Interpretable Sequence Classification Via Prototype Trajectory

We propose a novel interpretable recurrent neural network (RNN) model, called ProtoryNet, in which we introduce a new concept of prototype trajectories. Motivated by the prototype theory in modern linguistics, ProtoryNet makes a prediction by finding the most similar prototype for each sentence in a text sequence and feeding an RNN backbone with the proximity of each of the sentences to the prototypes. The RNN backbone then captures the temporal pattern of the prototypes, to which we refer as prototype trajectories. The prototype trajectories enable intuitive, fine-grained interpretation of how the model reached to the final prediction, resembling the process of how humans analyze paragraphs. Experiments conducted on multiple public data sets reveal that the proposed method not only is more interpretable but also is more accurate than the current state-of-the-art prototype-based method. Furthermore, we report a survey result indicating that human users find ProtoryNet more intuitive and easier to understand, compared to the other prototype-based methods

Deep learning for synthetic microstructure generation in a materials-by-design framework for heterogeneous energetic materials

The sensitivity of heterogeneous energetic (HE) materials (propellants, explosives, and pyrotechnics) is critically dependent on their microstructure. Initiation of chemical reactions occurs at hot spots due to energy localization at sites of porosities and other defects. Emerging multi-scale predictive models of HE response to loads account for the physics at the meso-scale, i.e. at the scale of statistically representative clusters of particles and other features in the microstructure. Meso-scale physics is infused in machine-learned closure models informed by resolved meso-scale simulations. Since microstructures are stochastic, ensembles of meso-scale simulations are required to quantify hot spot ignition and growth and to develop models for microstructure-dependent energy deposition rates. We propose utilizing generative adversarial networks (GAN) to spawn ensembles of synthetic heterogeneous energetic material microstructures. The method generates qualitatively and quantitatively realistic microstructures by learning from images of HE microstructures. We show that the proposed GAN method also permits the generation of new morphologies, where the porosity distribution can be controlled and spatially manipulated. Such control paves the way for the design of novel microstructures to engineer HE materials for targeted performance in a materials-by-design framework

Artificial intelligence approaches for materials-by-design of energetic materials: state-of-the-art, challenges, and future directions

Artificial intelligence (AI) is rapidly emerging as an enabling tool for solving various complex materials design problems. This paper aims to review recent advances in AI-driven materials-by-design and their applications to energetic materials (EM). Trained with data from numerical simulations and/or physical experiments, AI models can assimilate trends and patterns within the design parameter space, identify optimal material designs (micro-morphologies, combinations of materials in composites, etc.), and point to designs with superior/targeted property and performance metrics. We review approaches focusing on such capabilities with respect to the three main stages of materials-by-design, namely representation learning of microstructure morphology (i.e., shape descriptors), structure-property-performance (S-P-P) linkage estimation, and optimization/design exploration. We provide a perspective view of these methods in terms of their potential, practicality, and efficacy towards the realization of materials-by-design. Specifically, methods in the literature are evaluated in terms of their capacity to learn from a small/limited number of data, computational complexity, generalizability/scalability to other material species and operating conditions, interpretability of the model predictions, and the burden of supervision/data annotation. Finally, we suggest a few promising future research directions for EM materials-by-design, such as meta-learning, active learning, Bayesian learning, and semi-/weakly-supervised learning, to bridge the gap between machine learning research and EM research

Geology of a Stratigraphically Complex Natural Gas Play: Canyon Sandstones, Val Verde Basin, Southwest Texas

This report examines the influence of stratigraphy, diagenesis, natural fractures, and in situ stress on low-permeability, gas-bearing sandstone reservoirs of the Paleozoic Ozona and Sonora Canyon Sandstones of the Val Verde Basin, Texas. The main stratigraphic controls on the distribution and quality of Canyon Sandstone reservoirs are submarine fan depositional patterns. These patterns are revealed in regional facies and maximum sandstone maps. Siderite cement is key to good within-sandstone reservoir quality. Natural fractures are widespread in both Ozona and Sonora Canyon sandstones. They could be future targets for advanced drilling methods, and they need to be taken into account in hydraulic fracture treatment design and reservoir management.Bureau of Economic Geolog

A physics-aware deep learning model for energy localization in multiscale shock-to-detonation simulations of heterogeneous energetic materials

Predictive simulations of the shock-to-detonation transition (SDT) in heterogeneous energetic materials (EM) are vital to the design and control of their energy release and sensitivity. Due to the complexity of the thermo-mechanics of EM during the SDT, both macro-scale response and sub-grid mesoscale energy localization must be captured accurately. This work proposes an efficient and accurate multiscale framework for SDT simulations of EM. We employ deep learning to model the mesoscale energy localization of shock-initiated EM microstructures upon which prediction results are used to supply reaction progress rate information to the macroscale SDT simulation. The proposed multiscale modeling framework is divided into two stages. First, a physics-aware recurrent convolutional neural network (PARC) is used to model the mesoscale energy localization of shock-initiated heterogeneous EM microstructures. PARC is trained using direct numerical simulations (DNS) of hotspot ignition and growth within microstructures of pressed HMX material subjected to different input shock strengths. After training, PARC is employed to supply hotspot ignition and growth rates for macroscale SDT simulations. We show that PARC can play the role of a surrogate model in a multiscale simulation framework, while drastically reducing the computation cost and providing improved representations of the sub-grid physics. The proposed multiscale modeling approach will provide a new tool for material scientists in designing high-performance and safer energetic materials

Discovering study-specific gene regulatory networks

This article has been made available through the Brunel Open Access Publishing Fund.Microarrays are commonly used in biology because of their ability to simultaneously measure thousands of genes under different conditions. Due to their structure, typically containing a high amount of variables but far fewer samples, scalable network analysis techniques are often employed. In particular, consensus approaches have been recently used that combine multiple microarray studies in order to find networks that are more robust. The purpose of this paper, however, is to combine multiple microarray studies to automatically identify subnetworks that are distinctive to specific experimental conditions rather than common to them all. To better understand key regulatory mechanisms and how they change under different conditions, we derive unique networks from multiple independent networks built using glasso which goes beyond standard correlations. This involves calculating cluster prediction accuracies to detect the most predictive genes for a specific set of conditions. We differentiate between accuracies calculated using cross-validation within a selected cluster of studies (the intra prediction accuracy) and those calculated on a set of independent studies belonging to different study clusters (inter prediction accuracy). Finally, we compare our method's results to related state-of-the art techniques. We explore how the proposed pipeline performs on both synthetic data and real data (wheat and Fusarium). Our results show that subnetworks can be identified reliably that are specific to subsets of studies and that these networks reflect key mechanisms that are fundamental to the experimental conditions in each of those subsets

Predictive power of deep-learning segmentation based prognostication model in non-small cell lung cancer

PurposeThe study aims to create a model to predict survival outcomes for non-small cell lung cancer (NSCLC) after treatment with stereotactic body radiotherapy (SBRT) using deep-learning segmentation based prognostication (DESEP).MethodsThe DESEP model was trained using imaging from 108 patients with NSCLC with various clinical stages and treatment histories. The model generated predictions based on unsupervised features learned by a deep-segmentation network from computed tomography imaging to categorize patients into high and low risk groups for overall survival (DESEP-predicted-OS), disease specific survival (DESEP-predicted-DSS), and local progression free survival (DESEP-predicted-LPFS). Serial assessments were also performed using auto-segmentation based volumetric RECISTv1.1 and computer-based unidimensional RECISTv1.1 patients was performed.ResultsThere was a concordance between the DESEP-predicted-LPFS risk category and manually calculated RECISTv1.1 (φ=0.544, p=0.001). Neither the auto-segmentation based volumetric RECISTv1.1 nor the computer-based unidimensional RECISTv1.1 correlated with manual RECISTv1.1 (p=0.081 and p=0.144, respectively). While manual RECISTv1.1 correlated with LPFS (HR=6.97,3.51-13.85, c=0.70, p<0.001), it could not provide insight regarding DSS (p=0.942) or OS (p=0.662). In contrast, the DESEP-predicted methods were predictive of LPFS (HR=3.58, 1.66-7.18, c=0.60, p<0.001), OS (HR=6.31, 3.65-10.93, c=0.71, p<0.001) and DSS (HR=9.25, 4.50-19.02, c=0.69, p<0.001). The promising results of the DESEP model were reproduced for the independent, external datasets of Stanford University, classifying survival and ‘dead’ group in their Kaplan-Meyer curves (p = 0.019).ConclusionDeep-learning segmentation based prognostication can predict LPFS as well as OS, and DSS after SBRT for NSCLC. It can be used in conjunction with current standard of care, manual RECISTv1.1 to provide additional insights regarding DSS and OS in NSCLC patients receiving SBRT.SummaryWhile current standard of care, manual RECISTv1.1 correlated with local progression free survival (LPFS) (HR=6.97,3.51-13.85, c=0.70, p<0.001), it could not provide insight regarding disease specific survival (DSS) (p=0.942) or overall survival (OS) (p=0.662). In contrast, the deep-learning segmentation based prognostication (DESEP)-predicted methods were predictive of LPFS (HR=3.58, 1.66-7.18, c=0.60, p<0.001), OS (HR=6.31, 3.65-10.93, c=0.71, p<0.001) and DSS (HR=9.25, 4.50-19.02, c=0.69, p<0.001). DESEP can be used in conjunction with current standard of care, manual RECISTv1.1 to provide additional insights regarding DSS and OS in NSCLC patients

Signals for Non-Commutative QED in eγe \gamma and γγ\gamma \gamma Collisions

We study the effects of non-commutative QED (NCQED) in fermion pair production, gamma + gamma -> f + bar{f} and Compton scattering, e + gamma -> e + gamma. Non-commutative geometries appear naturally in the context of string/M-theory and gives rise to 3- and 4-point photon vertices and to momentum dependent phase factors in QED vertices which will have observable effects in high energy collisions. We consider e+ e- colliders with energies appropriate to the TeV Linear Collider proposals and the multi-TeV CLIC project operating in gamma gamma and e gamma modes. Non-commutative scales roughly equal to the center of mass energy of the e+ e- collider can be probed, with the exact value depending on the model parameters and experimental factors. However, we found that the Compton process is sensitive to Lambda_{NC} values roughly twice as large as those accessible to the pair production process.Comment: 24 pages, 11 eps figure files, RevTeX forma

Non-local heat transport in Alcator C-Mod ohmic L-mode plasmas

Non-local heat transport experiments were performed in Alcator C-Mod ohmic L-mode plasmas by inducing edge cooling with laser blow-off impurity (CaF2) injection. The non-local effect, a cooling of the edge electron temperature with a rapid rise of the central electron temperature, which contradicts the assumption of 'local' transport, was observed in low collisionality linear ohmic confinement (LOC) regime plasmas. Transport analysis shows this phenomenon can be explained either by a fast drop of the core diffusivity, or the sudden appearance of a heat pinch. In high collisionality saturated ohmic confinement (SOC) regime plasmas, the thermal transport becomes 'local': the central electron temperature drops on the energy confinement time scale in response to the edge cooling. Measurements from a high resolution imaging x-ray spectrometer show that the ion temperature has a similar behaviour as the electron temperature in response to edge cooling, and that the transition density of non-locality correlates with the rotation reversal critical density. This connection may indicate the possible connection between thermal and momentum transport, which is also linked to a transition in turbulence dominance between trapped electron modes (TEMs) and ion temperature gradient (ITG) modes. Experiments with repetitive cold pulses in one discharge were also performed to allow Fourier analysis and to provide details of cold front propagation. These modulation experiments showed in LOC plasmas that the electron thermal transport is not purely diffusive, while in SOC the electron thermal transport is more diffusive like. Linear gyrokinetic simulations suggest the turbulence outside r/a = 0.75 changes from TEM dominance in LOC plasmas to ITG mode dominance in SOC plasmas.United States. Dept. of Energy (DoE Contract No DE-FC02-99ER54512)Oak Ridge Institute for Science and Education (DOE Fusion Energy Postdoctoral Research Program