scholarly journals Machine Learning–Based Computational Models Derived From Large-Scale Radiographic-Radiomic Images Can Help Predict Adverse Histopathological Status of Gastric Cancer

2019 ◽  
Vol 10 (10) ◽  
pp. e00079 ◽  
Author(s):  
Qiong Li ◽  
Liang Qi ◽  
Qiu-Xia Feng ◽  
Chang Liu ◽  
Shu-Wen Sun ◽  
...  
2020 ◽  
Author(s):  
Ali Vakilian

Large volumes of available data have led to the emergence of new computational models for data analysis. One such model is captured by the notion of streaming algorithms: given a sequence of N items, the goal is to compute the value of a given function of the input items by a small number of passes and using a sublinear amount of space in N. Streaming algorithms have applications in many areas such as networking and large scale machine learning. Despite a huge amount of work on this area over the last two decades, there are multiple aspects of streaming algorithms that remained poorly understood, such as (a) streaming algorithms for combinatorial optimization problems and (b) incorporating modern machine learningtechniques in the design of streaming algorithms. In the first part of this thesis, we will describe (essentially) optimal streaming algorithms for set cover and maximum coverage, two classic problems in combinatorial optimization. Next, in the second part, we will show how to augment classic streaming algorithms of the frequency estimation and low-rank approximation problems with machine learning oracles in order to improve their space-accuracy tradeoffs. The new algorithms combine the benefits of machine learning with the formal guarantees available through algorithm design theory.


2013 ◽  
Author(s):  
Eric Cosatto ◽  
Pierre-Francois Laquerre ◽  
Christopher Malon ◽  
Hans-Peter Graf ◽  
Akira Saito ◽  
...  

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.


2021 ◽  
Author(s):  
Norberto Sánchez-Cruz ◽  
Jose L. Medina-Franco

<p>Epigenetic targets are a significant focus for drug discovery research, as demonstrated by the eight approved epigenetic drugs for treatment of cancer and the increasing availability of chemogenomic data related to epigenetics. This data represents a large amount of structure-activity relationships that has not been exploited thus far for the development of predictive models to support medicinal chemistry efforts. Herein, we report the first large-scale study of 26318 compounds with a quantitative measure of biological activity for 55 protein targets with epigenetic activity. Through a systematic comparison of machine learning models trained on molecular fingerprints of different design, we built predictive models with high accuracy for the epigenetic target profiling of small molecules. The models were thoroughly validated showing mean precisions up to 0.952 for the epigenetic target prediction task. Our results indicate that the herein reported models have considerable potential to identify small molecules with epigenetic activity. Therefore, our results were implemented as freely accessible and easy-to-use web application.</p>


2019 ◽  
Author(s):  
Ryther Anderson ◽  
Achay Biong ◽  
Diego Gómez-Gualdrón

<div>Tailoring the structure and chemistry of metal-organic frameworks (MOFs) enables the manipulation of their adsorption properties to suit specific energy and environmental applications. As there are millions of possible MOFs (with tens of thousands already synthesized), molecular simulation, such as grand canonical Monte Carlo (GCMC), has frequently been used to rapidly evaluate the adsorption performance of a large set of MOFs. This allows subsequent experiments to focus only on a small subset of the most promising MOFs. In many instances, however, even molecular simulation becomes prohibitively time consuming, underscoring the need for alternative screening methods, such as machine learning, to precede molecular simulation efforts. In this study, as a proof of concept, we trained a neural network as the first example of a machine learning model capable of predicting full adsorption isotherms of different molecules not included in the training of the model. To achieve this, we trained our neural network only on alchemical species, represented only by their geometry and force field parameters, and used this neural network to predict the loadings of real adsorbates. We focused on predicting room temperature adsorption of small (one- and two-atom) molecules relevant to chemical separations. Namely, argon, krypton, xenon, methane, ethane, and nitrogen. However, we also observed surprisingly promising predictions for more complex molecules, whose properties are outside the range spanned by the alchemical adsorbates. Prediction accuracies suitable for large-scale screening were achieved using simple MOF (e.g. geometric properties and chemical moieties), and adsorbate (e.g. forcefield parameters and geometry) descriptors. Our results illustrate a new philosophy of training that opens the path towards development of machine learning models that can predict the adsorption loading of any new adsorbate at any new operating conditions in any new MOF.</div>


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