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Protein characterization using nanopore-based devices promises to be a breakthrough method in basic research, diagnostics, and analytics. Current research includes the use of machine learning to achieve this task. In this work, a comprehensive statistical analysis of nanopore current signals is performed and demonstrated to be sufficient for classifying up to 42 peptides with 70 % accuracy. Two sets of features, the statistical moments and the catch22 set, are compared both in their representations and after training small classifier neural networks. We demonstrate that complex features of the events, captured in both the catch22 set and the central moments, are key in classifying peptides with otherwise similar mean currents. These results highlight the efficacy of purely statistical analysis of nanopore data and suggest a path forward for more sophisticated classification techniques.

This work introduces SwarmRL, a Python package designed to study intelligent active particles. SwarmRL provides an easy-to-use interface for developing models to control microscopic colloids using classical control and deep reinforcement learning approaches. These models may be deployed in simulations or real-world environments under a common framework. We explain the structure of the software and its key features and demonstrate how it can be used to accelerate research. With SwarmRL, we aim to streamline research into micro-robotic control while bridging the gap between experimental and simulation-driven sciences. SwarmRL is available open-source on GitHub at https://github.com/SwarmRL/SwarmRL., Comment: 16 pages, 3 figures

We demonstrate a novel approach to reservoir computer measurements using random matrices. We do so to motivate how atomic-scale devices might be used for real-world computing applications. Our approach uses random matrices to construct reservoir measurements, introducing a simple, scalable means for producing state descriptions. In our studies, two reservoirs, a five-atom Heisenberg spin chain, and a five-qubit quantum circuit, perform time series prediction and data interpolation. The performance of the measurement technique and current limitations are discussed in detail alongside an exploration of the diversity of measurements yielded by the random matrices. Additionally, we explore the role of the parameters of the reservoirs, adjusting coupling strength and the measurement dimension, yielding insights into how these learning machines might be automatically tuned for different problems. This research highlights using random matrices to measure simple quantum reservoirs for natural learning devices and outlines a path forward for improving their performance and experimental realization., Comment: 12 pages, 5 figures

Reinforcement learning (RL) is a flexible and efficient method for programming micro-robots in complex environments. Here we investigate whether reinforcement learning can provide insights into biological systems when trained to perform chemotaxis. Namely, whether we can learn about how intelligent agents process given information in order to swim towards a target. We run simulations covering a range of agent shapes, sizes, and swim speeds to determine if the physical constraints on biological swimmers, namely Brownian motion, lead to regions where reinforcement learners' training fails. We find that the RL agents can perform chemotaxis as soon as it is physically possible and, in some cases, even before the active swimming overpowers the stochastic environment. We study the efficiency of the emergent policy and identify convergence in agent size and swim speeds. Finally, we study the strategy adopted by the reinforcement learning algorithm to explain how the agents perform their tasks. To this end, we identify three emerging dominant strategies and several rare approaches taken. These strategies, whilst producing almost identical trajectories in simulation, are distinct and give insight into the possible mechanisms behind which biological agents explore their environment and respond to changing conditions., Comment: 12 pages, 6 figures

The quantum theory of atoms in molecules (QTAIM) gives access to well-defined local atomic energies. Due to their locality, these energies are potentially interesting in fitting atomistic machine learning models as they inform about physically relevant properties. However, computationally, quantum-mechanically accurate local energies are notoriously difficult to obtain for large systems. Here, we show that by employing semi-empirical correlations between different components of the total energy, we can obtain well-defined local energies at a moderate cost. We employ this methodology to investigate energetics in noble liquids or argon, krypton, and their mixture. Instead of using these local energies to fit atomistic models, we show how well these local energies are reproduced by machine-learned models trained on the total energies. The results of our investigation suggest that smaller neural networks, trained only on the total energy of an atomistic system, are more likely to reproduce the underlying local energy partitioning faithfully than larger networks. Furthermore, we demonstrate that networks more capable of this energy decomposition are, in turn, capable of transferring to previously unseen systems. Our results are a step towards understanding how much physics can be learned by neural networks and where this can be applied, particularly how a better understanding of physics aids in the transferability of these neural networks., Comment: 13 pages, 10 figures

The past decade has seen tremendous breakthroughs in computation and there is no indication that this will slow any time soon. Machine learning, large-scale computing resources, and increased industry focus have resulted in rising investments in computer-driven solutions for data management, simulations, and model generation. However, with this growth in computation has come an even larger expansion of data and with it, complexity in data storage, sharing, and tracking. In this work, we introduce ZnTrack, a Python-driven data versioning tool. ZnTrack builds upon established version control systems to provide a user-friendly and easy-to-use interface for tracking parameters in experiments, designing workflows, and storing and sharing data. From this ability to reduce large datasets to a simple Python script emerges the concept of Data as Code, a core component of the work presented here and an undoubtedly important concept as the age of computation continues to evolve. ZnTrack offers an open-source, FAIR data compatible Python package to enable users to harness these concepts of the future., Comment: 22 pages, 10 figures, 2MB PDF

This letter presents a novel approach for identifying uncorrelated atomic configurations from extensive data sets with a non-standard neural network workflow known as random network distillation (RND) for training machine-learned inter-atomic potentials (MLPs). This method is coupled with a DFT workflow wherein initial data is generated with cheaper classical methods before only the minimal subset is passed to a more computationally expensive ab initio calculation. This benefits training not only by reducing the number of expensive DFT calculations required but also by providing a pathway to the use of more accurate quantum mechanical calculations for training. The method's efficacy is demonstrated by constructing machine-learned inter-atomic potentials for the molten salts KCl and NaCl. Our RND method allows accurate models to be fit on minimal data sets, as small as 32 configurations, reducing the required structures by at least one order of magnitude compared to alternative methods., Comment: 9 pages, 8 figures, letter

Multi-Agent Reinforcement Learning (MARL) is a promising candidate for realizing efficient control of microscopic particles, of which micro-robots are a subset. However, the microscopic particles' environment presents unique challenges, such as Brownian motion at sufficiently small length-scales. In this work, we explore the role of temperature in the emergence and efficacy of strategies in MARL systems using particle-based Langevin molecular dynamics simulations as a realistic representation of micro-scale environments. To this end, we perform experiments on two different multi-agent tasks in microscopic environments at different temperatures, detecting the source of a concentration gradient and rotation of a rod. We find that at higher temperatures, the RL agents identify new strategies for achieving these tasks, highlighting the importance of understanding this regime and providing insight into optimal training strategies for bridging the generalization gap between simulation and reality. We also introduce a novel Python package for studying microscopic agents using reinforcement learning (RL) to accompany our results., Comment: 12 pages, 5 figures

A theory of neural networks (NNs) built upon collective variables would provide scientists with the tools to better understand the learning process at every stage. In this work, we introduce two such variables, the entropy and the trace of the empirical neural tangent kernel (NTK) built on the training data passed to the model. We empirically analyze the NN performance in the context of these variables and find that there exists correlation between the starting entropy, the trace of the NTK, and the generalization of the model computed after training is complete. This framework is then applied to the problem of optimal data selection for the training of NNs. To this end, random network distillation (RND) is used as a means of selecting training data which is then compared with random selection of data. It is shown that not only does RND select data-sets capable of outperforming random selection, but that the collective variables associated with the RND data-sets are larger than those of the randomly selected sets. The results of this investigation provide a stable ground from which the selection of data for NN training can be driven by this phenomenological framework., Comment: 13 pages, 7 figures

We present an investigation into data selection methods for the efficient sampling of configuration space as applied to the development of inter-atomic potentials for scale bridging in molecular dynamics (MD) simulations. This investigation suggests that the most efficient sampling techniques are those that incorporate information on an atomic level such as forces or atomic energies. Finally, we generate an inter-atomic potential for the a sodium chloride system using each data selection technique and find that the global selection methods result in non-physical simulations.