Wenzel, Markus
Synthetic Generation of Dermatoscopic Images with GAN and Closed-Form Factorization
Mekala, Rohan Reddy, Pahde, Frederik, Baur, Simon, Chandrashekar, Sneha, Diep, Madeline, Wenzel, Markus, Wisotzky, Eric L., Yolcu, Galip Ümit, Lapuschkin, Sebastian, Ma, Jackie, Eisert, Peter, Lindvall, Mikael, Porter, Adam, Samek, Wojciech
In the realm of dermatological diagnoses, where the analysis of dermatoscopic and microscopic skin lesion images is pivotal for the accurate and early detection of various medical conditions, the costs associated with creating diverse and high-quality annotated datasets have hampered the accuracy and generalizability of machine learning models. We propose an innovative unsupervised augmentation solution that harnesses Generative Adversarial Network (GAN) based models and associated techniques over their latent space to generate controlled "semiautomatically-discovered" semantic variations in dermatoscopic images. We created synthetic images to incorporate the semantic variations and augmented the training data with these images. With this approach, we were able to increase the performance of machine learning models and set a new benchmark amongst non-ensemble based models in skin lesion classification on the HAM10000 dataset; and used the observed analytics and generated models for detailed studies on model explainability, affirming the effectiveness of our solution.
Insights Into the Inner Workings of Transformer Models for Protein Function Prediction
Wenzel, Markus, Grüner, Erik, Strodthoff, Nils
Motivation: We explored how explainable AI (XAI) can help to shed light into the inner workings of neural networks for protein function prediction, by extending the widely used XAI method of integrated gradients such that latent representations inside of transformer models, which were finetuned to Gene Ontology term and Enzyme Commission number prediction, can be inspected too. Results: The approach enabled us to identify amino acids in the sequences that the transformers pay particular attention to, and to show that these relevant sequence parts reflect expectations from biology and chemistry, both in the embedding layer and inside of the model, where we identified transformer heads with a statistically significant correspondence of attribution maps with ground truth sequence annotations (e.g., transmembrane regions, active sites) across many proteins. Availability and Implementation: Source code can be accessed at https://github.com/markuswenzel/xai-proteins .
FUTURE-AI: International consensus guideline for trustworthy and deployable artificial intelligence in healthcare
Lekadir, Karim, Feragen, Aasa, Fofanah, Abdul Joseph, Frangi, Alejandro F, Buyx, Alena, Emelie, Anais, Lara, Andrea, Porras, Antonio R, Chan, An-Wen, Navarro, Arcadi, Glocker, Ben, Botwe, Benard O, Khanal, Bishesh, Beger, Brigit, Wu, Carol C, Cintas, Celia, Langlotz, Curtis P, Rueckert, Daniel, Mzurikwao, Deogratias, Fotiadis, Dimitrios I, Zhussupov, Doszhan, Ferrante, Enzo, Meijering, Erik, Weicken, Eva, González, Fabio A, Asselbergs, Folkert W, Prior, Fred, Krestin, Gabriel P, Collins, Gary, Tegenaw, Geletaw S, Kaissis, Georgios, Misuraca, Gianluca, Tsakou, Gianna, Dwivedi, Girish, Kondylakis, Haridimos, Jayakody, Harsha, Woodruf, Henry C, Aerts, Hugo JWL, Walsh, Ian, Chouvarda, Ioanna, Buvat, Irène, Rekik, Islem, Duncan, James, Kalpathy-Cramer, Jayashree, Zahir, Jihad, Park, Jinah, Mongan, John, Gichoya, Judy W, Schnabel, Julia A, Kushibar, Kaisar, Riklund, Katrine, Mori, Kensaku, Marias, Kostas, Amugongo, Lameck M, Fromont, Lauren A, Maier-Hein, Lena, Alberich, Leonor Cerdá, Rittner, Leticia, Phiri, Lighton, Marrakchi-Kacem, Linda, Donoso-Bach, Lluís, Martí-Bonmatí, Luis, Cardoso, M Jorge, Bobowicz, Maciej, Shabani, Mahsa, Tsiknakis, Manolis, Zuluaga, Maria A, Bielikova, Maria, Fritzsche, Marie-Christine, Linguraru, Marius George, Wenzel, Markus, De Bruijne, Marleen, Tolsgaard, Martin G, Ghassemi, Marzyeh, Ashrafuzzaman, Md, Goisauf, Melanie, Yaqub, Mohammad, Ammar, Mohammed, Abadía, Mónica Cano, Mahmoud, Mukhtar M E, Elattar, Mustafa, Rieke, Nicola, Papanikolaou, Nikolaos, Lazrak, Noussair, Díaz, Oliver, Salvado, Olivier, Pujol, Oriol, Sall, Ousmane, Guevara, Pamela, Gordebeke, Peter, Lambin, Philippe, Brown, Pieta, Abolmaesumi, Purang, Dou, Qi, Lu, Qinghua, Osuala, Richard, Nakasi, Rose, Zhou, S Kevin, Napel, Sandy, Colantonio, Sara, Albarqouni, Shadi, Joshi, Smriti, Carter, Stacy, Klein, Stefan, Petersen, Steffen E, Aussó, Susanna, Awate, Suyash, Raviv, Tammy Riklin, Cook, Tessa, Mutsvangwa, Tinashe E M, Rogers, Wendy A, Niessen, Wiro J, Puig-Bosch, Xènia, Zeng, Yi, Mohammed, Yunusa G, Aquino, Yves Saint James, Salahuddin, Zohaib, Starmans, Martijn P A
Despite major advances in artificial intelligence (AI) for medicine and healthcare, the deployment and adoption of AI technologies remain limited in real-world clinical practice. In recent years, concerns have been raised about the technical, clinical, ethical and legal risks associated with medical AI. To increase real world adoption, it is essential that medical AI tools are trusted and accepted by patients, clinicians, health organisations and authorities. This work describes the FUTURE-AI guideline as the first international consensus framework for guiding the development and deployment of trustworthy AI tools in healthcare. The FUTURE-AI consortium was founded in 2021 and currently comprises 118 inter-disciplinary experts from 51 countries representing all continents, including AI scientists, clinicians, ethicists, and social scientists. Over a two-year period, the consortium defined guiding principles and best practices for trustworthy AI through an iterative process comprising an in-depth literature review, a modified Delphi survey, and online consensus meetings. The FUTURE-AI framework was established based on 6 guiding principles for trustworthy AI in healthcare, i.e. Fairness, Universality, Traceability, Usability, Robustness and Explainability. Through consensus, a set of 28 best practices were defined, addressing technical, clinical, legal and socio-ethical dimensions. The recommendations cover the entire lifecycle of medical AI, from design, development and validation to regulation, deployment, and monitoring. FUTURE-AI is a risk-informed, assumption-free guideline which provides a structured approach for constructing medical AI tools that will be trusted, deployed and adopted in real-world practice. Researchers are encouraged to take the recommendations into account in proof-of-concept stages to facilitate future translation towards clinical practice of medical AI.
From Modern CNNs to Vision Transformers: Assessing the Performance, Robustness, and Classification Strategies of Deep Learning Models in Histopathology
Springenberg, Maximilian, Frommholz, Annika, Wenzel, Markus, Weicken, Eva, Ma, Jackie, Strodthoff, Nils
While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.
Focus Group on Artificial Intelligence for Health
Salathé, Marcel, Wiegand, Thomas, Wenzel, Markus
Artificial Intelligence (AI) - the phenomenon of machines being able to solve problems that require human intelligence - has in the past decade seen an enormous rise of interest due to significant advances in effectiveness and use. The health sector, one of the most important sectors for societies and economies worldwide, is particularly interesting for AI applications, given the ongoing digitalisation of all types of health information. The potential for AI assistance in the health domain is immense, because AI can support medical decision making at reduced costs, everywhere. However, due to the complexity of AI algorithms, it is difficult to distinguish good from bad AI-based solutions and to understand their strengths and weaknesses, which is crucial for clarifying responsibilities and for building trust. For this reason, the International Telecommunication Union (ITU) has established a new Focus Group on "Artificial Intelligence for Health" (FG-AI4H) in partnership with the World Health Organization (WHO). Health and care services are usually the responsibility of a government - even when provided through private insurance systems - and thus under the responsibility of WHO/ITU member states. FG-AI4H will identify opportunities for international standardization, which will foster the application of AI to health issues on a global scale. In particular, it will establish a standardized assessment framework with open benchmarks for the evaluation of AI-based methods for health, such as AI-based diagnosis, triage or treatment decisions.