Approaching coupled cluster accuracy with a general-purpose neural network potential through transfer learning.
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ABSTRACT:
SUBMITTER: Smith JS
PROVIDER: S-EPMC6602931 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Appropriately identifying and treating molecules and materials with significant multi-reference (MR) character is crucial for achieving high data fidelity in virtual high-throughput screening (VHTS). Despite development of numerous MR diagnostics, the extent to which a single value of such a diagnostic indicates the MR effect on a chemical property prediction is not well established. We evaluate MR diagnostics for over 10 000 transition-metal complexes (TMCs) and compare to those for organic molecules. We observe that only some MR diagnostics are transferable from one chemical space to another. By studying the influence of MR character on chemical properties (i.e., MR effect) that involve multiple potential energy surfaces (i.e., adiabatic spin splitting, ΔE H-L, and ionization potential, IP), we show that differences in MR character are more important than the cumulative degree of MR character in predicting the magnitude of an MR effect. Motivated by this observation, we build transfer learning models to predict CCSD(T)-level adiabatic ΔE H-L and IP from lower levels of theory. By combining these models with uncertainty quantification and multi-level modeling, we introduce a multi-pronged strategy that accelerates data acquisition by at least a factor of three while achieving coupled cluster accuracy (i.e., to within 1 kcal mol-1 MAE) for robust VHTS.
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Project description:Pneumonitis is an infectious disease that causes the inflammation of the air sac. It can be life-threatening to the very young and elderly. Detection of pneumonitis from X-ray images is a significant challenge. Early detection and assistance with diagnosis can be crucial. Recent developments in the field of deep learning have significantly improved their performance in medical image analysis. The superior predictive performance of the deep learning methods makes them ideal for pneumonitis classification from chest X-ray images. However, training deep learning models can be cumbersome and resource-intensive. Reusing knowledge representations of public models trained on large-scale datasets through transfer learning can help alleviate these challenges. In this paper, we compare various image classification models based on transfer learning with well-known deep learning architectures. The Kaggle chest X-ray dataset was used to evaluate and compare our models. We apply basic data augmentation and fine-tune our feed-forward classification head on the models pretrained on the ImageNet dataset. We observed that the DenseNet201 model outperforms other models with an AUROC score of 0.966 and a recall score of 0.99. We also visualize the class activation maps from the DenseNet201 model to interpret the patterns recognized by the model for prediction.
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Project description:Elemental phosphorus is attracting growing interest across fundamental and applied fields of research. However, atomistic simulations of phosphorus have remained an outstanding challenge. Here, we show that a universally applicable force field for phosphorus can be created by machine learning (ML) from a suitably chosen ensemble of quantum-mechanical results. Our model is fitted to density-functional theory plus many-body dispersion (DFT + MBD) data; its accuracy is demonstrated for the exfoliation of black and violet phosphorus (yielding monolayers of "phosphorene" and "hittorfene"); its transferability is shown for the transition between the molecular and network liquid phases. An application to a phosphorene nanoribbon on an experimentally relevant length scale exemplifies the power of accurate and flexible ML-driven force fields for next-generation materials modelling. The methodology promises new insights into phosphorus as well as other structurally complex, e.g., layered solids that are relevant in diverse areas of chemistry, physics, and materials science.
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Project description:As the industry gradually enters the stage of unmanned and intelligent, factories in the future need to realize intelligent monitoring and diagnosis and maintenance of parts and components. In order to achieve this goal, it is first necessary to accurately identify and classify the parts in the factory. However, the existing literature rarely studies the classification and identification of parts of the entire factory. Due to the lack of existing data samples, this paper studies the identification and classification of small samples of industrial machine parts. In order to solve this problem, this paper establishes a convolutional neural network model based on the InceptionNet-V3 pretrained model through migration learning. Through experimental design, the influence of data expansion, learning rate and optimizer algorithm on the model effectiveness is studied, and the optimal model was finally determined, and the test accuracy rate reaches 99.74%. By comparing with the accuracy of other classifiers, the experimental results prove that the convolutional neural network model based on transfer learning can effectively solve the problem of recognition and classification of industrial machine parts with small samples and the idea of transfer learning can also be further promoted.
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Project description:BackgroundTo diagnose key pathologies of age-related macular degeneration (AMD) and diabetic macular edema (DME) quickly and accurately, researchers attempted to develop effective artificial intelligence methods by using medical images.ResultsA convolutional neural network (CNN) with transfer learning capability is proposed and appropriate hyperparameters are selected for classifying optical coherence tomography (OCT) images of AMD and DME. To perform transfer learning, a pre-trained CNN model is used as the starting point for a new CNN model for solving related problems. The hyperparameters (parameters that have set values before the learning process begins) in this study were algorithm hyperparameters that affect learning speed and quality. During training, different CNN-based models require different algorithm hyperparameters (e.g., optimizer, learning rate, and mini-batch size). Experiments showed that, after transfer learning, the CNN models (8-layer Alexnet, 22-layer Googlenet, 16-layer VGG, 19-layer VGG, 18-layer Resnet, 50-layer Resnet, and a 101-layer Resnet) successfully classified OCT images of AMD and DME.ConclusionsThe experimental results further showed that, after transfer learning, the VGG19, Resnet101, and Resnet50 models with appropriate algorithm hyperparameters had excellent capability and performance in classifying OCT images of AMD and DME.
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Project description:To understand how the central nervous system performs computations using recurrent neuronal circuitry, simulations have become an indispensable tool for theoretical neuroscience. To study neuronal circuits and their ability to self-organize, increasing attention has been directed toward synaptic plasticity. In particular spike-timing-dependent plasticity (STDP) creates specific demands for simulations of spiking neural networks. On the one hand a high temporal resolution is required to capture the millisecond timescale of typical STDP windows. On the other hand network simulations have to evolve over hours up to days, to capture the timescale of long-term plasticity. To do this efficiently, fast simulation speed is the crucial ingredient rather than large neuron numbers. Using different medium-sized network models consisting of several thousands of neurons and off-the-shelf hardware, we compare the simulation speed of the simulators: Brian, NEST and Neuron as well as our own simulator Auryn. Our results show that real-time simulations of different plastic network models are possible in parallel simulations in which numerical precision is not a primary concern. Even so, the speed-up margin of parallelism is limited and boosting simulation speeds beyond one tenth of real-time is difficult. By profiling simulation code we show that the run times of typical plastic network simulations encounter a hard boundary. This limit is partly due to latencies in the inter-process communications and thus cannot be overcome by increased parallelism. Overall, these results show that to study plasticity in medium-sized spiking neural networks, adequate simulation tools are readily available which run efficiently on small clusters. However, to run simulations substantially faster than real-time, special hardware is a prerequisite.
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Project description:BACKGROUND: The implementation of new medical knowledge into general practice is a complex process. Blended learning may offer an effective and efficient educational intervention to reduce the knowledge-to-practice gap. The aim of this study was to compare knowledge acquisition about dementia management between a blended learning approach using online modules in addition to quality circles (QCs) and QCs alone. METHODS: In this cluster-randomised trial with QCs as clusters and general practitioners (GPs) as participants, 389 GPs from 26 QCs in the western part of Germany were invited to participate. Data on the GPs' knowledge were obtained at three points in time by means of a questionnaire survey. Primary outcome was the knowledge gain before and after the interventions. A subgroup analysis of the users of the online modules was performed. RESULTS: 166 GPs were available for analysis and filled out a knowledge test at least two times. A significant increase of knowledge was found in both groups that indicated positive learning effects of both approaches. However, there was no significant difference between the groups. A subgroup analysis of the GPs who self-reported that they had actually used the online modules showed that they had a significant increase in their knowledge scores. CONCLUSION: A blended learning approach was not superior to a QCs approach for improving knowledge about dementia management. However, a subgroup of GPs who were motivated to actually use the online modules had a gain in knowledge. TRIAL REGISTRATION: Current Controlled Trials ISRCTN36550981.
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Project description:BackgroundPredicting hepatocellular carcinoma (HCC) prognosis is important for treatment selection, and it is increasingly interesting to predict prognosis through gene expression data. Currently, the prognosis remains of low accuracy due to the high dimension but small sample size of liver cancer omics data. In previous studies, a transfer learning strategy has been developed by pre-training models on similar cancer types and then fine-tuning the pre-trained models on the target dataset. However, transfer learning has limited performance since other cancer types are similar at different levels, and it is not trivial to balance the relations with different cancer types.MethodsHere, we propose an adaptive transfer-learning-based deep Cox neural network (ATRCN), where cancers are represented by 12 phenotype and 10 genotype features, and suitable cancers were adaptively selected for model pre-training. In this way, the pre-trained model can learn valuable prior knowledge from other cancer types while reducing the biases.ResultsATRCN chose pancreatic and stomach adenocarcinomas as the pre-training cancers, and the experiments indicated that our method improved the C-index of 3.8% by comparing with traditional transfer learning methods. The independent tests on three additional HCC datasets proved the robustness of our model. Based on the divided risk subgroups, we identified 10 HCC prognostic markers, including one new prognostic marker, TTC36. Further wet experiments indicated that TTC36 is associated with the progression of liver cancer cells.ConclusionThese results proved that our proposed deep-learning-based method for HCC prognosis prediction is robust, accurate, and biologically meaningful.
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