A Hierarchical Transformer Encoder to Improve Entire Neoplasm Segmentation on Whole Slide Image of Hepatocellular Carcinoma

In digital histopathology, entire neoplasm segmentation on Whole Slide Image (WSI) of Hepatocellular Carcinoma (HCC) plays an important role, especially as a preprocessing filter to automatically exclude healthy tissue, in histological molecular correlations mining and other downstream histopathological tasks. The segmentation task remains challenging due to HCC's inherent high-heterogeneity and the lack of dependency learning in large field of view. In this article, we propose a novel deep learning architecture with a hierarchical Transformer encoder, HiTrans, to learn the global dependencies within expanded 4096$\times$4096 WSI patches. HiTrans is designed to encode and decode the patches with larger reception fields and the learned global dependencies, compared to the state-of-the-art Fully Convolutional Neural networks (FCNN). Empirical evaluations verified that HiTrans leads to better segmentation performance by taking into account regional and global dependency information.

Fine-tune your Classifier: Finding Correlations With Temperature

Temperature is a widely used hyperparameter in various tasks involving neural networks, such as classification or metric learning, whose choice can have a direct impact on the model performance. Most of existing works select its value using hyperparameter optimization methods requiring several runs to find the optimal value. We propose to analyze the impact of temperature on classification tasks by describing a dataset as a set of statistics computed on representations on which we can build a heuristic giving us a default value of temperature. We study the correlation between these extracted statistics and the observed optimal temperatures. This preliminary study on more than a hundred combinations of different datasets and features extractors highlights promising results towards the construction of a general heuristic for temperature.

Learning an Adaptation Function to Assess Image Visual Similarities

Human perception is routinely assessing the similarity between images, both for decision making and creative thinking. But the underlying cognitive process is not really well understood yet, hence difficult to be mimicked by computer vision systems. State-of-the-art approaches using deep architectures are often based on the comparison of images described as feature vectors learned for image categorization task. As a consequence, such features are powerful to compare semantically related images but not really efficient to compare images visually similar but semantically unrelated. Inspired by previous works on neural features adaptation to psycho-cognitive representations, we focus here on the specific task of learning visual image similarities when analogy matters. We propose to compare different supervised, semi-supervised and self-supervised networks, pre-trained on distinct scales and contents datasets (such as ImageNet-21k, ImageNet-1K or VGGFace2) to conclude which model may be the best to approximate the visual cortex and learn only an adaptation function corresponding to the approximation of the the primate IT cortex through the metric learning framework. Our experiments conducted on the Totally Looks Like image dataset highlight the interest of our method, by increasing the retrieval scores of the best model @1 by 2.25x. This research work was recently accepted for publication at the ICIP 2021 international conference [1]. In this new article, we expand on this previous work by using and comparing new pre-trained feature extractors on other datasets.