scholarly journals Machine learning for laser-induced electron diffraction imaging of molecular structures

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Xinyao Liu ◽  
Kasra Amini ◽  
Aurelien Sanchez ◽  
Blanca Belsa ◽  
Tobias Steinle ◽  
...  
Keyword(s):  
Machine Learning ◽  
Electron Diffraction ◽  
Learning Algorithm ◽  
Structural Complexity ◽  
Solution Space ◽  
Molecular Structures ◽  
Global Extremum ◽  
Dimensional Solution ◽  
Time Resolved ◽  
Diffraction Imaging

AbstractUltrafast diffraction imaging is a powerful tool to retrieve the geometric structure of gas-phase molecules with combined picometre spatial and attosecond temporal resolution. However, structural retrieval becomes progressively difficult with increasing structural complexity, given that a global extremum must be found in a multi-dimensional solution space. Worse, pre-calculating many thousands of molecular configurations for all orientations becomes simply intractable. As a remedy, here, we propose a machine learning algorithm with a convolutional neural network which can be trained with a limited set of molecular configurations. We demonstrate structural retrieval of a complex and large molecule, Fenchone (C10H16O), from laser-induced electron diffraction (LIED) data without fitting algorithms or ab initio calculations. Retrieval of such a large molecular structure is not possible with other variants of LIED or ultrafast electron diffraction. Combining electron diffraction with machine learning presents new opportunities to image complex and larger molecules in static and time-resolved studies.

scholarly journals Quantum state tomography of molecules by ultrafast diffraction

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ming Zhang ◽  
Shuqiao Zhang ◽  
Yanwei Xiong ◽  
Hankai Zhang ◽  
Anatoly A. Ischenko ◽  
...  
Keyword(s):  
Electron Diffraction ◽  
Quantum State ◽  
Degrees Of Freedom ◽  
Molecular Structures ◽  
Electron Diffraction Data ◽  
Ultrafast Electron Diffraction ◽  
Time Resolved ◽  
Quantum State Tomography ◽  
New Variant ◽  
State Tomography

AbstractUltrafast electron diffraction and time-resolved serial crystallography are the basis of the ongoing revolution in capturing at the atomic level of detail the structural dynamics of molecules. However, most experiments capture only the probability density of the nuclear wavepackets to determine the time-dependent molecular structures, while the full quantum state has not been accessed. Here, we introduce a framework for the preparation and ultrafast coherent diffraction from rotational wave packets of molecules, and we establish a new variant of quantum state tomography for ultrafast electron diffraction to characterize the molecular quantum states. The ability to reconstruct the density matrix, which encodes the amplitude and phase of the wavepacket, for molecules of arbitrary degrees of freedom, will enable the reconstruction of a quantum molecular movie from experimental x-ray or electron diffraction data.

Complete and representative training of neural networks: A generalization study using double noise injection and natural images

Geophysics ◽  
2021 ◽  
pp. 1-43
Author(s):  
Chao Zhang ◽  
Mirko van der Baan
Keyword(s):  
Machine Learning ◽  
Neural Networks ◽  
Seismic Data ◽  
Learning Algorithm ◽  
Random Noise ◽  
Solution Space ◽  
Natural Images ◽  
Training Data ◽  
Noisy Input ◽  
Noise Injection

Neural networks hold substantial promise to automate various processing and interpretation tasks. Yet their performance is often sub-optimal compared with standard but more closely guided approaches. Lack of performance is often attributed to poor generalization, in particular if fewer training examples are provided than free parameters exist in the machine learning algorithm. In this case the training data are typically memorized instead of the algorithm learning the underlying general trends. Network generalization is improved if the provided samples are representative, in that they describe all features of interest well. We argue that a more subtle condition preventing poor performance is that the provided examples must also be complete; the examples must span the full solution space. Ensuring completeness during training is challenging unless the target application is well understood. We illustrate that one possible solution is to make the problem more general if this greatly increases the number of available training data. For instance, if seismic images are treated as a subclass of natural images, then a deep-learning-based denoiser for seismic data can be trained using exclusively natural images. The latter are widely available. The resulting denoising algorithm has never seen any seismic data during the training stage; yet it displays a performance comparable to standard and advanced random-noise reduction methods. We exclude any seismic data during training to demonstrate the natural images are both complete and representative for this specific task. Furthermore, we apply a novel approach to increase the amount of training data known as double noise injection, providing both noisy input and output images during the training process. Given the importance of network generalization, we hope that insights gained in this study may help improve the performance of a range of machine learning applications in geophysics.

scholarly journals Interpretable Machine Learning for Perturbation Biology

2019 ◽  
Author(s):  
Bo Yuan ◽  
Ciyue Shen ◽  
Augustin Luna ◽  
Anil Korkut ◽  
Debora S. Marks ◽  
...  
Keyword(s):  
Machine Learning ◽  
Cell Biology ◽  
Computational Models ◽  
De Novo ◽  
Hybrid Approach ◽  
Solution Space ◽  
Training Data ◽  
Modeling Framework ◽  
Dimensional Solution ◽  
Wide Range

AbstractSystematic perturbation of cells followed by comprehensive measurements of molecular and phenotypic responses provides an informative data resource for constructing computational models of cell biology. Models that generalize well beyond training data can be used to identify combinatorial perturbations of potential therapeutic interest. Major challenges for machine learning on large biological datasets are to find global optima in an enormously complex multi-dimensional solution space and to mechanistically interpret the solutions. To address these challenges, we introduce a hybrid approach that combines explicit mathematical models of dynamic cell biological processes with a machine learning framework, implemented in Tensorflow. We tested the modeling framework on a perturbation-response dataset for a melanoma cell line after drug treatments. The models can be efficiently trained to accurately describe cellular behavior, as tested by cross-validation. Even though completely data-driven and independent of prior knowledge, the resulting de novo network models recapitulate some known interactions. The main predictive application is the identification of combinatorial candidates for cancer therapy. The approach is readily applicable to a wide range of kinetic models of cell biology.

Electron Channeling Patterns

1977 ◽  
Vol 35 ◽  
pp. 12-13
Author(s):  
David C. Joy
Keyword(s):  
Electron Diffraction ◽  
Incidence Angle ◽  
Photographic Plate ◽  
Diffraction Effect ◽  
Angle Of Incidence ◽  
Bulk Single Crystal ◽  
Time Resolved ◽  
Electron Channeling ◽  
Spatially Resolved ◽  
Large Bulk

Electron channeling patterns (ECP) were first found by Coates (1967) while observing a large bulk, single crystal of silicon in a scanning electron microscope. The geometric pattern visible was shown to be produced as a result of the changes in the angle of incidence, between the beam and the specimen surface normal, which occur when the sample is examined at low magnification (Booker, Shaw, Whelan and Hirsch 1967).A conventional electron diffraction pattern consists of an angularly resolved intensity distribution in space which may be directly viewed on a fluorescent screen or recorded on a photographic plate. An ECP, on the other hand, is produced as the result of changes in the signal collected by a suitable electron detector as the incidence angle is varied. If an integrating detector is used, or if the beam traverses the surface at a fixed angle, then no channeling contrast will be observed. The ECP is thus a time resolved electron diffraction effect. It can therefore be related to spatially resolved diffraction phenomena by an application of the concepts of reciprocity (Cowley 1969).

Machine Learning Algorithm to Predict Early Complications after Brain Tumor Surgery

2018 ◽  
Author(s):  
C.H.B. van Niftrik ◽  
F. van der Wouden ◽  
V. Staartjes ◽  
J. Fierstra ◽  
M. Stienen ◽  
...  
Keyword(s):  
Machine Learning ◽  
Brain Tumor ◽  
Learning Algorithm ◽  
Machine Learning Algorithm ◽  
Tumor Surgery ◽  
Early Complications ◽  
Brain Tumor Surgery

Design of English text-to-speech conversion algorithm based on machine learning

2020 ◽  
pp. 1-12
Author(s):  
Li Dongmei
Keyword(s):  
Machine Learning ◽  
Speech Synthesis ◽  
Feature Recognition ◽  
Learning Algorithm ◽  
Morphological Structure ◽  
English Text ◽  
Text To Speech ◽  
Part Of Speech ◽  
Modern Computer ◽  
Conversion Algorithm

English text-to-speech conversion is the key content of modern computer technology research. Its difficulty is that there are large errors in the conversion process of text-to-speech feature recognition, and it is difficult to apply the English text-to-speech conversion algorithm to the system. In order to improve the efficiency of the English text-to-speech conversion, based on the machine learning algorithm, after the original voice waveform is labeled with the pitch, this article modifies the rhythm through PSOLA, and uses the C4.5 algorithm to train a decision tree for judging pronunciation of polyphones. In order to evaluate the performance of pronunciation discrimination method based on part-of-speech rules and HMM-based prosody hierarchy prediction in speech synthesis systems, this study constructed a system model. In addition, the waveform stitching method and PSOLA are used to synthesize the sound. For words whose main stress cannot be discriminated by morphological structure, label learning can be done by machine learning methods. Finally, this study evaluates and analyzes the performance of the algorithm through control experiments. The results show that the algorithm proposed in this paper has good performance and has a certain practical effect.

Intelligent system of English composition scoring model based on improved machine learning algorithm

2020 ◽  
pp. 1-11
Author(s):  
Jie Liu ◽  
Lin Lin ◽  
Xiufang Liang
Keyword(s):  
Machine Learning ◽  
Evaluation System ◽  
Intelligent System ◽  
Learning Algorithm ◽  
Learning Algorithms ◽  
Machine Learning Algorithms ◽  
Assessment System ◽  
English Composition ◽  
Region Extraction ◽  
Constraint Model

The online English teaching system has certain requirements for the intelligent scoring system, and the most difficult stage of intelligent scoring in the English test is to score the English composition through the intelligent model. In order to improve the intelligence of English composition scoring, based on machine learning algorithms, this study combines intelligent image recognition technology to improve machine learning algorithms, and proposes an improved MSER-based character candidate region extraction algorithm and a convolutional neural network-based pseudo-character region filtering algorithm. In addition, in order to verify whether the algorithm model proposed in this paper meets the requirements of the group text, that is, to verify the feasibility of the algorithm, the performance of the model proposed in this study is analyzed through design experiments. Moreover, the basic conditions for composition scoring are input into the model as a constraint model. The research results show that the algorithm proposed in this paper has a certain practical effect, and it can be applied to the English assessment system and the online assessment system of the homework evaluation system algorithm system.

Feature extraction and prediction of Dengue Outbreaks

2020 ◽  
pp. 216-222
Author(s):  
Kunal Parikh ◽  
Tanvi Makadia ◽  
Harshil Patel
Keyword(s):  
Public Health ◽  
Machine Learning ◽  
Developing Countries ◽  
Feature Extraction ◽  
Predictive Analytics ◽  
Learning Algorithm ◽  
Machine Learning Algorithm ◽  
Health Concerns ◽  
The World ◽  
Dengue Outbreaks

Dengue is unquestionably one of the biggest health concerns in India and for many other developing countries. Unfortunately, many people have lost their lives because of it. Every year, approximately 390 million dengue infections occur around the world among which 500,000 people are seriously infected and 25,000 people have died annually. Many factors could cause dengue such as temperature, humidity, precipitation, inadequate public health, and many others. In this paper, we are proposing a method to perform predictive analytics on dengue’s dataset using KNN: a machine-learning algorithm. This analysis would help in the prediction of future cases and we could save the lives of many.

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