Generative Deep Learning for Targeted Compound Design.

Automated design synthesis has the potential to revolutionize the modern engineering design process and improve access to highly optimized and customized products across countless industries. Successfully adapting generative machine learning to design engineering may enable such automated design synthesis and is a research subject of great importance. We present a review and analysis of deep generative machine learning models in engineering design. Deep generative models (DGMs) typically leverage deep networks to learn from an input dataset and synthesize new designs. Recently, DGMs such as feedforward neural networks (NNs), generative adversarial networks (GANs), variational autoencoders (VAEs), and certain deep reinforcement learning (DRL) frameworks have shown promising results in design applications like structural optimization, materials design, and shape synthesis. The prevalence of DGMs in engineering design has skyrocketed since 2016. Anticipating the continued growth, we conduct a review of recent advances to benefit researchers interested in DGMs for design. We structure our review as an exposition of the algorithms, datasets, representation methods, and applications commonly used in the current literature. In particular, we discuss key works that have introduced new techniques and methods in DGMs, successfully applied DGMs to a design-related domain, or directly supported the development of DGMs through datasets or auxiliary methods. We further identify key challenges and limitations currently seen in DGMs across design fields, such as design creativity, handling constraints and objectives, and modeling both form and functional performance simultaneously. In our discussion, we identify possible solution pathways as key areas on which to target the future work.

Drug discovery is a multi-stage process, often beginning with the identification of active molecules from a high-throughput screen or machine learning model. Once structure activity relationship trends become well established, identifying new analogs with better properties is important. Synthesizing these new compounds is a logical next step, and is key to research groups that have a synthetic chemistry team or external collaborators. Generative machine learning models have become widely adopted to generate new molecules and explore molecular space, with the goal of discovering novel compounds with desires properties. These generative models have been composed from recurrent neural networks (RNNs), Variational Autoencoders (VAEs), and Generative Adversarial Networks (GANs) and are often combined with transfer learning or scoring of physicochemical properties to steer generative design. While these generative models have proven useful in generating new molecular libraries, often they are not capable of addressing a wide variety of potential problems, and often converge into similar molecular space when combined with a scoring function for desired properties. In addition, generated compounds are often not synthetically feasible, reducing their capabilities outside of virtual composition and limiting their usefulness in real-world scenarios. Here we introduce a suite of automated tools called MegaSyn representing 3 components: a new hill-climb algorithm which makes use of SMILES-based RNN generative models, analog generation software, and retrosynthetic analysis coupled with fragment analysis to score molecules for their synthetic feasibility. We now describe the development and testing of this suite of tools and propose how they might be used to optimize molecules or prioritize promising lead compounds using test case examples.

In recent years, Deep Learning (DL), such as the algorithms of Convolutional Neural Networks (CNN), Recurrent Neural Networks (RNN) and Generative Adversarial Networks (GAN), has been widely studied and applied in various fields including agriculture. Researchers in the fields of agriculture often use software frameworks without sufficiently examining the ideas and mechanisms of a technique. This article provides a concise summary of major DL algorithms, including concepts, limitations, implementation, training processes, and example codes, to help researchers in agriculture to gain a holistic picture of major DL techniques quickly. Research on DL applications in agriculture is summarized and analyzed, and future opportunities are discussed in this paper, which is expected to help researchers in agriculture to better understand DL algorithms and learn major DL techniques quickly, and further to facilitate data analysis, enhance related research in agriculture, and thus promote DL applications effectively. Keywords: deep learning, smart agriculture, neural network, convolutional neural networks, recurrent neural networks, generative adversarial networks, artificial intelligence, image processing, pattern recognition DOI: 10.25165/j.ijabe.20181104.4475 Citation: Zhu N Y, Liu X, Liu Z Q, Hu K, Wang Y K, Tan J L, et al. Deep learning for smart agriculture: Concepts, tools, applications, and opportunities. Int J Agric & Biol Eng, 2018; 11(4): 32-44.

Personalized medicine represents a paradigm shift in healthcare, aiming to tailor treatment strategies to the unique genetic, environmental, and lifestyle characteristics of individual patients. This approach holds immense potential for improving therapeutic efficacy and minimizing adverse drug reactions. With the rapid advancement of artificial intelligence, deep learning has emerged as a transformative tool in pharmacology, enabling precise modeling of complex biological data and uncovering hidden patterns in patient-specific information. This study investigates the application of deep learning techniques - such as Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs), Transformer architectures, and Generative Adversarial Networks (GANs) - in optimizing personalized treatment strategies. Using a diverse dataset comprising electronic health records (EHRs), genomic sequences, and clinical indicators, we developed and trained deep learning models for tasks including drug response prediction, biomarker identification, and adverse drug reaction (ADR) forecasting. Among the models evaluated, Transformer-based architectures demonstrated superior performance, achieving an accuracy of 91.2% and an AUC-ROC of 0.92 in drug response prediction tasks. Moreover, the integration of deep learning models into the treatment pipeline resulted in a 20-30% improvement in drug-patient matching efficiency compared to traditional statistical methods. The findings underscore the potential of AI-powered systems to enhance clinical decision-making and enable precision pharmacotherapy. However, challenges such as data privacy, model interpretability, and regulatory compliance remain critical barriers to widespread adoption. The study also explores future directions, including the implementation of explainable AI (XAI) and federated learning, to address these limitations and facilitate the integration of deep learning into routine clinical practice.

Deep generative models (GMs) have transformed the exploration of drug-like chemical space (CS) by generating novel molecules through complex, nontransparent processes, bypassing direct structural similarity. This review examines five key architectures for CS exploration: recurrent neural networks (RNNs), variational autoencoders (VAEs), generative adversarial networks (GANs), normalizing flows (NF), and Transformers. It discusses molecular representation choices, training strategies for focused CS exploration, evaluation criteria for CS coverage, and related challenges. Future directions include refining models, exploring new notations, improving benchmarks, and enhancing interpretability to better understand biologically relevant molecular properties.

Predicting crop yield based on the environmental, soil, water and crop parameters has been a potential research topic. Deep-learning-based models are broadly used to extract significant crop features for prediction. Though these methods could resolve the yield prediction problem there exist the following inadequacies: Unable to create a direct non-linear or linear mapping between the raw data and crop yield values; and the performance of those models highly relies on the quality of the extracted features. Deep reinforcement learning provides direction and motivation for the aforementioned shortcomings. Combining the intelligence of reinforcement learning and deep learning, deep reinforcement learning builds a complete crop yield prediction framework that can map the raw data to the crop prediction values. The proposed work constructs a Deep Recurrent Q-Network model which is a Recurrent Neural Network deep learning algorithm over the Q-Learning reinforcement learning algorithm to forecast the crop yield. The sequentially stacked layers of Recurrent Neural network is fed by the data parameters. The Q- learning network constructs a crop yield prediction environment based on the input parameters. A linear layer maps the Recurrent Neural Network output values to the Q-values. The reinforcement learning agent incorporates a combination of parametric features with the threshold that assist in predicting crop yield. Finally, the agent receives an aggregate score for the actions performed by minimizing the error and maximizing the forecast accuracy. The proposed model efficiently predicts the crop yield outperforming existing models by preserving the original data distribution with an accuracy of 93.7%.

Discovering new chemical compounds with specific properties can provide advantages for fields that rely on materials for their development, although this task comes at a high cost in terms of complexity and resources. Since the beginning of the data age, deep learning techniques have revolutionized the process of designing molecules by analyzing and learning from representations of molecular data, greatly reducing the resources and time involved. Various deep learning approaches have been developed to date, using a variety of architectures and strategies, in order to explore the extensive and discontinuous chemical space, providing benefits for generating compounds with specific properties. In this study, we present a systematic review that offers a statistical description and comparison of the strategies utilized to generate molecules through deep learning techniques, utilizing the metrics proposed in Molecular Sets (MOSES) or Guacamol. The study included 48 articles retrieved from a query-based search of Scopus and Web of Science and 25 articles retrieved from citation search, yielding a total of 72 retrieved articles, of which 62 correspond to chemical language models approaches to molecule generation and other 10 retrieved articles correspond to molecular graph representations. Transformers, recurrent neural networks (RNNs), generative adversarial networks (GANs), Structured Space State Sequence (S4) models, and variational autoencoders (VAEs) are considered the main deep learning architectures used for molecule generation in the set of retrieved articles. In addition, transfer learning, reinforcement learning, and conditional learning are the most employed techniques for biased model generation and exploration of specific chemical space regions. Finally, this analysis focuses on the central themes of molecular representation, databases, training dataset size, validity-novelty trade-off, and performance of unbiased and biased chemical language models. These themes were selected to conduct a statistical analysis utilizing graphical representation and statistical tests. The resulting analysis reveals the main challenges, advantages, and opportunities in the field of chemical language models over the past four years.

The de novo design of molecular structures using deep learning generative models introduces an encouraging solution to drug discovery in the face of the continuously increased cost of new drug development. From the generation of original texts, images, and videos, to the scratching of novel molecular structures the creativity of deep learning generative models exhibits the height machine intelligence can achieve. The purpose of this paper is to review the latest advances in generative chemistry which relies on generative modeling to expedite the drug discovery process. This review starts with a brief history of artificial intelligence in drug discovery to outline this emerging paradigm. Commonly used chemical databases, molecular representations, and tools in cheminformatics and machine learning are covered as the infrastructure for generative chemistry. The detailed discussions on utilizing cutting-edge generative architectures, including recurrent neural network, variational autoencoder, adversarial autoencoder, and generative adversarial network for compound generation are focused. Challenges and future perspectives follow.

In this paper, we propose an improved hybrid approach for text generation that combines the strengths of generative adversarial networks (GANs) and recurrent neural networks (RNNs). The proposed model, named TextGen-GAN, uses a GAN to generate high-level semantic representations of text, which are then passed through an RNN decoder to produce coherent and diverse text. The suggested method produces superior results in terms of both quality and diversity when tested on a number of benchmark datasets. The obtained results show that the combination of GAN and RNN outperforms GAN alone, RNN only, baseline, and state-of-the-art models, demonstrating the effectiveness of the proposed hybrid approach.

This paper surveys the growing interest in utilizing deep learning (DL) as a powerful tool to address challenging problems in earthquake engineering. Despite decades of advancement in domain knowledge, issues such as uncertainty in earthquake occurrence, unpredictable seismic loads, nonlinear structural responses, and community engagement remain difficult to tackle using domain-specific methods. DL offers promising solutions by leveraging its data-driven capacity for nonlinear mapping, sequential data modeling, automatic feature extraction, dimensionality reduction, optimal decision-making, and so on. However, the literature lacks a comprehensive review that systematically covers a consistent scope intersecting DL and earthquake engineering. To bridge this gap, this paper first discusses methodological advances to elucidate various applicable DL techniques, such as multilayer perceptron, convolutional neural network (CNN), recurrent neural network (RNN), generative adversarial network, autoencoder, transfer learning, reinforcement learning (RL), and graph neural network. A thorough research landscape is then disclosed by exploring various DL applications across different research topics, including vision-based seismic damage assessment and structural characterization, seismic demand and damage state prediction, seismic response history prediction, regional seismic risk assessment and community resilience, ground motion (GM) for engineering use, seismic response control, and the inverse problem of system/damage identification. Suitable DL techniques for each research topic are identified, emphasizing the preeminence of CNN for vision-based tasks, RNN for sequential data, RL for community resilience, and unsupervised learning for GM analysis. The paper also discusses opportunities and challenges for leveraging DL in earthquake engineering research and practice, highlighting the need for open-access multimodal big data and efforts to enhance model interpretability and incorporate physics information into DL. Finally, the paper advocates for DL applications to further advance the research frontier of uncertainty quantification in performance-based earthquake engineering.

Prediction concept needs human-like thinking and ideas. ANN helps make a program for describing the solutions to the prediction problems. To gain accurate prediction, there is a need for deep thinking in the knowledge system discovered. Deep learning helps form such next-level type of ANN thinking. Deep learning models do not require humans for programming the problems. It can determine the prediction by itself by learning the dataset. This paper describes the prediction by considering sequential model for continuous accessing of data with the help of multi-layers. Deep learning is very helpful for predicting larger dataset. This paper proposes an algorithmic model known as a Comprehensive Deep Recurrent Artificial Neural Networks (CDRANN) by hybridizing LSTM (long short-term memory) with RNN (recurrent neural network) backtrack solver for better future stock prediction. This paper also explains the need for hybridizing evolutionary model CDRANN to create a novel change in future prediction.KeywordsCDRANN (Comprehensive Deep Recurrent Artificial Neural Networks)LSTM (long short-term memory)RNN (recurrent neural network)Stock marketPrediction

A method for evaluating deep generative models of images for hallucinations in high-order spatial context

ABSTRACTRenewable energy systems represented by photovoltaic power generation systems have strong weather sensitivity, and weather factors are important reasons for the high uncertainty. This paper proposes a power flow analysis method based on a weather scenario generation model, which generates a massive amount of hourly weather scenarios with real probability characteristics, temporal features, and diverse variations throughout the year to fully analyse power flow. The proposed model, named “BL‐StyleGAN”, combines generative adversarial networks (GAN), bidirectional long short‐term memory networks (Bi‐LSTM), and style transfer strategies to accurately learn the probability, diversity, and temporality of real temperature, direct radiation, and diffuse radiation data. Compared with other deep generative models based on GANs, the proposed model has significant advantages in learning the temporal and diverse characteristics of weather data. We applied this weather scenario generation model to the power grid in a certain location in Guangdong Province, China for power flow analysis. Experimental results demonstrate that the proposed BL‐StyleGAN model surpasses other deep generative models in the accuracy of power flow analysis.

This paper proposes a novel approach for generating 3-dimensional complex geological facies models based on deep generative models. It can reproduce a wide range of conceptual geological models while possessing the flexibility necessary to honor constraints such as well data. Compared with existing geostatistics-based modeling methods, our approach produces realistic subsurface facies architecture in 3D using a state-of-the-art deep learning method called Generative Adversarial Networks (GANs). GANs couple a generator with a discriminator and each uses a deep Convolutional Neural Network (CNN). The networks are trained in an adversarial manner until the generator can create "fake" images that the discriminator cannot distinguish from "real" images. We extend the original GAN approach to 3D geological modeling at the reservoir scale. The GANs are trained using a library of 3D facies models. Once the GANs have been trained, they can generate a variety of geologically realistic facies models constrained by well data interpretations. This geomodelling approach using GANs has been tested on models of both complex fluvial depositional systems and carbonate reservoirs that exhibit progradational and aggradational trends. The results demonstrate that this deep learning-driven modeling approach can capture more realistic facies architectures and associations than existing geostatistical modeling methods, which often fail to reproduce heterogeneous nonstationary sedimentary facies with apparent depositional trend.

Medical image reconstruction is typically an ill-posed inverse problem. In order to address such ill-posed problems, the prior distribution of the sought after object property is usually incorporated by means of some sparsity-promoting regularization. Recently, prior distributions for images estimated using generative adversarial networks (GANs) have shown great promise in regularizing some of these image reconstruction problems. In this work, we apply an image-adaptive GAN-based reconstruction method (IAGAN) to reconstruct high fidelity images from incomplete medical imaging data. It is observed that the IAGAN method can potentially recover fine structures in the object that are relevant for medical diagnosis but may be oversmoothed in reconstructions with traditional sparsity-promoting regularization.