We define a neural network as a septuple consisting of (1) a state vector, (2) an input projection, (3) an output projection, (4) a weight matrix, (5) a bias vector, (6) an activation map and (7) a loss function. We argue that the loss function can be imposed either on the boundary (i.e. input and/or output neurons) or in the bulk (i.e. hidden neurons) for both supervised and unsupervised systems.

Allostery is considered important in regulating protein’s activity. Drug development depends on the understanding of allosteric mechanisms, especially the identification of allosteric sites, which is a prerequisite in drug discovery and design. Many computational methods have been developed for allosteric site prediction using pocket features and protein dynamics. Here, we present an ensemble learning

Two-qubit systems typically employ 36 projective measurements for high-fidelity tomographic estimation. The overcomplete nature of the 36 measurements suggests possible robustness of the estimation procedure to missing measurements. In this paper, we explore the resilience of machine-learning-based quantum state estimation techniques to missing measurements by creating a pipeline of stacked machine

Current beam orientation optimization algorithms for radiotherapy, such as column generation (CG), are typically heuristic or greedy in nature because of the size of the combinatorial problem, which leads to suboptimal solutions. We propose a reinforcement learning strategy using a Monte Carlo Tree Search (MCTS) that can find a better beam orientation set in less time than CG. We utilize a reinforcement

The neural ordinary differential equation (neural ODE) is a novel machine learning architecture whose weights are smooth functions of the continuous depth. We apply the neural ODE to holographic QCD by regarding the weight functions as a bulk metric, and train the machine with lattice QCD data of chiral condensate at finite temperature. The machine finds consistent bulk geometry at various values of

The requirement for accelerated and quantitatively accurate screening of nuclear magnetic resonance spectra across the small molecules chemical compound space is two-fold: (1) a robust ‘local’ machine learning (ML) strategy capturing the effect of the neighborhood on an atom’s ‘near-sighted’ property—chemical shielding; (2) an accurate reference dataset generated with a state-of-the-art first-principles

Machine learning has been proven to have the potential to bridge the gap between the accuracy of ab initio methods and the efficiency of empirical force fields. Neural networks are one of the most frequently used approaches to construct high-dimensional potential energy surfaces. Unfortunately, they lack an inherent uncertainty estimation which is necessary for efficient and automated sampling through

Completing a data tensor with structured missing components is a challenging task where the missing components are not distributed randomly but they admit some regular patterns, e.g. missing columns and rows or missing blocks/patches. Many of the existing tensor completion algorithms are not able to handle such scenarios. In this paper, we propose a novel and efficient approach for matrix/tensor completion

Containment of epidemic outbreaks entails great societal and economic costs. Cost-effective containment strategies rely on efficiently identifying infected individuals, making the best possible use of the available testing resources. Therefore, quickly identifying the optimal testing strategy is of critical importance. Here, we demonstrate that machine learning can be used to identify which individuals

Artificial intelligence is driving one of the most important revolutions in organic chemistry. Multiple platforms, including tools for reaction prediction and synthesis planning based on machine learning, have successfully become part of the organic chemists’ daily laboratory, assisting in domain-specific synthetic problems. Unlike reaction prediction and retrosynthetic models, the prediction of reaction

We describe the current and future plans for using artificial intelligence and machine learning (AI/ML) methods at the National Synchrotron Light Source II (NSLS-II), a scientific user facility at the Brookhaven National Laboratory. We discuss the opportunity for using the AI/ML tools and techniques developed in the data and computational science areas to greatly improve the scientific output of large

We propose a theoretical understanding of neural networks in terms of Wilsonian effective field theory. The correspondence relies on the fact that many asymptotic neural networks are drawn from Gaussian processes (GPs), the analog of non-interacting field theories. Moving away from the asymptotic limit yields a non-Gaussian process (NGP) and corresponds to turning on particle interactions, allowing

In recent years the development of machine learning potentials (MLPs) has become a very active field of research. Numerous approaches have been proposed, which allow one to perform extended simulations of large systems at a small fraction of the computational costs of electronic structure calculations. The key to the success of modern MLPs is the close-to first principles quality description of the

We describe a neural network-based tool for the automatic estimation of thin film thicknesses and scattering length densities from neutron reflectivity curves. The neural network sits within a data pipeline, that takes raw data from a neutron reflectometer, and outputs data and parameter estimates into a fitting program for end user analysis. Our tool deals with simple cases, predicting the number

In the next decade, the demands for computing in large scientific experiments are expected to grow tremendously. During the same time period, CPU performance increases will be limited. At the CERN Large Hadron Collider (LHC), these two issues will confront one another as the collider is upgraded for high luminosity running. Alternative processors such as graphics processing units (GPUs) can resolve

Control of the stochastic dynamics of a quantum system is indispensable in fields such as quantum information processing and metrology. However, there is no general ready-made approach to the design of efficient control strategies. Here, we propose a framework for the automated design of control schemes based on differentiable programming. We apply this approach to the state preparation and stabilization

With recent technological advances, large-scale experimental facilities generate huge datasets, into the petabyte range, every year, thereby creating the Big Data deluge effect. Data management, including the collection, management, and curation of these large datasets, is a significantly intensive precursor step in relation to the data analysis that underpins scientific investigations. The rise of

Neutron reflectometry (NR) is a powerful tool for probing thin films at length scales down to nanometers. We investigated the use of a neural network to predict a two-layer thin film structure to model a given measured reflectivity curve. Application of this neural network to predict a thin film structure revealed that it was accurate and could provide an excellent starting point for traditional fitting

We introduce natural language processing into the study of knot theory, as made natural by the braid word representation of knots. We study the UNKNOT problem of determining whether or not a given knot is the unknot. After describing an algorithm to randomly generate N-crossing braids and their knot closures and discussing the induced prior on the distribution of knots, we apply binary classification

The goal of specular neutron and x-ray reflectometry is to infer a material’s scattering length density (SLD) profile from its experimental reflectivity curves. This paper focuses on the investigation of an original approach to the ill-posed non-invertible problem which involves the use of artificial neural networks (ANNs). In particular, the numerical experiments described here deal with large data

Several applications in the scientific simulation of physical systems can be formulated as control/optimization problems. The computational models for such systems generally contain hyperparameters, which control solution fidelity and computational expense. The tuning of these parameters is non-trivial and the general approach is to manually ‘spot-check’ for good combinations. This is because optimal

Monte Carlo (MC) simulation is considered the gold standard method for radiotherapy dose calculation. However, achieving high precision requires a large number of simulation histories, which is time-consuming. The use of computer graphics processing units (GPUs) has greatly accelerated MC simulation and allows dose calculation within a few minutes for a typical radiotherapy treatment plan. However

X-ray computed tomography (CT) is a nondestructive imaging technique to reconstruct cross-sectional images of an object using x-ray measurements taken from different view angles for medical diagnosis, therapeutic planning, security screening, and other applications. In clinical practice, the x-ray tube emits polychromatic x-rays, and the x-ray detector array operates in the energy-integrating mode

Neutron computed tomography (NCT), a 3D non-destructive characterization technique, is carried out at nuclear reactor or spallation neutron source-based user facilities. Because neutrons are not severely attenuated by heavy elements and are sensitive to light elements like hydrogen, neutron radiography and computed tomography offer a complementary contrast to x-ray CT conducted at a synchrotron user

Mixing cations has been a successful strategy in perovskite synthesis by solution-processing, delivering improvements in the thermodynamic stability as well as in the lattice parameter control. Unfortunately, the relation between a given cation mixture and the associated structural deformation is not well-established, a fact that hinders an adequate identification of the optimum chemical compositions

Efficient, physically-inspired descriptors of the structure and composition of molecules and materials play a key role in the application of machine-learning techniques to atomistic simulations. The proliferation of approaches, as well as the fact that each choice of features can lead to very different behavior depending on how they are used, e.g. by introducing non-linear kernels and non-Euclidean

Machine learning with application to questions in the physical sciences has become a widely used tool, successfully applied to classification, regression and optimization tasks in many areas. Research focus mostly lies in improving the accuracy of the machine learning models in numerical predictions, while scientific understanding is still almost exclusively generated by human researchers analysing

We introduce a new family of energy-based probabilistic graphical models for efficient unsupervised learning. Its definition is motivated by the control of the spin-glass properties of the Ising model described by the weights of Boltzmann machines. We use it to learn the Bars and Stripes dataset of various sizes and the MNIST dataset, and show how they quickly achieve the performance offered by standard

Bridging systems biology and drug design, we propose a deep learning framework for de novo discovery of molecules tailored to bind with given protein targets. Our methodology is exemplified by the task of designing antiviral candidates to target SARS-CoV-2 related proteins. Crucially, our framework does not require fine-tuning for specific proteins but is demonstrated to generalize in proposing ligands

Atomic environment fingerprints are widely used in computational materials science, from machine learning potentials to the quantification of similarities between atomic configurations. Many approaches to the construction of such fingerprints, also called structural descriptors, have been proposed. In this work, we compare the performance of fingerprints based on the overlap matrix, the smooth overlap

Pencil beam (PB) dose calculation is fast but inaccurate due to the approximations when dealing with inhomogeneities. Monte Carlo (MC) dose calculation is the most accurate method but it is time consuming. The aim of this study was to develop a deep learning model that can boost the accuracy of PB dose calculation to the level of MC dose by converting PB dose to MC dose for different tumor sites. The

Beamline experiments at central facilities are increasingly demanding of remote, high-throughput, and adaptive operation conditions. To accommodate such needs, new approaches must be developed that enable on-the-fly decision making for data intensive challenges. Reinforcement learning (RL) is a domain of AI that holds the potential to enable autonomous operations in a feedback loop between beamline

Deep learning methods applied to chemistry can be used to accelerate the discovery of new molecules. This work introduces GraphINVENT, a platform developed for graph-based molecular design using graph neural networks (GNNs). GraphINVENT uses a tiered deep neural network architecture to probabilistically generate new molecules a single bond at a time. All models implemented in GraphINVENT can quickly

Quantum machine learning is a relatively new research field that aims to combine the dramatic performance advantage offered by quantum computing and the ability of machine learning algorithms to learn complex distributions of high-dimensional data. The primary focus of this domain is the implementation of classical machine learning algorithms in the quantum mechanical domain and study of the speedup

We introduce and explore an approach for constructing force fields for small molecules, which combines intuitive low body order empirical force field terms with the concepts of data driven statistical fits of recent machine learned potentials. We bring these two key ideas together to bridge the gap between established empirical force fields that have a high degree of transferability on the one hand

We introduce a neural network inspired by Google’s Inception model to compute the Hodge number h 1,1 of complete intersection Calabi–Yau (CICY) 3-folds. This architecture improves largely the accuracy of the predictions over existing results, giving already 97% of accuracy with just 30% of the data for training. Accuracy climbs to 99% when using 80% of the data for training. This proves that neural

Is a deep learning model capable of representing systems governed by certain first principle physics laws by only observing the system’s output? In an effort to simulate two-dimensional subsurface fluid dynamics in porous media, we found that an accurate deep-learning-based proxy model can be taught efficiently by a computationally expensive finite-volume-based simulator. We pose the problem as an

Despite 2D materials holding great promise for a broad range of applications, the proliferation of devices and their fulfillment of real-life demands are still far from being realized. Experimentally obtainable samples commonly experience a wide range of perturbations (ripples and wrinkles, point and line defects, grain boundaries, strain field, doping, water intercalation, oxidation, edge reconstructions)

We investigate how the training curve of isotropic kernel methods depends on the symmetry of the task to be learned, in several settings. (i) We consider a regression task, where the target function is a Gaussian random field that depends only on variables, fewer than the input dimension d. We compute the expected test error ϵ that follows where p is the size of the training set. We find that β ∼ 1/d

All species of scorpions can inject venom, some of them even with the possibility of killing a human. Therefore, early detection and identification are essential to minimize scorpion stings. In this paper, we propose a novel automatic system for the detection and recognition of scorpions using computer vision and machine learning (ML) approaches. Two complementary image-processing techniques were used

Data augmentation has led to substantial improvements in the performance and generalization of deep models, and remains a highly adaptable method to evolving model architectures and varying amounts of data—in particular, extremely scarce amounts of available training data. In this paper, we present a novel method of applying Mbius transformations to augment input images during training. Mbius transformations

Lagrangian methods to solve the inviscid Euler equations produce numerical oscillations near shock waves. A common approach to reducing these oscillations is to add artificial viscosity (AV) to the discrete equations. The AV term acts as a dissipative mechanism that attenuates oscillations by smearing the shock across a finite number of computational cells. However, AV introduces several control parameters

Single particle imaging (SPI) is a promising method of native structure determination, which has undergone fast progress with the development of x-ray free-electron lasers. Large amounts of data are collected during SPI experiments, driving the need for automated data analysis. The necessary data analysis pipeline has a number of steps including binary object classification (single versus non-single

Non-negative matrix factorization (NMF) has proven to be a powerful unsupervised learning method for uncovering hidden features in complex and noisy data sets with applications in data mining, text recognition, dimension reduction, face recognition, anomaly detection, blind source separation, and many other fields. An important input for NMF is the latent dimensionality of the data, that is, the number

We extend the ability of an unitary quantum circuit by interfacing it with a classical autoregressive neural network. The combined model parametrizes a variational density matrix as a classical mixture of quantum pure states, where the autoregressive network generates bitstring samples as input states to the quantum circuit. We devise an efficient variational algorithm to jointly optimize the classical

Optical multi-layer thin films are widely used in optical and energy applications requiring photonic designs. Engineers often design such structures based on their physical intuition. However, solely relying on human experts can be time-consuming and may lead to sub-optimal designs, especially when the design space is large. In this work, we frame the multi-layer optical design task as a sequence generation

Transfer learning refers to the use of knowledge gained while solving a machine learning task and applying it to the solution of a closely related problem. Such an approach has enabled scientific breakthroughs in computer vision and natural language processing where the weights learned in state-of-the-art models can be used to initialize models for other tasks which dramatically improve their performance

Particle physics is a branch of science aiming at discovering the fundamental laws of matter and forces. Graph neural networks are trainable functions which operate on graphs—sets of elements and their pairwise relations—and are a central method within the broader field of geometric deep learning. They are very expressive and have demonstrated superior performance to other classical deep learning approaches

Quantum hardware and quantum-inspired algorithms are becoming increasingly popular for combinatorial optimization. However, these algorithms may require careful hyperparameter tuning for each problem instance. We use a reinforcement learning agent in conjunction with a quantum-inspired algorithm to solve the Ising energy minimization problem, which is equivalent to the Maximum Cut problem. The agent

Topological error correcting codes, and particularly the surface code, currently provide the most feasible road-map towards large-scale fault-tolerant quantum computation. As such, obtaining fast and flexible decoding algorithms for these codes, within the experimentally realistic and challenging context of faulty syndrome measurements, without requiring any final read-out of the physical qubits, is

This paper discusses two cases of applying artificial neural networks to the capacitance–voltage characteristics of InAsSb-based barrier infrared detectors. In the first case, we discuss a methodology for training a fully-connected feedforward network to predict the capacitance of the device as a function of the absorber, barrier, and contact doping densities, the barrier thickness, and the applied

The subject of this paper is the technology (the ‘how’) of constructing machine-learning interatomic potentials, rather than science (the ‘what’ and ‘why’) of atomistic simulations using machine-learning potentials. Namely, we illustrate how to construct moment tensor potentials using active learning as implemented in the MLIP package, focusing on the efficient ways to automatically sample configurations

The massive amount of data produced during simulation on high-performance computers has grown exponentially over the past decade, exacerbating the need for streaming compression and decompression methods for efficient storage and transfer of this data—key to realizing the full potential of large-scale computational science. Lossy compression approaches such as JPEG when applied to scientific simulation

We present PyXtal_FF—a package based on Python programming language—for developing machine learning potentials (MLPs). The aim of PyXtal_FF is to promote the application of atomistic simulations through providing several choices of atom-centered descriptors and machine learning regressions in one platform. Based on the given choice of descriptors (including the atom-centered symmetry functions, embedded

Machine-learning force fields have been increasingly employed in order to extend the possibility of current first-principles calculations. However, the transferability of the obtained potential cannot always be guaranteed in situations that are outside the original database. To study such limitation, we examined the very difficult case of the interactions in gold–iron nanoparticles. For the machine-learning

A notion of quantum natural evolution strategies is introduced, which provides a geometric synthesis of a number of known quantum/classical algorithms for performing classical black-box optimization. The recent work of Gomes et al (2019 arXiv:1910.10675) on heuristic combinatorial optimization using neural quantum states is pedagogically reviewed in this context, emphasizing the connection with natural

An InfoCGAN neural network is trained on 2D square Ising configurations conditioned on the external applied magnetic field and the temperature. The network is composed of two main sub-networks. The generator network learns to generate convincing Ising configurations and the discriminator network learns to discriminate between ‘real’ and ‘fake’ configurations with an additional categorical assignment

Multi-band insulating Bloch Hamiltonians with internal or spatial symmetries, such as particle-hole or inversion, may have topologically disconnected sectors of trivial atomic-limit (momentum-independent) Hamiltonians. We present a neural-network-based protocol for finding topologically relevant indices that are invariant under transformations between such trivial atomic-limit Hamiltonians, thus corresponding

Machine learning surrogate models for quantum mechanical simulations have enabled the field to efficiently and accurately study material and molecular systems. Developed models typically rely on a substantial amount of data to make reliable predictions of the potential energy landscape or careful active learning (AL) and uncertainty estimates. When starting with small datasets, convergence of AL approaches

Non-negative matrix factorization (NMF) is a popular method for finding a low rank approximation of a matrix, thereby revealing the latent components behind it. In genomics, NMF is widely used to interpret mutation data and derive the underlying mutational processes and their activities. A key challenge in the use of NMF is determining the number of components, or rank of the factorization. Here we