncover how these instructors navigated the dynamic nature of pedagogical decision making in and across contexts. 

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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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