Explainable Techniques for Analyzing Flow Cytometry Cell Transformers

Explainability for Deep Learning Models is especially important for clinical applications, where decisions of automated systems have far-reaching consequences. While various post-hoc explainable methods, such as attention visualization and saliency maps, already exist for common data modalities, including natural language and images, little work has been done to adapt them to the modality of Flow CytoMetry (FCM) data. In this work, we evaluate the usage of a transformer architecture called ReluFormer that ease attention visualization as well as we propose a gradient- and an attention-based visualization technique tailored for FCM. We qualitatively evaluate the visualization techniques for cell classification and polygon regression on pediatric Acute Lymphoblastic Leukemia (ALL) FCM samples. The results outline the model's decision process and demonstrate how to utilize the proposed techniques to inspect the trained model. The gradient-based visualization not only identifies cells that are most significant for a particular prediction but also indicates the directions in the FCM feature space in which changes have the most impact on the prediction. The attention visualization provides insights on the transformer's decision process when handling FCM data. We show that different attention heads specialize by attending to different biologically meaningful sub-populations in the data, even though the model retrieved solely supervised binary classification signals during training.

ECSIC: Epipolar Cross Attention for Stereo Image Compression

In this paper, we present ECSIC, a novel learned method for stereo image compression. Our proposed method compresses the left and right images in a joint manner by exploiting the mutual information between the images of the stereo image pair using a novel stereo cross attention (SCA) module and two stereo context modules. The SCA module performs cross-attention restricted to the corresponding epipolar lines of the two images and processes them in parallel. The stereo context modules improve the entropy estimation of the second encoded image by using the first image as a context. We conduct an extensive ablation study demonstrating the effectiveness of the proposed modules and a comprehensive quantitative and qualitative comparison with existing methods. ECSIC achieves state-of-the-art performance among stereo image compression models on the two popular stereo image datasets Cityscapes and InStereo2k while allowing for fast encoding and decoding, making it highly practical for real-time applications.

Automated Identification of Cell Populations in Flow Cytometry Data with Transformers

Acute Lymphoblastic Leukemia (ALL) is the most frequent hematologic malignancy in children and adolescents. A strong prognostic factor in ALL is given by the Minimal Residual Disease (MRD), which is a measure for the number of leukemic cells persistent in a patient. Manual MRD assessment from Multiparameter Flow Cytometry (FCM) data after treatment is time-consuming and subjective. In this work, we present an automated method to compute the MRD value directly from FCM data. We present a novel neural network approach based on the transformer architecture that learns to directly identify blast cells in a sample. We train our method in a supervised manner and evaluate it on publicly available ALL FCM data from three different clinical centers. Our method reaches a median f1 score of ~0.93 when tested on 200 B-ALL samples.