Evolutionary Multi-Objective Design of SARS-CoV-2 Protease Inhibitor Candidates

Computational drug design based on artificial intelligence is an emerging research area. At the time of writing this paper, the world suffers from an outbreak of the coronavirus SARS-CoV-2. A promising way to stop the virus replication is via protease inhibition. We propose an evolutionary multi-objective algorithm (EMOA) to design potential protease inhibitors for SARS-CoV-2's main protease. Based on the SELFIES representation the EMOA maximizes the binding of candidate ligands to the protein using the docking tool QuickVina 2, while at the same time taking into account further objectives like drug-likeliness or the fulfillment of filter constraints. The experimental part analyzes the evolutionary process and discusses the inhibitor candidates.

Learned Weight Sharing for Deep Multi-Task Learning by Natural Evolution Strategy and Stochastic Gradient Descent

In deep multi-task learning, weights of task-specific networks are shared between tasks to improve performance on each single one. Since the question, which weights to share between layers, is difficult to answer, human-designed architectures often share everything but a last task-specific layer. In many cases, this simplistic approach severely limits performance. Instead, we propose an algorithm to learn the assignment between a shared set of weights and task-specific layers. To optimize the non-differentiable assignment and at the same time train the differentiable weights, learning takes place via a combination of natural evolution strategy and stochastic gradient descent. The end result are task-specific networks that share weights but allow independent inference. They achieve lower test errors than baselines and methods from literature on three multi-task learning datasets.

Acute Lymphoblastic Leukemia Classification from Microscopic Images using Convolutional Neural Networks

Examining blood microscopic images for leukemia is necessary when expensive equipment for flow cytometry is unavailable. Automated systems can ease the burden on medical experts for performing this examination and may be especially helpful to quickly screen a large number of patients. We present a simple, yet effective classification approach using a ResNeXt convolutional neural network with Squeeze-and-Excitation modules. The approach was evaluated in the C-NMC online challenge and achieves a weighted F1-score of 88.91% on the test set. Code is available at https://github.com/jprellberg/isbi2019cancer

Limited Evaluation Evolutionary Optimization of Large Neural Networks

Stochastic gradient descent is the most prevalent algorithm to train neural networks. However, other approaches such as evolutionary algorithms are also applicable to this task. Evolutionary algorithms bring unique trade-offs that are worth exploring, but computational demands have so far restricted exploration to small networks with few parameters. We implement an evolutionary algorithm that executes entirely on the GPU, which allows to efficiently batch-evaluate a whole population of networks. Within this framework, we explore the limited evaluation evolutionary algorithm for neural network training and find that its batch evaluation idea comes with a large accuracy trade-off. In further experiments, we explore crossover operators and find that unprincipled random uniform crossover performs extremely well. Finally, we train a network with 92k parameters on MNIST using an EA and achieve 97.6 % test accuracy compared to 98 % test accuracy on the same network trained with Adam. Code is available at https://github.com/jprellberg/gpuea.

Lamarckian Evolution of Convolutional Neural Networks

Convolutional neural networks belong to the most successul image classifiers, but the adaptation of their network architecture to a particular problem is computationally expensive. We show that an evolutionary algorithm saves training time during the network architecture optimization, if learned network weights are inherited over generations by Lamarckian evolution. Experiments on typical image datasets show similar or significantly better test accuracies and improved convergence speeds compared to two different baselines without weight inheritance. On CIFAR-10 and CIFAR-100 a 75 % improvement in data efficiency is observed.

Multi-label Classification of Surgical Tools with Convolutional Neural Networks

Automatic tool detection from surgical imagery has a multitude of useful applications, such as real-time computer assistance for the surgeon. Using the successful residual network architecture, a system that can distinguish 21 different tools in cataract surgery videos is created. The videos are provided as part of the 2017 CATARACTS challenge and pose difficulties found in many real-world datasets, for example a strong class imbalance. The construction of the detection system is guided by a wide array of experiments that explore different design decisions.