Quantum Machine Learning Predicting ADME-Tox Properties in Drug Discovery.

In the drug discovery paradigm, the evaluation of absorption, distribution, metabolism, and excretion (ADME) and toxicity properties of new chemical entities is one of the most critical issues, which is a time-consuming process, immensely expensive, and poses formidable challenges in pharmaceutical R&D. In recent years, emerging technologies like artificial intelligence (AI), big data, and cloud technologies have garnered great attention to predict the ADME and toxicity of molecules. Currently, the blend of quantum computation and machine learning has attracted considerable attention in almost every field ranging from chemistry to biomedicine and several engineering disciplines as well. Quantum computers have the potential to bring advances in high-throughput experimental techniques and in screening billions of molecules by reducing development costs and time associated with the drug discovery process. Motivated by the efficiency of quantum kernel methods, we proposed a quantum machine learning (QML) framework consisting of a classical support vector classifier algorithm with a kernel-based quantum classifier. To demonstrate the feasibility of the proposed QML framework, the simplified molecular input line entry system (SMILES) notation-based string kernel, combined with a quantum support vector classifier, is used for the evaluation of chemical/drug ADME-Tox properties. The proposed quantum machine learning framework is validated and assessed via large-scale simulations. Based on our results from numerical simulations, the quantum model achieved the best performance as compared to classical counterparts in terms of the area under the curve of the receiver operating characteristic curve (AUC ROC; 0.80-0.95) for predicting outcomes on ADME-Tox data sets for small molecules, with a different number of features. The deployment of the proposed framework in the pharmaceutical industry would be extremely valuable in making the best decisions possible.

Matrix Product State-Based Quantum Classifier.

Interest in quantum computing has increased significantly. Tensor network theory has become increasingly popular and widely used to simulate strongly entangled correlated systems. Matrix product state (MPS) is a well-designed class of tensor network states that plays an important role in processing quantum information. In this letter, we show that MPS, as a one-dimensional array of tensors, can be used to classify classical and quantum data. We have performed binary classification of the classical machine learning data set Iris encoded in a quantum state. We have also investigated its performance by considering different parameters on the ibmqx4 quantum computer and proved that MPS circuits can be used to attain better accuracy. Furthermore the learning ability of an MPS quantum classifier is tested to classify evapotranspiration (ET o ) for the Patiala meteorological station located in northern Punjab (India), using three years of a historical data set (Agri). We have used different performance metrics of classification to measure its capability. Finally, the results are plotted and the degree of correspondence among values of each sample is shown.

Variational quantum classifiers through the lens of the Hessian.

In quantum computing, the variational quantum algorithms (VQAs) are well suited for finding optimal combinations of things in specific applications ranging from chemistry all the way to finance. The training of VQAs with gradient descent optimization algorithm has shown a good convergence. At an early stage, the simulation of variational quantum circuits on noisy intermediate-scale quantum (NISQ) devices suffers from noisy outputs. Just like classical deep learning, it also suffers from vanishing gradient problems. It is a realistic goal to study the topology of loss landscape, to visualize the curvature information and trainability of these circuits in the existence of vanishing gradients. In this paper, we calculate the Hessian and visualize the loss landscape of variational quantum classifiers at different points in parameter space. The curvature information of variational quantum classifiers (VQC) is interpreted and the loss function's convergence is shown. It helps us better understand the behavior of variational quantum circuits to tackle optimization problems efficiently. We investigated the variational quantum classifiers via Hessian on quantum computers, starting with a simple 4-bit parity problem to gain insight into the practical behavior of Hessian, then thoroughly analyzed the behavior of Hessian's eigenvalues on training the variational quantum classifier for the Diabetes dataset. Finally, we show how the adaptive Hessian learning rate can influence the convergence while training the variational circuits.

Cyanobacteria blue-green algae prediction enhancement using hybrid machine learning-based gamma test variable selection and empirical wavelet transform.

This study aims to evaluate the usefulness and effectiveness of four machine learning (ML) models for modelling cyanobacteria blue-green algae (CBGA) at two rivers located in the USA. The proposed modelling framework was based on establishing a link between five water quality variables and the concentration of CBGA. For this purpose, artificial neural network (ANN), extreme learning machine (ELM), random forest regression (RFR), and random vector functional link (RVFL) are developed. First, the four models were developed using only water quality variables. Second, based on the results of the first, a new modelling strategy was introduced based on preprocessing signal decomposition. Hence, the empirical mode decomposition (EMD), the variational mode decomposition (VMD), and the empirical wavelet transform (EWT) were used for decomposing the water quality variables into several subcomponents, and the obtained intrinsic mode functions (IMFs) and multiresolution analysis (MRA) components were used as new input variables for the ML models. Results of the present investigation show that (i) using single models, good predictive accuracy was obtained using the RFR model exhibiting an R and NSE values of ≈0.914 and ≈0.833 for the first station, and ≈0.944 and ≈0.884 for the second station, while the others models, i.e., ANN, RVFL, and ELM, have failed to provide a good estimation of the CBGA; (ii) the decomposition methods have contributed to a significant improvement of the individual models performances; (iii) among the thee decomposition methods, the EMD was found to be superior to the VMD and EWT; and (iv) the ANN and RFR were found to be more accurate compared to the ELM and RVFL models, exhibiting high numerical performances with R and NSE values of approximately ≈0.983, ≈0.967, and ≈0.989 and ≈0.976, respectively.

The impact of climate changes on the water footprint of wheat and maize production in the Nile Delta, Egypt.

Spatial-temporal information of different water resources is essential to rationally manage, sustainably develop, and optimally utilize water. This study focused on simulating future water footprint (WF) of two agronomically important crops (i.e., wheat and maize) using deep neural networks (DNN) method in Nile delta. DNN model was calibrated and validated by using 2006-2014 and 2015-2017 datasets. Moreover, future data (2022-2040) were obtained from three Representative Concentration Pathways (RCP) 2.6, 4.5, and 8.5, and incorporated into DNN prediction set. The findings showed that determination-coefficient between historical-predicted crop evapotranspiration (ETc) varied from 0.92 to 0.97 for two crops. The yield prediction values of wheat-maize deviated within the ranges of -3.21% to 3.47% and -4.93% to 5.88%, respectively. Based on the ensemble of RCP, precipitation was forecasted to decease by 667.40% and 261.73% in winter and summer in western as compared to eastern, respectively, which will ultimately be dropped to 105.02% and 60.87%, respectively parallel to historical. Therefore, the substantial fluctuations in precipitation caused an obvious decrease in green WF of wheat (i.e., 24.96% and 37.44%) in western and eastern, respectively. Additionally, for maize, it induced a 103.93% decrease in western and an 8.96% increase in eastern. Furthermore, increasing ETc by 8.46% and 12.45% gave rise to substantially increasing (i.e., 8.96% and 17.21%) in western for wheat-maize compared to the east, respectively. Likewise, grey wheat-maize WF findings reveals that there was an increase of 3.07% and 5.02% in western as compared to -14.51% and 12.37% in eastern. Hence, our results highly recommend the optimal use of the eastern delta to save blue-water by 16.58% and 40.25% of total requirements for wheat-maize in contrast to others. Overall, the current research framework and results derived from the adopted methodology will help in optimal planning of future water under climate change in the agricultural sector.

Implementing the Principle of the 3 Rs Through the Indian Pharmacopoeia.

Quality and safety tests are required for regulatory approval of drugs and pharmaceuticals in the country to guarantee minimum safety standards, and most of these tests include animal usage. In the case of biological medicines, these safety and quality tests have to be performed on a batch-to-batch basis and require a large number of animals. Russell and Burch's 1959 principle of the 3 Rs- replacement, reduction, and refinement-is now being increasingly adopted worldwide, and various national and international pharmacopoeias have taken initiatives to safeguard animals. This article details the Indian Pharmacopoeia Commission's initiative to implement the 3 Rs through the Indian Pharmacopoeia. Explored are the deletion of animal tests, such as the abnormal toxicity test at final lot for biologicals; the replacement of in vivo methods by in vitro methods; the reduction in the number of animals used where deletion of the animal test is not possible; and the refinement of tests to cause minimal suffering to the animals. In Indian Pharmacopoeia 2014, pyrogen testing using rabbits has been replaced by the bacterial endotoxin test in the majority of biological monographs-keeping in view international trends and, especially for vaccine monographs, validated in vitro tests such as the bacterial endotoxin test as an alternative to the pyrogen test where justified and authorized. Steps are taken for introducing a single-dilution assay for the potency testing of diphtheria and tetanus vaccine (adsorbed) with the aim of minimizing number of animals used. The justified and authorized use of animals in drug manufacturing, analytic laboratories, and research will not only help in the expedited development/production of drugs but also be useful in protecting and promoting animal health.