Accurate determination of a small molecule candidate (ligand) binding pose in its target protein pocket is important for computer-aided drug discovery. Typical rigid-body docking methods ignore the pocket flexibility of protein, while the more accurate pose generation using molecular dynamics is hindered by slow protein dynamics. We develop a tiered tensor transform (3T) algorithm to rapidly generate diverse protein-ligand complex conformations for both pose and affinity estimation in drug screening, requiring neither machine learning training nor lengthy dynamics computation, while maintaining both coarse-grain-like coordinated protein dynamics and atomistic-level details of the complex pocket. The 3T conformation structures we generate are closer to experimental co-crystal structures than those generated by docking software, and more importantly achieve significantly higher accuracy in active ligand classification than traditional ensemble docking using hundreds of experimental protein conformations. 3T structure transformation is decoupled from the system physics, making future usage in other computational scientific domains possible.

Computational units in artificial neural networks follow a simplified model of biological neurons. In the biological model, the output signal of a neuron runs down the axon, splits following the many branches at its end, and passes identically to all the downward neurons of the network. Each of the downward neurons will use their copy of this signal as one of many inputs dendrites, integrate them all and fire an output, if above some threshold. In the artificial neural network, this translates to the fact that the nonlinear filtering of the signal is performed in the upward neuron, meaning that in practice the same activation is shared between all the downward neurons that use that signal as their input. Dendrites thus play a passive role. We propose a slightly more complex model for the biological neuron, where dendrites play an active role: the activation in the output of the upward neuron becomes optional, and instead the signals going through each dendrite undergo independent nonlinear filterings, before the linear combination. We implement this new model into a ReLU computational unit and discuss its biological plausibility. We compare this new computational unit with the standard one and describe it from a geometrical point of view. We provide a Keras implementation of this unit into fully connected and convolutional layers and estimate their FLOPs and weights change. We then use these layers in ResNet architectures on CIFAR-10, CIFAR-100, Imagenette, and Imagewoof, obtaining performance improvements over standard ResNets up to 1.73%. Finally, we prove a universal representation theorem for continuous functions on compact sets and show that this new unit has more representational power than its standard counterpart.

Deep-learning of artificial neural networks (ANNs) is creating highly functional tools that are, unfortunately, as hard to interpret as their natural counterparts. While it is possible to identify functional modules in natural brains using technologies such as fMRI, we do not have at our disposal similarly robust methods for artificial neural networks. Ideally, understanding which parts of an artificial neural network perform what function might help us to address a number of vexing problems in ANN research, such as catastrophic forgetting and overfitting. Furthermore, revealing a network's modularity could improve our trust in them by making these black boxes more transparent. Here we introduce a new information-theoretic concept that proves useful in understanding and analyzing a network's functional modularity: the relay information $I_R$. The relay information measures how much information groups of neurons that participate in a particular function (modules) relay from inputs to outputs. Combined with a greedy search algorithm, relay information can be used to {\em identify} computational modules in neural networks. We also show that the functionality of modules correlates with the amount of relay information they carry.

Cellular automata (CA) captivate researchers due to teh emergent, complex individualized behavior that simple global rules of interaction enact. Recent advances in the field have combined CA with convolutional neural networks to achieve self-regenerating images. This new branch of CA is called neural cellular automata [1]. The goal of this project is to use the idea of idea of neural cellular automata to grow prediction machines. We place many different convolutional neural networks in a grid. Each conv net cell outputs a prediction of what the next state will be, and minimizes predictive error. Cells received their neighbors' colors and fitnesses as input. Each cell's fitness score described how accurate its predictions were. Cells could also move to explore their environment and some stochasticity was applied to movement.

Cognitive Computing (COC) aims to build highly cognitive machines with low computational resources that respond in real-time. However, scholarly literature shows varying research areas and various interpretations of COC. This calls for a cohesive architecture that delineates the nature of COC. We argue that if Herbert Simon considered the design science is the science of artificial, cognitive systems are the products of cognitive science or 'the newest science of the artificial'. Therefore, building a conceptual basis for COC is an essential step into prospective cognitive computing-based systems. This paper proposes an architecture of COC through analyzing the literature on COC using a myriad of statistical analysis methods. Then, we compare the statistical analysis results with previous qualitative analysis results to confirm our findings. The study also comprehensively surveys the recent research on COC to identify the state of the art and connect the advances in varied research disciplines in COC. The study found that there are three underlaying computing paradigms, Von-Neuman, Neuromorphic Engineering and Quantum Computing, that comprehensively complement the structure of cognitive computation. The research discuss possible applications and open research directions under the COC umbrella.

Real-world applications often require learning continuously from a stream of data under ever-changing conditions. When trying to learn from such non-stationary data, deep neural networks (DNNs) undergo catastrophic forgetting of previously learned information. Among the common approaches to avoid catastrophic forgetting, rehearsal-based methods have proven effective. However, they are still prone to forgetting due to task-interference as all parameters respond to all tasks. To counter this, we take inspiration from sparse coding in the brain and introduce dynamic modularity and sparsity (Dynamos) for rehearsal-based general continual learning. In this setup, the DNN learns to respond to stimuli by activating relevant subsets of neurons. We demonstrate the effectiveness of Dynamos on multiple datasets under challenging continual learning evaluation protocols. Finally, we show that our method learns representations that are modular and specialized, while maintaining reusability by activating subsets of neurons with overlaps corresponding to the similarity of stimuli.

The surrogate loss of variational autoencoders (VAEs) poses various challenges to their training, inducing the imbalance between task fitting and representation inference. To avert this, the existing strategies for VAEs focus on adjusting the tradeoff by introducing hyperparameters, deriving a tighter bound under some mild assumptions, or decomposing the loss components per certain neural settings. VAEs still suffer from uncertain tradeoff learning.We propose a novel evolutionary variational autoencoder (eVAE) building on the variational information bottleneck (VIB) theory and integrative evolutionary neural learning. eVAE integrates a variational genetic algorithm into VAE with variational evolutionary operators including variational mutation, crossover, and evolution. Its inner-outer-joint training mechanism synergistically and dynamically generates and updates the uncertain tradeoff learning in the evidence lower bound (ELBO) without additional constraints. Apart from learning a lossy compression and representation of data under the VIB assumption, eVAE presents an evolutionary paradigm to tune critical factors of VAEs and deep neural networks and addresses the premature convergence and random search problem by integrating evolutionary optimization into deep learning. Experiments show that eVAE addresses the KL-vanishing problem for text generation with low reconstruction loss, generates all disentangled factors with sharp images, and improves the image generation quality,respectively. eVAE achieves better reconstruction loss, disentanglement, and generation-inference balance than its competitors.

Thorough testing of safety-critical autonomous systems, such as self-driving cars, autonomous robots, and drones, is essential for detecting potential failures before deployment. One crucial testing stage is model-in-the-loop testing, where the system model is evaluated by executing various scenarios in a simulator. However, the search space of possible parameters defining these test scenarios is vast, and simulating all combinations is computationally infeasible. To address this challenge, we introduce AmbieGen, a search-based test case generation framework for autonomous systems. AmbieGen uses evolutionary search to identify the most critical scenarios for a given system, and has a modular architecture that allows for the addition of new systems under test, algorithms, and search operators. Currently, AmbieGen supports test case generation for autonomous robots and autonomous car lane keeping assist systems. In this paper, we provide a high-level overview of the framework's architecture and demonstrate its practical use cases.

Novel topological spin textures, such as magnetic skyrmions, benefit from their inherent stability, acting as the ground state in several magnetic systems. In the current study of atomic monolayer magnetic materials, reasonable initial guesses are still needed to search for those magnetic patterns. This situation underlines the need to develop a more effective way to identify the ground states. To solve this problem, in this work, we propose a genetic-tunneling-driven variance-controlled optimization approach, which combines a local energy minimizer back-end and a metaheuristic global searching front-end. This algorithm is an effective optimization solution for searching for magnetic ground states at extremely low temperatures and is also robust for finding low-energy degenerated states at finite temperatures. We demonstrate here the success of this method in searching for magnetic ground states of 2D monolayer systems with both artificial and calculated interactions from density functional theory. It is also worth noting that the inherent concurrent property of this algorithm can significantly decrease the execution time. In conclusion, our proposed method builds a useful tool for low-dimensional magnetic system energy optimization.

This is paper for the smooth function approximation by neural networks (NN). Mathematical or physical functions can be replaced by NN models through regression. In this study, we get NNs that generate highly accurate and highly smooth function, which only comprised of a few weight parameters, through discussing a few topics about regression. First, we reinterpret inside of NNs for regression; consequently, we propose a new activation function--integrated sigmoid linear unit (ISLU). Then special charateristics of metadata for regression, which is different from other data like image or sound, is discussed for improving the performance of neural networks. Finally, the one of a simple hierarchical NN that generate models substituting mathematical function is presented, and the new batch concept ``meta-batch" which improves the performance of NN several times more is introduced. The new activation function, meta-batch method, features of numerical data, meta-augmentation with metaparameters, and a structure of NN generating a compact multi-layer perceptron(MLP) are essential in this study.