Seegerer, Philipp
Atlas: A Novel Pathology Foundation Model by Mayo Clinic, Charit\'e, and Aignostics
Alber, Maximilian, Tietz, Stephan, Dippel, Jonas, Milbich, Timo, Lesort, Timothée, Korfiatis, Panos, Krügener, Moritz, Cancer, Beatriz Perez, Shah, Neelay, Möllers, Alexander, Seegerer, Philipp, Carpen-Amarie, Alexandra, Standvoss, Kai, Dernbach, Gabriel, de Jong, Edwin, Schallenberg, Simon, Kunft, Andreas, von Ankershoffen, Helmut Hoffer, Schaeferle, Gavin, Duffy, Patrick, Redlon, Matt, Jurmeister, Philipp, Horst, David, Ruff, Lukas, Müller, Klaus-Robert, Klauschen, Frederick, Norgan, Andrew
Recent advances in digital pathology have demonstrated the effectiveness of foundation models across diverse applications. In this report, we present Atlas, a novel vision foundation model based on the RudolfV approach. Our model was trained on a dataset comprising 1.2 million histopathology whole slide images, collected from two medical institutions: Mayo Clinic and Charit\'e - Universt\"atsmedizin Berlin. Comprehensive evaluations show that Atlas achieves state-of-the-art performance across twenty-one public benchmark datasets, even though it is neither the largest model by parameter count nor by training dataset size.
iNNvestigate neural networks!
Alber, Maximilian, Lapuschkin, Sebastian, Seegerer, Philipp, Hägele, Miriam, Schütt, Kristof T., Montavon, Grégoire, Samek, Wojciech, Müller, Klaus-Robert, Dähne, Sven, Kindermans, Pieter-Jan
In recent years, deep neural networks have revolutionized many application domains of machine learning and are key components of many critical decision or predictive processes. Therefore, it is crucial that domain specialists can understand and analyze actions and pre- dictions, even of the most complex neural network architectures. Despite these arguments neural networks are often treated as black boxes. In the attempt to alleviate this short- coming many analysis methods were proposed, yet the lack of reference implementations often makes a systematic comparison between the methods a major effort. The presented library iNNvestigate addresses this by providing a common interface and out-of-the- box implementation for many analysis methods, including the reference implementation for PatternNet and PatternAttribution as well as for LRP-methods. To demonstrate the versatility of iNNvestigate, we provide an analysis of image classifications for variety of state-of-the-art neural network architectures.