Christian Abbet

Thomas Stegmüller, Christian Abbet, Behzad Bozorgtabar et al.

Screening Papanicolaou test samples has proven to be highly effective in reducing cervical cancer-related mortality. However, the lack of trained cytopathologists hinders its widespread implementation in low-resource settings. Deep learning-based telecytology diagnosis emerges as an appealing alternative, but it requires the collection of large annotated training datasets, which is costly and time-consuming. In this paper, we demonstrate that the abundance of unlabeled images that can be extracted from Pap smear test whole slide images presents a fertile ground for self-supervised learning methods, yielding performance improvements relative to readily available pre-trained models for various downstream tasks. In particular, we propose \textbf{C}ervical \textbf{C}ell \textbf{C}opy-\textbf{P}asting ($\texttt{C}^{3}\texttt{P}$) as an effective augmentation method, which enables knowledge transfer from open-source and labeled single-cell datasets to unlabeled tiles. Not only does $\texttt{C}^{3}\texttt{P}$ outperforms naive transfer from single-cell images, but we also demonstrate its advantageous integration into multiple instance learning methods. Importantly, all our experiments are conducted on our introduced \textit{in-house} dataset comprising liquid-based cytology Pap smear images obtained using low-cost technologies. This aligns with our objective of leveraging deep learning-based telecytology for diagnosis in low-resource settings.

Christian Abbet, Linda Studer, Andreas Fischer et al.

Supervised learning is constrained by the availability of labeled data, which are especially expensive to acquire in the field of digital pathology. Making use of open-source data for pre-training or using domain adaptation can be a way to overcome this issue. However, pre-trained networks often fail to generalize to new test domains that are not distributed identically due to tissue stainings, types, and textures variations. Additionally, current domain adaptation methods mainly rely on fully-labeled source datasets. In this work, we propose Self-Rule to Multi-Adapt (SRMA), which takes advantage of self-supervised learning to perform domain adaptation, and removes the necessity of fully-labeled source datasets. SRMA can effectively transfer the discriminative knowledge obtained from a few labeled source domain's data to a new target domain without requiring additional tissue annotations. Our method harnesses both domains' structures by capturing visual similarity with intra-domain and cross-domain self-supervision. Moreover, we present a generalized formulation of our approach that allows the framework to learn from multiple source domains. We show that our proposed method outperforms baselines for domain adaptation of colorectal tissue type classification \new{in single and multi-source settings}, and further validate our approach on an in-house clinical cohort. The code and trained models are available open-source: https://github.com/christianabbet/SRA.

Christian Abbet, Inti Zlobec, Behzad Bozorgtabar et al.

With the long-term rapid increase in incidences of colorectal cancer (CRC), there is an urgent clinical need to improve risk stratification. The conventional pathology report is usually limited to only a few histopathological features. However, most of the tumor microenvironments used to describe patterns of aggressive tumor behavior are ignored. In this work, we aim to learn histopathological patterns within cancerous tissue regions that can be used to improve prognostic stratification for colorectal cancer. To do so, we propose a self-supervised learning method that jointly learns a representation of tissue regions as well as a metric of the clustering to obtain their underlying patterns. These histopathological patterns are then used to represent the interaction between complex tissues and predict clinical outcomes directly. We furthermore show that the proposed approach can benefit from linear predictors to avoid overfitting in patient outcomes predictions. To this end, we introduce a new well-characterized clinicopathological dataset, including a retrospective collective of 374 patients, with their survival time and treatment information. Histomorphological clusters obtained by our method are evaluated by training survival models. The experimental results demonstrate statistically significant patient stratification, and our approach outperformed the state-of-the-art deep clustering methods.

Christian Abbet, Meryem M'hamdi, Athanasios Giannakopoulos et al.

We propose a new method to detect when users express the intent to leave a service, also known as churn. While previous work focuses solely on social media, we show that this intent can be detected in chatbot conversations. As companies increasingly rely on chatbots they need an overview of potentially churny users. To this end, we crowdsource and publish a dataset of churn intent expressions in chatbot interactions in German and English. We show that classifiers trained on social media data can detect the same intent in the context of chatbots. We introduce a classification architecture that outperforms existing work on churn intent detection in social media. Moreover, we show that, using bilingual word embeddings, a system trained on combined English and German data outperforms monolingual approaches. As the only existing dataset is in English, we crowdsource and publish a novel dataset of German tweets. We thus underline the universal aspect of the problem, as examples of churn intent in English help us identify churn in German tweets and chatbot conversations.