Elisabeth Rumetshofer

Johannes Lehner, Benedikt Alkin, Andreas Fürst et al.

Masked Image Modeling (MIM) methods, like Masked Autoencoders (MAE), efficiently learn a rich representation of the input. However, for adapting to downstream tasks, they require a sufficient amount of labeled data since their rich features code not only objects but also less relevant image background. In contrast, Instance Discrimination (ID) methods focus on objects. In this work, we study how to combine the efficiency and scalability of MIM with the ability of ID to perform downstream classification in the absence of large amounts of labeled data. To this end, we introduce Masked Autoencoder Contrastive Tuning (MAE-CT), a sequential approach that utilizes the implicit clustering of the Nearest Neighbor Contrastive Learning (NNCLR) objective to induce abstraction in the topmost layers of a pre-trained MAE. MAE-CT tunes the rich features such that they form semantic clusters of objects without using any labels. Notably, MAE-CT does not rely on hand-crafted augmentations and frequently achieves its best performances while using only minimal augmentations (crop & flip). Further, MAE-CT is compute efficient as it requires at most 10% overhead compared to MAE re-training. Applied to large and huge Vision Transformer (ViT) models, MAE-CT excels over previous self-supervised methods trained on ImageNet in linear probing, k-NN and low-shot classification accuracy as well as in unsupervised clustering accuracy. With ViT-H/16 MAE-CT achieves a new state-of-the-art in linear probing of 82.2%.

Markus Hofmarcher, Andreas Mayr, Elisabeth Rumetshofer et al.

Due to the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, there is an urgent need for novel therapies and drugs. We conducted a large-scale virtual screening for small molecules that are potential CoV-2 inhibitors. To this end, we utilized "ChemAI", a deep neural network trained on more than 220M data points across 3.6M molecules from three public drug-discovery databases. With ChemAI, we screened and ranked one billion molecules from the ZINC database for favourable effects against CoV-2. We then reduced the result to the 30,000 top-ranked compounds, which are readily accessible and purchasable via the ZINC database. Additionally, we screened the DrugBank using ChemAI to allow for drug repurposing, which would be a fast way towards a therapy. We provide these top-ranked compounds of ZINC and DrugBank as a library for further screening with bioassays at https://github.com/ml-jku/sars-cov-inhibitors-chemai.

Andreas Fürst, Elisabeth Rumetshofer, Johannes Lehner et al.

CLIP yielded impressive results on zero-shot transfer learning tasks and is considered as a foundation model like BERT or GPT3. CLIP vision models that have a rich representation are pre-trained using the InfoNCE objective and natural language supervision before they are fine-tuned on particular tasks. Though CLIP excels at zero-shot transfer learning, it suffers from an explaining away problem, that is, it focuses on one or few features, while neglecting other relevant features. This problem is caused by insufficiently extracting the covariance structure in the original multi-modal data. We suggest to use modern Hopfield networks to tackle the problem of explaining away. Their retrieved embeddings have an enriched covariance structure derived from co-occurrences of features in the stored embeddings. However, modern Hopfield networks increase the saturation effect of the InfoNCE objective which hampers learning. We propose to use the InfoLOOB objective to mitigate this saturation effect. We introduce the novel "Contrastive Leave One Out Boost" (CLOOB), which uses modern Hopfield networks for covariance enrichment together with the InfoLOOB objective. In experiments we compare CLOOB to CLIP after pre-training on the Conceptual Captions and the YFCC dataset with respect to their zero-shot transfer learning performance on other datasets. CLOOB consistently outperforms CLIP at zero-shot transfer learning across all considered architectures and datasets.

Susanne Kimeswenger, Elisabeth Rumetshofer, Markus Hofmarcher et al.

Diagnosing basal cell carcinomas (BCC), one of the most common cutaneous malignancies in humans, is a task regularly performed by pathologists and dermato-pathologists. Improving histological diagnosis by providing diagnosis suggestions, i.e. computer-assisted diagnoses is actively researched to improve safety, quality and efficiency. Increasingly, machine learning methods are applied due to their superior performance. However, typical images obtained by scanning histological sections often have a resolution that is prohibitive for processing with current state-of-the-art neural networks. Furthermore, the data pose a problem of weak labels, since only a tiny fraction of the image is indicative of the disease class, whereas a large fraction of the image is highly similar to the non-disease class. The aim of this study is to evaluate whether it is possible to detect basal cell carcinomas in histological sections using attention-based deep learning models and to overcome the ultra-high resolution and the weak labels of whole slide images. We demonstrate that attention-based models can indeed yield almost perfect classification performance with an AUC of 0.99.