TopologyNet: Topology based deep convolutional neural networks for biomolecular property predictions

Although deep learning approaches have had tremendous success in image, video and audio processing, computer vision, and speech recognition, their applications to three-dimensional (3D) biomolecular structural data sets have been hindered by the entangled geometric complexity and biological complexity. We introduce topology, i.e., element specific persistent homology (ESPH), to untangle geometric complexity and biological complexity. ESPH represents 3D complex geometry by one-dimensional (1D) topological invariants and retains crucial biological information via a multichannel image representation. It is able to reveal hidden structure-function relationships in biomolecules. We further integrate ESPH and convolutional neural networks to construct a multichannel topological neural network (TopologyNet) for the predictions of protein-ligand binding affinities and protein stability changes upon mutation. To overcome the limitations to deep learning arising from small and noisy training sets, we present a multitask topological convolutional neural network (MT-TCNN). We demonstrate that the present TopologyNet architectures outperform other state-of-the-art methods in the predictions of protein-ligand binding affinities, globular protein mutation impacts, and membrane protein mutation impacts.Comment: 20 pages, 8 figures, 5 table

Evolutionary polymorphic neural networks in chemical engineering modeling

Evolutionary Polymorphic Neural Network (EPNN) is a novel approach to modeling chemical, biochemical and physical processes. This approach has its basis in modern artificial intelligence, especially neural networks and evolutionary computing. EPNN can perform networked symbolic regressions for input-output data, while providing information about both the structure and complexity of a process during its own evolution. In this work three different processes are modeled: 1. A dynamic neutralization process. 2. An aqueous two-phase system. 3. Reduction of a biodegradation model. In all three cases, EPNN shows better or at least equal performances over published data than traditional thermodynamics /transport or neural network models. Furthermore, in those cases where traditional modeling parameters are difficult to determine, EPNN can be used as an auxiliary tool to produce equivalent empirical formulae for the target process. Feedback links in EPNN network can be formed through training (evolution) to perform multiple steps ahead predictions for dynamic nonlinear systems. Unlike existing applications combining neural networks and genetic algorithms, symbolic formulae can be extracted from EPNN modeling results for further theoretical analysis and process optimization. EPNN system can also be used for data prediction tuning. In which case, only a minimum number of initial system conditions need to be adjusted. Therefore, the network structure of EPNN is more flexible and adaptable than traditional neural networks. Due to the polymorphic and evolutionary nature of the EPNN system, the initially randomized values of constants in EPNN networks will converge to the same or similar forms of functions in separate runs until the training process ends. The EPNN system is not sensitive to differences in initial values of the EPNN population. However, if there exists significant larger noise in one or more data sets in the whole data composition, the EPNN system will probably fail to converge to a satisfactory level of prediction on these data sets. EPNN networks with a relatively small number of neurons can achieve similar or better performance than both traditional thermodynamic and neural network models. The developed EPNN approach provides alternative methods for efficiently modeling complex, dynamic or steady-state chemical processes. EPNN is capable of producing symbolic empirical formulae for chemical processes, regardless of whether or not traditional thermodynamic models are available or can be applied. The EPNN approach does overcome some of the limitations of traditional thermodynamic /transport models and traditional neural network models

A Review of using Data Mining Techniques in Power Plants

Data mining techniques and their applications have developed rapidly during the last two decades. This paper reviews application of data mining techniques in power systems, specially in power plants, through a survey of literature between the year 2000 and 2015. Keyword indices, articles’ abstracts and conclusions were used to classify more than 86 articles about application of data mining in power plants, from many academic journals and research centers. Because this paper concerns about application of data mining in power plants; the paper started by providing a brief introduction about data mining and power systems to give the reader better vision about these two different disciplines. This paper presents a comprehensive survey of the collected articles and classifies them according to three categories: the used techniques, the problem and the application area. From this review we found that data mining techniques (classification, regression, clustering and association rules) could be used to solve many types of problems in power plants, like predicting the amount of generated power, failure prediction, failure diagnosis, failure detection and many others. Also there is no standard technique that could be used for a specific problem. Application of data mining in power plants is a rich research area and still needs more exploration

Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Knowing the catalytic turnover numbers of enzymes is essential for understanding the growth rate, proteome composition, and physiology of organisms, but experimental data on enzyme turnover numbers is sparse and noisy. Here, we demonstrate that machine learning can successfully predict catalytic turnover numbers in Escherichia coli based on integrated data on enzyme biochemistry, protein structure, and network context. We identify a diverse set of features that are consistently predictive for both in vivo and in vitro enzyme turnover rates, revealing novel protein structural correlates of catalytic turnover. We use our predictions to parameterize two mechanistic genome-scale modelling frameworks for proteome-limited metabolism, leading to significantly higher accuracy in the prediction of quantitative proteome data than previous approaches. The presented machine learning models thus provide a valuable tool for understanding metabolism and the proteome at the genome scale, and elucidate structural, biochemical, and network properties that underlie enzyme kinetics

Experimental investigation and modelling of the heating value and elemental composition of biomass through artificial intelligence

Abstract: Knowledge advancement in artificial intelligence and blockchain technologies provides new potential predictive reliability for biomass energy value chain. However, for the prediction approach against experimental methodology, the prediction accuracy is expected to be high in order to develop a high fidelity and robust software which can serve as a tool in the decision making process. The global standards related to classification methods and energetic properties of biomass are still evolving given different observation and results which have been reported in the literature. Apart from these, there is a need for a holistic understanding of the effect of particle sizes and geospatial factors on the physicochemical properties of biomass to increase the uptake of bioenergy. Therefore, this research carried out an experimental investigation of some selected bioresources and also develops high-fidelity models built on artificial intelligence capability to accurately classify the biomass feedstocks, predict the main elemental composition (Carbon, Hydrogen, and Oxygen) on dry basis and the Heating value in (MJ/kg) of biomass...Ph.D. (Mechanical Engineering Science

Predicting Skin Permeability by means of Computational Approaches : Reliability and Caveats in Pharmaceutical Studies

© 2019 American Chemical Society.The skin is the main barrier between the internal body environment and the external one. The characteristics of this barrier and its properties are able to modify and affect drug delivery and chemical toxicity parameters. Therefore, it is not surprising that permeability of many different compounds has been measured through several in vitro and in vivo techniques. Moreover, many different in silico approaches have been used to identify the correlation between the structure of the permeants and their permeability, to reproduce the skin behavior, and to predict the ability of specific chemicals to permeate this barrier. A significant number of issues, like interlaboratory variability, experimental conditions, data set building rationales, and skin site of origin and hydration, still prevent us from obtaining a definitive predictive skin permeability model. This review wants to show the main advances and the principal approaches in computational methods used to predict this property, to enlighten the main issues that have arisen, and to address the challenges to develop in future research.Peer reviewedFinal Accepted Versio

Surface tension of binary mixtures containing environmentally friendly ionic liquids: Insights from artifcial intelligence

The surface tension (ST) of ionic liquids (ILs) and their accompanying mixtures allows engineers to accurately arrange new processes on the industrial scale. Without any doubt, experimental methods for the specification of the ST of every supposable IL and its mixtures with other compounds would be an arduous job. Also, experimental measurements are effortful and prohibitive; thus, a precise estimation of the property via a dependable method would be greatly desirable. For doing this task, a new modeling method according to artificial neural network (ANN) disciplined by four optimization algorithms, namely teaching�learning-based optimization (TLBO), particle swarm optimization (PSO), genetic algorithm (GA) and imperialist competitive algorithm (ICA), has been suggested to estimate ST of the binary ILs mixtures. For training and testing the applied network, a set of 748 data points of binary ST of IL systems within the temperature range of 283.1�348.15 K was utilized. Furthermore, an outlier analysis was used to discover doubtful data points. Gained values of MSE & R2 were 0.0000007 and 0.993, 0.0000002 and 0.998, 0.0000004 and 0.996 and 0.0000006 and 0.994 for the ICA-ANN, TLBO-ANN, PSO-ANN and GA-ANN, respectively. Results demonstrated that the experimental data and predicted values of the TLBO-ANN model for such target are wholly matched

Benchmarking Materials Property Prediction Methods: The Matbench Test Set and Automatminer Reference Algorithm

We present a benchmark test suite and an automated machine learning procedure for evaluating supervised machine learning (ML) models for predicting properties of inorganic bulk materials. The test suite, Matbench, is a set of 13 ML tasks that range in size from 312 to 132k samples and contain data from 10 density functional theory-derived and experimental sources. Tasks include predicting optical, thermal, electronic, thermodynamic, tensile, and elastic properties given a materials composition and/or crystal structure. The reference algorithm, Automatminer, is a highly-extensible, fully-automated ML pipeline for predicting materials properties from materials primitives (such as composition and crystal structure) without user intervention or hyperparameter tuning. We test Automatminer on the Matbench test suite and compare its predictive power with state-of-the-art crystal graph neural networks and a traditional descriptor-based Random Forest model. We find Automatminer achieves the best performance on 8 of 13 tasks in the benchmark. We also show our test suite is capable of exposing predictive advantages of each algorithm - namely, that crystal graph methods appear to outperform traditional machine learning methods given ~10^4 or greater data points. The pre-processed, ready-to-use Matbench tasks and the Automatminer source code are open source and available online (http://hackingmaterials.lbl.gov/automatminer/). We encourage evaluating new materials ML algorithms on the MatBench benchmark and comparing them against the latest version of Automatminer.Comment: Main text, supplemental inf