QSAR study of amidino bis-benzimidazole derivatives as potent anti-malarial agents against Plasmodium falciparum

2013 ◽  
Vol 67 (11) ◽  
Author(s):  
Apilak Worachartcheewan ◽  
Chanin Nantasenamat ◽  
Chartchalerm Isarankura-Na-Ayudhya ◽  
Virapong Prachayasittikul
Keyword(s):  
Plasmodium Falciparum ◽  
Correlation Coefficient ◽  
Cross Validation ◽  
Mean Squared Error ◽  
Sum Of Squares ◽  
Atomic Masses ◽  
Root Mean Squared Error ◽  
Squared Error ◽  
Qsar Models ◽  
Leave One Out

AbstractA data set of amidino bis-benzimidazoles, in particular 2′-arylsubstituted-1H,1′H-[2,5′]bisbenzimidazolyl-5-carboximidine derivatives with anti-malarial activity against Plasmodium falciparum was employed in investigating the quantitative structure-activity relationship (QSAR). Quantum chemical and molecular descriptors were obtained from B3LYP/6-31g(d) calculations and Dragon software, respectively. Significant variables, which included total energy (E T), highest occupied molecular orbital (HOMO), Moran autocorrelation-lag3/weighted by atomic masses (MATS3m), Geary autocorrelation-lag8/weighted by atomic masses (GATS8m), and 3D-MoRSEsignal 11/weighted by atomic Sanderson electronegativities (Mor11e), were used in the construction of QSAR models using multiple linear regression (MLR) and artificial neural network (ANN). The results indicated that the predictive models for both the MLR and ANN approaches using leave-one-out cross-validation afforded a good performance in modelling the anti-malarial activity against P. falciparum as observed by correlation coefficients of leave-one-out cross-validation (R LOO-CV) of 0.9760 and 0.9821, respectively, root mean squared error of leave-one-out cross-validation (RMSELOO-CV) of 0.1301 and 0.1102, respectively, and predictivity of leave-one-out cross-validation (Q LOO-CV2) of 0.9526 and 0.9645, respectively. Model validation was performed using an external testing set and the results suggested that the model provided good predictivity for both MLR and ANN models with correlation coefficient of the external set (R Ext) values of 0.9978 and 0.9844, respectively, root mean squared error of the external set (RMSEExt) of 0.0764 and 0.1302 respectively, and predictivity of the external set (Q Ext2) of 0.9956 and 0.9690, respectively. Furthermore, the robustness of the QSAR models is corroborated by a number of statistical parameters, comprising adjusted correlation coefficient (R Adj2), standard deviation (s), predicted residual sum of squares (PRESS), standard error of prediction (SDEP), total sum of squares deviation (SSY), and quality factor (Q). The QSAR models so constructed provide pertinent insights for the future design of anti-malarial agents.

Cross-Validation of Field-Based Assessments of Body Composition for Individuals with Down Syndrome

2005 ◽  
Vol 22 (2) ◽  
pp. 198-206 ◽  
Author(s):  
Phillip C. Usera ◽  
John T. Foley ◽  
Joonkoo Yun
Keyword(s):  
Body Composition ◽  
Down Syndrome ◽  
Body Fat ◽  
Cross Validation ◽  
Mean Squared Error ◽  
The Body ◽  
Anthropometric Measurements ◽  
Prediction Equations ◽  
Root Mean Squared Error ◽  
Squared Error

The purpose of this study was to cross-validate skinfold and anthropometric measurements for individuals with Down syndrome (DS). Estimated body fat of 14 individuals with DS and 13 individuals without DS was compared between criterion measurement (BOP POD®) and three prediction equations. Correlations between criterion and field-based tests for non-DS group and DS groups ranged from .81 – .94 and .11 – .54, respectively. Root-Mean-Squared-Error was employed to examine the amount of error on the field-based measurements. A MANOVA indicated significant differences in accuracy between groups for Jackson’s equation and Lohman’s equation. Based on the results, efforts should now be directed toward developing new equations that can assess the body composition of individuals with DS in a clinically feasible way.

scholarly journals Multivariate calibration applied in UV-Vis spectroscopy data to determine total acidity in wines

2015 ◽  
Vol 6 (1) ◽  
pp. 70 ◽  
Author(s):  
Cristiane Da Silva Morais ◽  
Luiza Mariano Leme ◽  
Patrícia Valderrama ◽  
Paulo Henrique Março
Keyword(s):  
Correlation Coefficient ◽  
Multivariate Calibration ◽  
Mean Squared Error ◽  
Reference Method ◽  
Total Acidity ◽  
Waste Generation ◽  
Root Mean Squared Error ◽  
Squared Error ◽  
Vis Spectroscopy ◽  
Significant Difference

<p>Classical methods, as titration to evaluate acidity, bring disadvantage to waste generation and mainly time consumption. Therefore, is necessary to develop an alternative methodology for measuring total acidity of wine samples. The Ultraviolet and Visible spectrophotometric technique can be introduced in the industry to monitoring this parameter because it enables rapid and efficient analysis without waste generation. Thereby, in this study were developed multivariate calibration models using the Partial Least Squares (PLS) regression between the UV-Vis spectra of wines and total acidity values determined by the reference method. The figures of merit for the models were Root Mean Squared Error of Calibration (RMSEC), Root Mean Squared Error of Prediction (RMSEP) and correlation coefficient (R). To the white wines, the model obtained showed RMSEC and RMSEP of 5.87 meq L<sup>-1</sup> and 6.58 meq L<sup>-1</sup>, respectively. To the red wines, the model presented RMSEC 0.71 meq L<sup>-1</sup> and RMSEP 6.93 meq L<sup>-1</sup>. Both models presented correlation coefficient of 0.71. A paired t-test showed no significant difference between titration and spectrophotometric methods at a confidence level of 95%. Therefore, the advantages offered by the UV-Vis method are attractive to industrial requirements, suggesting that studies focused on optical methods and multivariate calibration can be interesting and deserve to be observed in further studies.</p><p>&nbsp;</p><p>DOI: 10.14685/rebrapa.v6i1.193</p><p>&nbsp;</p>

scholarly journals PENERAPAN ALGORITMA RANDOM FOREST UNTUK IDENTIFIKASI DEHIDRASI BERBASIS CITRA URINE

2020 ◽  
Vol 6 (3) ◽  
pp. 49-54
Author(s):  
Niyalatul Muna ◽  
Faisal Lutfi Afriansyah ◽  
Ameng Bagus Suprayogy
Keyword(s):  
Random Forest ◽  
Cross Validation ◽  
Mean Squared Error ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Root Mean Squared Error ◽  
Squared Error

Tingkat dehidrasi tidak hanya bisa dirasakan secara langsung akan tetapi dapat diamati dan dilihat secara fisik berbasis visual. Secara visual salah satu gejala dari dehidrasi dapat dilihat dari warna urine. Gejala ini biasanya tidak begitu diperhatikan dan dianggap biasa. Padahal gejala hipohidrasi atau dehidrasi merupakan dampak yang merugikan dari asupan air yang tidak memadai sehingga mempengaruhi warna urine yang dihasilkan. Kesulitan panca indra manusia membedakan gejala dehidrasi dan melihat perbedaan warna urine secara visual sering diterjemahkan berbeda-beda, dikarenakan tingkat kemiripan warna yang dihasilkan. Beberapa penelitian menunjukkan adanya pemanfaatan teknologi kamera dengan sistem cerdas dapat membantu kesulitan dan keterbatasan panca indra manusia. Penelitian ini menggunakan citra urine diambil dari sample orang dewasa yang dikelompokkan berdasarkan kategori warna urine hasil penelitian terdahulu. Pengambilan fitur dari setiap citra urine diambil nilai warna dari  YCbCr. Model warna yang dihasilkan dari setiap sampel akan diidentifikasi menggunakan algoritma Random Forest dengan cross-validation. Hasil dari percobaan yang dilakukan menunjukkan akurasi 90% dari 30 dataset yang diujikan dengan nilai precision 90.2%, recall 90%, Mean absolute error 0.2473, dan Root mean squared error sebesar 0.3208.

Use of reflectance spectroscopy to estimate the organic carbon and CaCO3 contents of soils

2012 ◽  
Vol 61 (2) ◽  
pp. 277-290 ◽  
Author(s):  
Ádám Csorba ◽  
Vince Láng ◽  
László Fenyvesi ◽  
Erika Michéli
Keyword(s):  
Organic Carbon ◽  
Least Squares ◽  
Partial Least Squares ◽  
Partial Least Squares Regression ◽  
Mean Squared Error ◽  
Reflectance Spectroscopy ◽  
Least Squares Regression ◽  
Root Mean Squared Error ◽  
Squared Error

Napjainkban egyre nagyobb igény mutatkozik olyan technológiák és módszerek kidolgozására és alkalmazására, melyek lehetővé teszik a gyors, költséghatékony és környezetbarát talajadat-felvételezést és kiértékelést. Ezeknek az igényeknek felel meg a reflektancia spektroszkópia, mely az elektromágneses spektrum látható (VIS) és közeli infravörös (NIR) tartományában (350–2500 nm) végzett reflektancia-mérésekre épül. Figyelembe véve, hogy a talajokról felvett reflektancia spektrum információban nagyon gazdag, és a vizsgált tartományban számos talajalkotó rendelkezik karakterisztikus spektrális „ujjlenyomattal”, egyetlen görbéből lehetővé válik nagyszámú, kulcsfontosságú talajparaméter egyidejű meghatározása. Dolgozatunkban, a reflektancia spektroszkópia alapjaira helyezett, a talajok ösz-szetételének meghatározását célzó módszertani fejlesztés első lépéseit mutatjuk be. Munkánk során talajok szervesszén- és CaCO3-tartalmának megbecslését lehetővé tévő többváltozós matematikai-statisztikai módszerekre (részleges legkisebb négyzetek módszere, partial least squares regression – PLSR) épülő prediktív modellek létrehozását és tesztelését végeztük el. A létrehozott modellek tesztelése során megállapítottuk, hogy az eljárás mindkét talajparaméter esetében magas R2értéket [R2(szerves szén) = 0,815; R2(CaCO3) = 0,907] adott. A becslés pontosságát jelző közepes négyzetes eltérés (root mean squared error – RMSE) érték mindkét paraméter esetében közepesnek mondható [RMSE (szerves szén) = 0,467; RMSE (CaCO3) = 3,508], mely a reflektancia mérési előírások standardizálásával jelentősen javítható. Vizsgálataink alapján arra a következtetésre jutottunk, hogy a reflektancia spektroszkópia és a többváltozós kemometriai eljárások együttes alkalmazásával, gyors és költséghatékony adatfelvételezési és -értékelési módszerhez juthatunk.

Comparative study of the pencil-and-paper and digital formats of the Spanish DARS scale

2021 ◽  
pp. 1-21
Author(s):  
Elsa Arrua-Duarte ◽  
Marta Migoya-Borja ◽  
Igor Barahona ◽  
Lena C. Quilty ◽  
Sakina J. Rizvi ◽  
...  
Keyword(s):  
Rating Scale ◽  
Mean Squared Error ◽  
Intraclass Correlation ◽  
Test Validity ◽  
Wilcoxon Test ◽  
Digital Version ◽  
Root Mean Squared Error ◽  
Squared Error ◽  
Digital Format ◽  
Paper And Pencil

Abstract Objective: The Dimensional Anhedonia Rating Scale (DARS) is a novel questionnaire to assess anhedonia of recent validation. In this work we aim to study the equivalence between the traditional paper-and-pencil and the digital format of DARS. Methods: 69 patients filled the DARS in a paper-based and digital versions. We assessed differences between formats (Wilcoxon test), validity of the scales (Kappa and Intraclass Correlation Coefficients), and reliability (Cronbach’s alpha and Guttman’s coefficient). We calculated the Comparative Fit Index and the Root Mean Squared Error associated with the proposed one-factor structure. Results: Total scores were higher for paper-based format. Significant differences between both formats were found for three items. The weighted Kappa coefficient was approximately 0.40 for most of the items. Internal consistency was greater than 0.94, and the Intraclass Correlation Coefficient for the digital version was 0.95 and 0.94 for the paper-and-pencil version (F= 16.7, p < 0.001). Comparative Adjustment Index was 0.97 for the digital DARS and 0.97 for the paper-and-pencil DARS, and Root Mean Squared Error was 0.11 for the digital DARS and 0.10 for the paper-and-pencil DARS. Conclusion: The digital DARS is consistent in many respects to the paper-and-pencil questionnaire, but equivalence with this format cannot be assumed without caution.

scholarly journals Prediction of the Toxicity of Binary Mixtures by QSAR Approach Using the Hypothetical Descriptors

2018 ◽  
Vol 19 (11) ◽  
pp. 3423 ◽  
Author(s):  
Ting Wang ◽  
Lili Tang ◽  
Feng Luan ◽  
M. Natália D. S. Cordeiro
Keyword(s):  
Correlation Coefficient ◽  
Binary Mixtures ◽  
Quantitative Structure Activity Relationship ◽  
Training Set ◽  
Statistical Parameters ◽  
Test Set ◽  
Qsar Models ◽  
Forward Stepwise ◽  
Leave One Out ◽  
External Test

Organic compounds are often exposed to the environment, and have an adverse effect on the environment and human health in the form of mixtures, rather than as single chemicals. In this paper, we try to establish reliable and developed classical quantitative structure–activity relationship (QSAR) models to evaluate the toxicity of 99 binary mixtures. The derived QSAR models were built by forward stepwise multiple linear regression (MLR) and nonlinear radial basis function neural networks (RBFNNs) using the hypothetical descriptors, respectively. The statistical parameters of the MLR model provided were N (number of compounds in training set) = 79, R2 (the correlation coefficient between the predicted and observed activities)= 0.869, LOOq2 (leave-one-out correlation coefficient) = 0.864, F (Fisher’s test) = 165.494, and RMS (root mean square) = 0.599 for the training set, and Next (number of compounds in external test set) = 20, R2 = 0.853, qext2 (leave-one-out correlation coefficient for test set)= 0.825, F = 30.861, and RMS = 0.691 for the external test set. The RBFNN model gave the statistical results, namely N = 79, R2 = 0.925, LOOq2 = 0.924, F = 950.686, RMS = 0.447 for the training set, and Next = 20, R2 = 0.896, qext2 = 0.890, F = 155.424, RMS = 0.547 for the external test set. Both of the MLR and RBFNN models were evaluated by some statistical parameters and methods. The results confirm that the built models are acceptable, and can be used to predict the toxicity of the binary mixtures.

scholarly journals Prediksi Indeks Harga Saham Gabungan (IHSG) Menggunakan Algoritma Neural Network

2018 ◽  
Vol 4 (1) ◽  
pp. 24
Author(s):  
Imam Halimi ◽  
Wahyu Andhyka Kusuma
Keyword(s):  
Neural Network ◽  
Data Mining ◽  
Linear Regression ◽  
Mean Squared Error ◽  
Composite Index ◽  
T Test ◽  
Sliding Windows ◽  
Root Mean Squared Error ◽  
Squared Error

Investasi saham merupakan hal yang tidak asing didengar maupun dilakukan. Ada berbagai macam saham di Indonesia, salah satunya adalah Indeks Harga Saham Gabungan (IHSG) atau dalam bahasa inggris disebut Indonesia Composite Index, ICI, atau IDX Composite. IHSG merupakan parameter penting yang dipertimbangkan pada saat akan melakukan investasi mengingat IHSG adalah saham gabungan. Penelitian ini bertujuan memprediksi pergerakan IHSG dengan teknik data mining menggunakan algoritma neural network dan dibandingkan dengan algoritma linear regression, yang dapat dijadikan acuan investor saat akan melakukan investasi. Hasil dari penelitian ini berupa nilai Root Mean Squared Error (RMSE) serta label tambahan angka hasil prediksi yang didapatkan setelah dilakukan validasi menggunakan sliding windows validation dengan hasil paling baik yaitu pada pengujian yang menggunakan algoritma neural network yang menggunakan windowing yaitu sebesar 37,786 dan pada pengujian yang tidak menggunakan windowing sebesar 13,597 dan untuk pengujian algoritma linear regression yang menggunakan windowing yaitu sebesar 35,026 dan pengujian yang tidak menggunakan windowing sebesar 12,657. Setelah dilakukan pengujian T-Test menunjukan bahwa pengujian menggunakan neural network yang dibandingkan dengan linear regression memiliki hasil yang tidak signifikan dengan nilai T-Test untuk pengujian dengan windowing dan tanpa windowing hasilnya sama, yaitu sebesar 1,000.

Two-Run Genetic Programming for Predicting Slump Flow of Concrete

2014 ◽  
Vol 590 ◽  
pp. 321-325
Author(s):  
Li Chen ◽  
Chang Huan Kou ◽  
Kuan Ting Chen ◽  
Shih Wei Ma
Keyword(s):  
Nonlinear Systems ◽  
Genetic Programming ◽  
High Performance ◽  
Mean Squared Error ◽  
High Performance Concrete ◽  
Local Optimum ◽  
Root Mean Squared Error ◽  
Squared Error ◽  
Slump Flow ◽  
Low Dimensional

A two-run genetic programming (GP) is proposed to estimate the slump flow of high-performance concrete (HPC) using several significant concrete ingredients in this study. GP optimizes functions and their associated coefficients simultaneously and is suitable to automatically discover relationships between nonlinear systems. Basic-GP usually suffers from premature convergence, which cannot acquire satisfying solutions and show satisfied performance only on low dimensional problems. Therefore it was improved by an automatically incremental procedure to improve the search ability and avoid local optimum. The results demonstrated that two-run GP generates an accurate formula through and has 7.5 % improvement on root mean squared error (RMSE) for predicting the slump flow of HPC than Basic-GP.

Machine learning and Grad-Cam based vascular aging assessment using photoplethysmogram (Preprint)

2021 ◽  
Author(s):  
Hangsik Shin
Keyword(s):  
Machine Learning ◽  
Correlation Coefficient ◽  
Age Estimation ◽  
Mean Squared Error ◽  
Mean Absolute Error ◽  
Absolute Error ◽  
Coefficient Of Determination ◽  
Vascular Aging ◽  
Squared Error ◽  
Vascular Age

BACKGROUND Arterial stiffness due to vascular aging is a major indicator for evaluating cardiovascular risk. OBJECTIVE In this study, we propose a method of estimating age by applying machine learning to photoplethysmogram for non-invasive vascular age assessment. METHODS The machine learning-based age estimation model that consists of three convolutional layers and two-layer fully connected layers, was developed using segmented photoplethysmogram by pulse from a total of 752 adults aged 19–87 years. The performance of the developed model was quantitatively evaluated using mean absolute error, root-mean-squared-error, Pearson’s correlation coefficient, coefficient of determination. The Grad-Cam was used to explain the contribution of photoplethysmogram waveform characteristic in vascular age estimation. RESULTS Mean absolute error of 8.03, root mean squared error of 9.96, 0.62 of correlation coefficient, and 0.38 of coefficient of determination were shown through 10-fold cross validation. Grad-Cam, used to determine the weight that the input signal contributes to the result, confirmed that the contribution to the age estimation of the photoplethysmogram segment was high around the systolic peak. CONCLUSIONS The machine learning-based vascular aging analysis method using the PPG waveform showed comparable or superior performance compared to previous studies without complex feature detection in evaluating vascular aging. CLINICALTRIAL 2015-0104

scholarly journals Evaluation of GEOS-Simulated L-Band Microwave Brightness Temperature Using Aquarius Observations over Non-Frozen Land across North America

2020 ◽  
Vol 12 (18) ◽  
pp. 3098
Author(s):  
Jongmin Park ◽  
Barton A. Forman ◽  
Rolf H. Reichle ◽  
Gabrielle De Lannoy ◽  
Saad B. Tarik
Keyword(s):  
North America ◽  
Brightness Temperature ◽  
Mean Squared Error ◽  
Transfer Model ◽  
Vegetation Types ◽  
Large Variability ◽  
Root Mean Squared Error ◽  
Squared Error ◽  
L Band ◽  
Soil Hydraulic

L-band brightness temperature (Tb) is one of the key remotely-sensed variables that provides information regarding surface soil moisture conditions. In order to harness the information in Tb observations, a radiative transfer model (RTM) is investigated for eventual inclusion into a data assimilation framework. In this study, Tb estimates from the RTM implemented in the NASA Goddard Earth Observing System (GEOS) were evaluated against the nearly four-year record of daily Tb observations collected by L-band radiometers onboard the Aquarius satellite. Statistics between the modeled and observed Tb were computed over North America as a function of soil hydraulic properties and vegetation types. Overall, statistics showed good agreement between the modeled and observed Tb with a relatively low, domain-average bias (0.79 K (ascending) and −2.79 K (descending)), root mean squared error (11.0 K (ascending) and 11.7 K (descending)), and unbiased root mean squared error (8.14 K (ascending) and 8.28 K (descending)). In terms of soil hydraulic parameters, large porosity and large wilting point both lead to high uncertainty in modeled Tb due to the large variability in dielectric constant and surface roughness used by the RTM. The performance of the RTM as a function of vegetation type suggests better agreement in regions with broadleaf deciduous and needleleaf forests while grassland regions exhibited the worst accuracy amongst the five different vegetation types.

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