Hopfield Networks is All You Need

We show that the transformer attention mechanism is the update rule of a modern Hopfield network with continuous states. This new Hopfield network can store exponentially (with the dimension) many patterns, converges with one update, and has exponentially small retrieval errors. The number of stored patterns is traded off against convergence speed and retrieval error. The new Hopfield network has three types of energy minima (fixed points of the update): (1) global fixed point averaging over all patterns, (2) metastable states averaging over a subset of patterns, and (3) fixed points which store a single pattern. Transformer and BERT models operate in their first layers preferably in the global averaging regime, while they operate in higher layers in metastable states. The gradient in transformers is maximal for metastable states, is uniformly distributed for global averaging, and vanishes for a fixed point near a stored pattern. Using the Hopfield network interpretation, we analyzed learning of transformer and BERT models. Learning starts with attention heads that average and then most of them switch to metastable states. However, the majority of heads in the first layers still averages and can be replaced by averaging, e.g. our proposed Gaussian weighting. In contrast, heads in the last layers steadily learn and seem to use metastable states to collect information created in lower layers. These heads seem to be a promising target for improving transformers. Neural networks with Hopfield networks outperform other methods on immune repertoire classification, where the Hopfield net stores several hundreds of thousands of patterns. We provide a new PyTorch layer called "Hopfield", which allows to equip deep learning architectures with modern Hopfield networks as a new powerful concept comprising pooling, memory, and attention. GitHub: https://github.com/ml-jku/hopfield-layers

Large-scale ligand-based virtual screening for SARS-CoV-2 inhibitors using deep neural networks

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.

Detecting cutaneous basal cell carcinomas in ultra-high resolution and weakly labelled histopathological images

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.

Using LSTMs for climate change assessment studies on droughts and floods

Climate change affects occurrences of floods and droughts worldwide. However, predicting climate impacts over individual watersheds is difficult, primarily because accurate hydrological forecasts require models that are calibrated to past data. In this work we present a large-scale LSTM-based modeling approach that -- by training on large data sets -- learns a diversity of hydrological behaviors. Previous work shows that this model is more accurate than current state-of-the-art models, even when the LSTM-based approach operates out-of-sample and the latter in-sample. In this work, we show how this model can assess the sensitivity of the underlying systems with regard to extreme (high and low) flows in individual watersheds over the continental US.

Quantum Optical Experiments Modeled by Long Short-Term Memory

We demonstrate how machine learning is able to model experiments in quantum physics. Quantum entanglement is a cornerstone for upcoming quantum technologies such as quantum computation and quantum cryptography. Of particular interest are complex quantum states with more than two particles and a large number of entangled quantum levels. Given such a multiparticle high-dimensional quantum state, it is usually impossible to reconstruct an experimental setup that produces it. To search for interesting experiments, one thus has to randomly create millions of setups on a computer and calculate the respective output states. In this work, we show that machine learning models can provide significant improvement over random search. We demonstrate that a long short-term memory (LSTM) neural network can successfully learn to model quantum experiments by correctly predicting output state characteristics for given setups without the necessity of computing the states themselves. This approach not only allows for faster search but is also an essential step towards automated design of multiparticle high-dimensional quantum experiments using generative machine learning models.

Patch Refinement -- Localized 3D Object Detection

We introduce Patch Refinement a two-stage model for accurate 3D object detection and localization from point cloud data. Patch Refinement is composed of two independently trained Voxelnet-based networks, a Region Proposal Network (RPN) and a Local Refinement Network (LRN). We decompose the detection task into a preliminary Bird's Eye View (BEV) detection step and a local 3D detection step. Based on the proposed BEV locations by the RPN, we extract small point cloud subsets ("patches"), which are then processed by the LRN, which is less limited by memory constraints due to the small area of each patch. Therefore, we can apply encoding with a higher voxel resolution locally. The independence of the LRN enables the use of additional augmentation techniques and allows for an efficient, regression focused training as it uses only a small fraction of each scene. Evaluated on the KITTI 3D object detection benchmark, our submission from January 28, 2019, outperformed all previous entries on all three difficulties of the class car, using only 50 % of the available training data and only LiDAR information.