VN-EGNN: E(3)-Equivariant Graph Neural Networks with Virtual Nodes Enhance Protein Binding Site Identification

Being able to identify regions within or around proteins, to which ligands can potentially bind, is an essential step to develop new drugs. Binding site identification methods can now profit from the availability of large amounts of 3D structures in protein structure databases or from AlphaFold predictions. Current binding site identification methods heavily rely on graph neural networks (GNNs), usually designed to output E(3)-equivariant predictions. Such methods turned out to be very beneficial for physics-related tasks like binding energy or motion trajectory prediction. However, the performance of GNNs at binding site identification is still limited potentially due to the lack of dedicated nodes that model hidden geometric entities, such as binding pockets. In this work, we extend E(n)-Equivariant Graph Neural Networks (EGNNs) by adding virtual nodes and applying an extended message passing scheme. The virtual nodes in these graphs are dedicated quantities to learn representations of binding sites, which leads to improved predictive performance. In our experiments, we show that our proposed method VN-EGNN sets a new state-of-the-art at locating binding site centers on COACH420, HOLO4K and PDBbind2020.

GNN-VPA: A Variance-Preserving Aggregation Strategy for Graph Neural Networks

Graph neural networks (GNNs), and especially message-passing neural networks, excel in various domains such as physics, drug discovery, and molecular modeling. The expressivity of GNNs with respect to their ability to discriminate non-isomorphic graphs critically depends on the functions employed for message aggregation and graph-level readout. By applying signal propagation theory, we propose a variance-preserving aggregation function (VPA) that maintains expressivity, but yields improved forward and backward dynamics. Experiments demonstrate that VPA leads to increased predictive performance for popular GNN architectures as well as improved learning dynamics. Our results could pave the way towards normalizer-free or self-normalizing GNNs.

Principled Weight Initialisation for Input-Convex Neural Networks

Input-Convex Neural Networks (ICNNs) are networks that guarantee convexity in their input-output mapping. These networks have been successfully applied for energy-based modelling, optimal transport problems and learning invariances. The convexity of ICNNs is achieved by using non-decreasing convex activation functions and non-negative weights. Because of these peculiarities, previous initialisation strategies, which implicitly assume centred weights, are not effective for ICNNs. By studying signal propagation through layers with non-negative weights, we are able to derive a principled weight initialisation for ICNNs. Concretely, we generalise signal propagation theory by removing the assumption that weights are sampled from a centred distribution. In a set of experiments, we demonstrate that our principled initialisation effectively accelerates learning in ICNNs and leads to better generalisation. Moreover, we find that, in contrast to common belief, ICNNs can be trained without skip-connections when initialised correctly. Finally, we apply ICNNs to a real-world drug discovery task and show that they allow for more effective molecular latent space exploration.

Quantification of Uncertainty with Adversarial Models

Quantifying uncertainty is important for actionable predictions in real-world applications. A crucial part of predictive uncertainty quantification is the estimation of epistemic uncertainty, which is defined as an integral of the product between a divergence function and the posterior. Current methods such as Deep Ensembles or MC dropout underperform at estimating the epistemic uncertainty, since they primarily consider the posterior when sampling models. We suggest Quantification of Uncertainty with Adversarial Models (QUAM) to better estimate the epistemic uncertainty. QUAM identifies regions where the whole product under the integral is large, not just the posterior. Consequently, QUAM has lower approximation error of the epistemic uncertainty compared to previous methods. Models for which the product is large correspond to adversarial models (not adversarial examples!). Adversarial models have both a high posterior as well as a high divergence between their predictions and that of a reference model. Our experiments show that QUAM excels in capturing epistemic uncertainty for deep learning models and outperforms previous methods on challenging tasks in the vision domain.

Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language

Activity and property prediction models are the central workhorses in drug discovery and materials sciences, but currently they have to be trained or fine-tuned for new tasks. Without training or fine-tuning, scientific language models could be used for such low-data tasks through their announced zero- and few-shot capabilities. However, their predictive quality at activity prediction is lacking. In this work, we envision a novel type of activity prediction model that is able to adapt to new prediction tasks at inference time, via understanding textual information describing the task. To this end, we propose a new architecture with separate modules for chemical and natural language inputs, and a contrastive pre-training objective on data from large biochemical databases. In extensive experiments, we show that our method CLAMP yields improved predictive performance on few-shot learning benchmarks and zero-shot problems in drug discovery. We attribute the advances of our method to the modularized architecture and to our pre-training objective.

CLOOB: Modern Hopfield Networks with InfoLOOB Outperform CLIP

Contrastive learning with the InfoNCE objective is exceptionally successful in various self-supervised learning tasks. Recently, the CLIP model yielded impressive results on zero-shot transfer learning when using InfoNCE for learning visual representations from natural language supervision. However, InfoNCE as a lower bound on the mutual information has been shown to perform poorly for high mutual information. In contrast, the InfoLOOB upper bound (leave one out bound) works well for high mutual information but suffers from large variance and instabilities. We introduce "Contrastive Leave One Out Boost" (CLOOB), where modern Hopfield networks boost learning with the InfoLOOB objective. Modern Hopfield networks replace the original embeddings by retrieved embeddings in the InfoLOOB objective. The retrieved embeddings give InfoLOOB two assets. Firstly, the retrieved embeddings stabilize InfoLOOB, since they are less noisy and more similar to one another than the original embeddings. Secondly, they are enriched by correlations, since the covariance structure of embeddings is reinforced through retrievals. We compare CLOOB to CLIP after learning 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.

Modern Hopfield Networks for Few- and Zero-Shot Reaction Prediction

An essential step in the discovery of new drugs and materials is the synthesis of a molecule that exists so far only as an idea to test its biological and physical properties. While computer-aided design of virtual molecules has made large progress, computer-assisted synthesis planning (CASP) to realize physical molecules is still in its infancy and lacks a performance level that would enable large-scale molecule discovery. CASP supports the search for multi-step synthesis routes, which is very challenging due to high branching factors in each synthesis step and the hidden rules that govern the reactions. The central and repeatedly applied step in CASP is reaction prediction, for which machine learning methods yield the best performance. We propose a novel reaction prediction approach that uses a deep learning architecture with modern Hopfield networks (MHNs) that is optimized by contrastive learning. An MHN is an associative memory that can store and retrieve chemical reactions in each layer of a deep learning architecture. We show that our MHN contrastive learning approach enables few- and zero-shot learning for reaction prediction which, in contrast to previous methods, can deal with rare, single, or even no training example(s) for a reaction. On a well established benchmark, our MHN approach pushes the state-of-the-art performance up by a large margin as it improves the predictive top-100 accuracy from $0.858\pm0.004$ to $0.959\pm0.004$. This advance might pave the way to large-scale molecule discovery.

MC-LSTM: Mass-Conserving LSTM

The success of Convolutional Neural Networks (CNNs) in computer vision is mainly driven by their strong inductive bias, which is strong enough to allow CNNs to solve vision-related tasks with random weights, meaning without learning. Similarly, Long Short-Term Memory (LSTM) has a strong inductive bias towards storing information over time. However, many real-world systems are governed by conservation laws, which lead to the redistribution of particular quantities -- e.g. in physical and economical systems. Our novel Mass-Conserving LSTM (MC-LSTM) adheres to these conservation laws by extending the inductive bias of LSTM to model the redistribution of those stored quantities. MC-LSTMs set a new state-of-the-art for neural arithmetic units at learning arithmetic operations, such as addition tasks, which have a strong conservation law, as the sum is constant over time. Further, MC-LSTM is applied to traffic forecasting, modelling a pendulum, and a large benchmark dataset in hydrology, where it sets a new state-of-the-art for predicting peak flows. In the hydrology example, we show that MC-LSTM states correlate with real-world processes and are therefore interpretable.

Uncertainty Estimation with Deep Learning for Rainfall-Runoff Modelling

Deep Learning is becoming an increasingly important way to produce accurate hydrological predictions across a wide range of spatial and temporal scales. Uncertainty estimations are critical for actionable hydrological forecasting, and while standardized community benchmarks are becoming an increasingly important part of hydrological model development and research, similar tools for benchmarking uncertainty estimation are lacking. We establish an uncertainty estimation benchmarking procedure and present four Deep Learning baselines, out of which three are based on Mixture Density Networks and one is based on Monte Carlo dropout. Additionally, we provide a post-hoc model analysis to put forward some qualitative understanding of the resulting models. Most importantly however, we show that accurate, precise, and reliable uncertainty estimation can be achieved with Deep Learning.