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Lindvall, M. (2021). Designing with Machine Learning in Digital Pathology: Augmenting Medical Specialists through Interaction Design. (Doctoral dissertation). Linköping: Linköping University Electronic Press
Open this publication in new window or tab >>Designing with Machine Learning in Digital Pathology: Augmenting Medical Specialists through Interaction Design
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

Recent advancements in machine learning (ML) have led to a dramatic increase in AI capabilities for medical diagnostic tasks. Despite technical advances, developers of predictive AI models struggle to integrate their work into routine clinical workflows. Inefficient human-AI interactions, poor sociotechnical fit and a lack of interactive strategies for dealing with the imperfect nature of predictions are known factors contributing to this lack of adoption.

User-centred design methods are typically aimed at discovering and realising desirable qualities in use, pragmatically oriented around finding solutions despite the limitations of material- and human resources. However, existing methods often rely on designers possessing knowledge of suitable interactive metaphors and idioms, as well as skills in evaluating ideas through low-fidelity prototyping and rapid iteration methods—all of which are challenged by the data-driven nature of machine learning and the unpredictable outputs from AI models.

Using a constructive design research approach, my work explores how we might design systems with AI components that aid clinical decision-making in a human-centred and iterative fashion. Findings are derived from experiments and experiences from four exploratory projects conducted in collaboration with professional physicians, all aiming to probe this design space by producing novel interactive systems for or with ML components.

Contributions include identifying practical and theoretical design challenges, suggesting novel interaction strategies for human-AI collaboration, framing ML competence for designers and presenting empirical descriptions of conducted design processes. Specifically, this compilation thesis contains three works that address effective human-machine teaching and two works that address the challenge of designing interactions that afford successful decision-making despite the uncertainty and imperfections inherent in machine predictions.

Finally, two works directly address design-researchers working with ML, arguing for a systematic approach to increase the repertoire available for theoretical annotation and understanding of the properties of ML as a designerly material.

Place, publisher, year, edition, pages
Linköping: Linköping University Electronic Press, 2021
Series
Linköping Studies in Science and Technology. Dissertations, ISSN 0345-7524 ; 2157
National Category
Design Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-176117 (URN)10.3384/diss.diva-176117 (DOI)978-91-7929-604-9 (ISBN)
Public defence
2021-09-23, K3, Kåkenhus, Campus Norrköping, Norrköping, 09:00 (English)
Opponent
Supervisors
Available from: 2021-08-30 Created: 2021-06-07 Last updated: 2025-02-25Bibliographically approved
Tsirikoglou, A., Stacke, K., Eilertsen, G., Lindvall, M. & Unger, J. (2020). A Study of Deep Learning Colon Cancer Detection in Limited Data Access Scenarios. In: : . Paper presented at International Conference on Learning Representations (ICLR) Workshop on AI for Overcoming Global Disparities in Cancer Care (AI4CC).
Open this publication in new window or tab >>A Study of Deep Learning Colon Cancer Detection in Limited Data Access Scenarios
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2020 (English)Conference paper, Poster (with or without abstract) (Refereed)
National Category
Medical Imaging
Identifiers
urn:nbn:se:liu:diva-169838 (URN)
Conference
International Conference on Learning Representations (ICLR) Workshop on AI for Overcoming Global Disparities in Cancer Care (AI4CC)
Funder
Wallenberg AI, Autonomous Systems and Software Program (WASP)
Available from: 2020-09-20 Created: 2020-09-20 Last updated: 2025-02-09
Lindvall, M. & Molin, J. (2020). Designing for the Long Tail of Machine Learning.
Open this publication in new window or tab >>Designing for the Long Tail of Machine Learning
2020 (English)Manuscript (preprint) (Other academic)
Abstract [en]

Recent technical advances has made machine learning (ML) a promising component to include in end user facing systems. However, user experience (UX) practitioners face challenges in relating ML to existing user-centered design processes and how to navigate the possibilities and constraints of this design space. Drawing on our own experience, we characterize designing within this space as navigating trade-offs between data gathering, model development and designing valuable interactions for a given model performance. We suggest that the theoretical description of how machine learning performance scales with training data can guide designers in these trade-offs as well as having implications for prototyping. We exemplify the learning curve's usage by arguing that a useful pattern is to design an initial system in a bootstrap phase that aims to exploit the training effect of data collected at increasing orders of magnitude.

Keywords
digital design, interaction design, machine learning
National Category
Design Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-163530 (URN)
Note

Accepted for presentation in poster format for the ACM CHI'19 Workshop <Emerging Perspectives in Human-Centered Machine Learning>

Available from: 2020-02-07 Created: 2020-02-07 Last updated: 2025-02-25Bibliographically approved
Maras, G., Lindvall, M. & Lundström, C. (2020). Regional lymph node metastasis in colon adenocarcinoma, second collection series.
Open this publication in new window or tab >>Regional lymph node metastasis in colon adenocarcinoma, second collection series
2020 (English)Data set
Abstract [en]

Whole slide pathology images from regional lymph node metastasis in colon adenocarcinoma produced at Region Gävleborg Clinical Pathology and Cytology department. Consists of fifty chronologically consecutive cases.

Keywords
Pathology, Whole slide imaging, Lymph nodes, Cancer, Colon, Adenocarcinoma
National Category
Clinical Laboratory Medicine
Identifiers
urn:nbn:se:liu:diva-166325 (URN)10.23698/aida/lnco2 (DOI)
Funder
Vinnova, 2017-02447
Note

Lymph glands have been identified by an experienced pathologist and annotated using region-of-interest boxes.

Available from: 2020-06-11 Created: 2020-06-11 Last updated: 2020-06-29Bibliographically approved
Lindvall, M., Sanner, A., Petré, F., Lindman, K., Treanor, D., Lundström, C. & Löwgren, J. (2020). TissueWand, a rapid histopathology annotation tool. Journal of Pathology Informatics, 11(27)
Open this publication in new window or tab >>TissueWand, a rapid histopathology annotation tool
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2020 (English)In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 11, no 27Article in journal (Refereed) Published
Abstract [en]

Background: Recent advancements in machine learning (ML) bring great possibilities for the development of tools to assist with diagnostic tasks within histopathology. However, these approaches typically require a large amount of ground truth training data in the form of image annotations made by human experts. As such annotation work is a very time-consuming task, there is a great need for tools that can assist in this process, saving time while not sacrificing annotation quality. Methods: In an iterative design process, we developed TissueWand – an interactive tool designed for efficient annotation of gigapixel-sized histopathological images, not being constrained to a predefined annotation task. Results: Several findings regarding appropriate interaction concepts were made, where a key design component was semi-automation based on rapid interaction feedback in a local region. In a user study, the resulting tool was shown to cause substantial speed-up compared to manual work while maintaining quality. Conclusions: The TissueWand tool shows promise to replace manual methods for early stages of dataset curation where no task-specific ML model yet exists to aid the effort.

Place, publisher, year, edition, pages
Medknow Publications, 2020
Keywords
Annotation, digital pathology, usability, user interface design, machine learning
National Category
Design Human Computer Interaction
Identifiers
urn:nbn:se:liu:diva-168487 (URN)10.4103/jpi.jpi_5_20 (DOI)
Funder
Wallenberg AI, Autonomous Systems and Software Program (WASP)
Available from: 2020-08-25 Created: 2020-08-25 Last updated: 2025-02-25Bibliographically approved
Lindvall, M. & Molin, J. (2020). Verification Staircase: a Design Strategy for Actionable Explanations. In: Alison Smith-Renner and Styliani Kleanthous and Brian Lim and Tsvi Kuflik and Simone Stumpf and Jahna Otterbacher and Advait Sarkar and Casey Dugan and Avital Shulner Tal (Ed.), Proceedings of the Workshop on Explainable Smart Systems for Algorithmic Transparency in Emerging Technologies co-located with 25th International Conference on Intelligent User Interfaces (IUI 2020), Cagliari, Italy, March 17, 2020: . Paper presented at Workshop on Explainable Smart Systems for Algorithmic Transparency in Emerging Technologies co-located with 25th International Conference on Intelligent User Interfaces (IUI 2020), Cagliari, Italy, March 17–20, 2020. Aachen: CEUR-WS.org, 2582
Open this publication in new window or tab >>Verification Staircase: a Design Strategy for Actionable Explanations
2020 (English)In: Proceedings of the Workshop on Explainable Smart Systems for Algorithmic Transparency in Emerging Technologies co-located with 25th International Conference on Intelligent User Interfaces (IUI 2020), Cagliari, Italy, March 17, 2020 / [ed] Alison Smith-Renner and Styliani Kleanthous and Brian Lim and Tsvi Kuflik and Simone Stumpf and Jahna Otterbacher and Advait Sarkar and Casey Dugan and Avital Shulner Tal, Aachen: CEUR-WS.org , 2020, Vol. 2582Conference paper, Published paper (Refereed)
Abstract [en]

What if the trust in the output of a predictive model could be acted upon in richer ways than a simple binary decision of accept or reject? Designing assistive AI tools for medical specialists entails supporting a complex but safety-critical decision process. It is common that decisions in this domain can be decomposed to a combination of many smaller decisions. In this paper, we present Verification Staircase – a design strategy that can be used for such scenarios. The verification staircase is when multiple interactive assistive tools are combined to allow for a nuanced amount of automation to aid the user. This can support a wide range of prediction quality scenarios, spanning from unproblematic minor mistakes to misleading major failures. By presenting the information in a hierarchical way, the user is able to learn how underlying predictions are connected to overall case predictions, and over time, calibrate their trust so that they can choose the appropriate level of automatic support.

Place, publisher, year, edition, pages
Aachen: CEUR-WS.org, 2020
Series
CEUR Workshop Proceedings, ISSN 1613-0073
Keywords
digital design, interaction design, machine learning, artificial intelligence, explainable artificial intelligence
National Category
Design Human Computer Interaction Computer Sciences
Identifiers
urn:nbn:se:liu:diva-165763 (URN)
Conference
Workshop on Explainable Smart Systems for Algorithmic Transparency in Emerging Technologies co-located with 25th International Conference on Intelligent User Interfaces (IUI 2020), Cagliari, Italy, March 17–20, 2020
Funder
Wallenberg AI, Autonomous Systems and Software Program (WASP)
Note

Accepted for oral presentation at Workshop on Explainable Smart Systems for Algorithmic Transparency in Emerging Technologies co-located with 25th International Conference on Intelligent User Interfaces (IUI 2020), Cagliari, Italy, March 17, 2020

Available from: 2020-05-20 Created: 2020-05-20 Last updated: 2025-02-25Bibliographically approved
Skoglund, K., Rose, J., Lindvall, M., Lundström, C. & Treanor, D. (2019). Annotations, ontologies, and whole slide images: Development of an annotated ontology-driven whole slide image library of normal and abnormal human tissue. Journal of Pathology Informatics, 10(22)
Open this publication in new window or tab >>Annotations, ontologies, and whole slide images: Development of an annotated ontology-driven whole slide image library of normal and abnormal human tissue
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2019 (English)In: Journal of Pathology Informatics, ISSN 2229-5089, E-ISSN 2153-3539, Vol. 10, no 22Article in journal (Refereed) Published
Abstract [en]

Objective: Digital pathology is today a widely used technology, and the digitalization of microscopic slides into whole slide images (WSIs) allows the use of machine learning algorithms as a tool in the diagnostic process. In recent years, “deep learning” algorithms for image analysis have been applied to digital pathology with great success. The training of these algorithms requires a large volume of high-quality images and image annotations. These large image collections are a potent source of information, and to use and share the information, standardization of the content through a consistent terminology is essential. The aim of this project was to develop a pilot dataset of exhaustive annotated WSI of normal and abnormal human tissue and link the annotations to appropriate ontological information. 

Materials and Methods: Several biomedical ontologies and controlled vocabularies were investigated with the aim of selecting the most suitable ontology for this project. The selection criteria required an ontology that covered anatomical locations, histological subcompartments, histopathologic diagnoses, histopathologic terms, and generic terms such as normal, abnormal, and artifact. WSIs of normal and abnormal tissue from 50 colon resections and 69 skin excisions, diagnosed 2015-2016 at the Department of Clinical Pathology in Linköping, were randomly collected. These images were manually and exhaustively annotated at the level of major subcompartments, including normal or abnormal findings and artifacts. 

Results: Systemized nomenclature of medicine clinical terms (SNOMED CT) was chosen, and the annotations were linked to its codes and terms. Two hundred WSI were collected and annotated, resulting in 17,497 annotations, covering a total area of 302.19 cm2, equivalent to 107,7 gigapixels. Ninety-five unique SNOMED CT codes were used. The time taken to annotate a WSI varied from 45 s to over 360 min, a total time of approximately 360 h. 

Conclusion: This work resulted in a dataset of 200 exhaustive annotated WSIs of normal and abnormal tissue from the colon and skin, and it has informed plans to build a comprehensive library of annotated WSIs. SNOMED CT was found to be the best ontology for annotation labeling. This project also demonstrates the need for future development of annotation tools in order to make the annotation process more efficient.

Place, publisher, year, edition, pages
Medknow Publications, 2019
Keywords
Annotation, digital pathology, image database, ontology, whole slide images
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:liu:diva-160146 (URN)10.4103/jpi.jpi_81_18 (DOI)
Available from: 2019-09-09 Created: 2019-09-09 Last updated: 2020-05-20Bibliographically approved
Jarkman, S., Lindvall, M., Hedlund, J., Treanor, D., Lundström, C. & van der Laak, J. (2019). Axillary lymph nodes in breast cancer cases.
Open this publication in new window or tab >>Axillary lymph nodes in breast cancer cases
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2019 (English)Data set, Primary data
Keywords
Pathology, Whole slide imaging, Breast, Lymph nodes, Cancer, Sentinel nodes, Immunohistochemical staining, cytokeratin, CKAE1/AE3
National Category
Radiology, Nuclear Medicine and Medical Imaging
Identifiers
urn:nbn:se:liu:diva-165757 (URN)10.23698/aida/brln (DOI)
Available from: 2020-05-19 Created: 2020-05-19 Last updated: 2021-09-22Bibliographically approved
Skoglund, K., Lindvall, M., Bivik Stadler, C., Lundström, C. & Treanor, D. (2019). Colon data from the Visual Sweden project DROID.
Open this publication in new window or tab >>Colon data from the Visual Sweden project DROID
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2019 (English)Data set
Abstract [en]

The dataset consists of 101 H&E-stained colon whole slide images (WSI) - 52 abnormal and 49 benign cases. All significant abnormal findings identified are outlined and categorized into 15 types such as hyperplastic polyp, high grade adenocarcinoma and necrosis. Other tissue components such as mucosa, submucosa, as well as the surgical margin are delineated to create a complete histological map. In total, 756 separate annotations have been made to segment the different tissue structures and link them to ontological information.

Keywords
Pathology, Colon, Cancer, Whole slide imaging, Annotated
National Category
Clinical Laboratory Medicine
Identifiers
urn:nbn:se:liu:diva-166322 (URN)10.23698/aida/drco (DOI)
Funder
Vinnova, 2015-07051
Note

One physician was responsible for the manual annotations controlled by a second pathologist. Accurate annotations were made over the whole tissues. 756 separate annotations were made.

Following abnormal findings were annotated for the malign cases: acute and chronic inflammation, acute inflammation, adenocarcinoma, atrophy, chronic inflammation, diverticula, diverticulitis, dysplasia, edema, fibrosis, granulations tissue, hemorrhage, hyalinization, hyperplasia, hyperplastic polyp, inflammation, lymphoma, mucinous adenocarcinoma, necrosis, serrated adenoma, stasis, tubular adenoma, tubulovillous adenoma and ulceration.

Other areas annotated: abnormal, artifact, cecum, colon, colonic mucous membrane, colonic muscularis propria, colonic submucosa, colonic subserosa, descending colon, ileum, normal, rectum, sigmoid colon and transverse colon.

For the benign cases following areas were annotated: artifact, cecum, colon, colonic mucous membrane, colonic muscularis propria, colonic submucosa, colonic subserosa, descending colon, ileum, normal, rectum, sigmoid colon and transverse colon.

Available from: 2020-06-11 Created: 2020-06-11 Last updated: 2020-06-17Bibliographically approved
Maras, G., Lindvall, M. & Lundström, C. (2019). Regional lymph node metastasis in colon adenocarcinoma.
Open this publication in new window or tab >>Regional lymph node metastasis in colon adenocarcinoma
2019 (English)Data set
Abstract [en]

Whole slide pathology images from regional lymph node metastasis in colon adenocarcinoma produced at Region Gävleborg Clinical Pathology and Cytology department and Region Östergötland Clinical Pathology department. Annotations for AI training produced as part of AIDA clinical fellowship project investigating AI decision support in metastasis detection.

Keywords
Pathology, Whole slide imaging, Annotated, Lymph nodes, Cancer, Colon, Adenocarcinoma
National Category
Clinical Laboratory Medicine
Identifiers
urn:nbn:se:liu:diva-166324 (URN)10.23698/aida/lnco (DOI)
Funder
Vinnova, 2017-02447
Note

Lymph nodes manually classified into two groups, either with or without tumor metastases. Tumors have been non-exhaustively annotated in lymph nodes that have them, so only lymph nodes without tumor present can be reliably used as examples of normal tissue. Regions deemed not suitable for AI training have been annotated for exclusion (eg missing or poor quality material), or as preparation artefact (eg folded tissue sample).

Available from: 2020-06-11 Created: 2020-06-11 Last updated: 2020-06-29Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-7014-8874

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