Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine of Cornell University, New York, NY, USA Key Words Machine Learning Biosynthesis Artificial Neural Networks Enzyme pathway Deep Learning DBTL cycle ART Abstract In the modern world, technology is at its peak. Different avenues in programming and technology have been explored for data analysis, automation, and robotics. Machine learning is key to optimize data analysis, make accurate predictions, and hasten/improve existing functions. Thus, presently, the field of machine learning in artificial intelligence is being developed and its uses in varying fields are being explored. One field in which its uses stand out is that of microbial biosynthesis. In this paper, a comprehensive overview of the differing machine learning programs used in biosynthesis is provided, alongside brief descriptions of the fields of machine learning and microbial biosynthesis separately. This information includes past trends, modern developments, future improvements, explanations of processes, and current problems they face. Thus, this paper's main contribution is to distill developments in, and provide a holistic explanation of, 2 key fields and their applicability to improve industry/research. It also highlights challenges and research directions, acting to instigate more research and development in the growing fields. Finally, the paper aims to act as a reference for academics performing research, industry professionals improving their processes, and students looking to understand the concept of machine learning in biosynthesis. Introduction In 1944, the field of microbial biosynthesis was first established industrially, with the antibiotic penicillin being mass produced by a fungi belonging to the Penicillium genus.[1]

Modern automated surveillance techniques are heavily reliant on deep learning methods. Despite the superior performance, these learning systems are inherently vulnerable to adversarial attacks - maliciously crafted inputs that are designed to mislead, or trick, models into making incorrect predictions. An adversary can physically change their appearance by wearing adversarial t-shirts, glasses, or hats or by specific behavior, to potentially avoid various forms of detection, tracking and recognition of surveillance systems; and obtain unauthorized access to secure properties and assets. This poses a severe threat to the security and safety of modern surveillance systems. This paper reviews recent attempts and findings in learning and designing physical adversarial attacks for surveillance applications. In particular, we propose a framework to analyze physical adversarial attacks and provide a comprehensive survey of physical adversarial attacks on four key surveillance tasks: detection, identification, tracking, and action recognition under this framework. Furthermore, we review and analyze strategies to defend against the physical adversarial attacks and the methods for evaluating the strengths of the defense. The insights in this paper present an important step in building resilience within surveillance systems to physical adversarial attacks.

This article presents a comprehensive overview of the digital twin technology and its capability levels, with a specific focus on its applications in the wind energy industry. It consolidates the definitions of digital twin and its capability levels on a scale from 0-5; 0-standalone, 1-descriptive, 2-diagnostic, 3-predictive, 4-prescriptive, 5-autonomous. It then, from an industrial perspective, identifies the current state of the art and research needs in the wind energy sector. The article proposes approaches to the identified challenges from the perspective of research institutes and offers a set of recommendations for diverse stakeholders to facilitate the acceptance of the technology. The contribution of this article lies in its synthesis of the current state of knowledge and its identification of future research needs and challenges from an industry perspective, ultimately providing a roadmap for future research and development in the field of digital twin and its applications in the wind energy industry.

Deep generative models such as Variational Autoencoders (VAEs), Generative Adversarial Networks (GANs), Diffusion Models, and Transformers, have shown great promise in a variety of applications, including image and speech synthesis, natural language processing, and drug discovery. However, when applied to engineering design problems, evaluating the performance of these models can be challenging, as traditional statistical metrics based on likelihood may not fully capture the requirements of engineering applications. This paper doubles as a review and practical guide to evaluation metrics for deep generative models (DGMs) in engineering design. We first summarize the well-accepted `classic' evaluation metrics for deep generative models grounded in machine learning theory. Using case studies, we then highlight why these metrics seldom translate well to design problems but see frequent use due to the lack of established alternatives. Next, we curate a set of design-specific metrics which have been proposed across different research communities and can be used for evaluating deep generative models. These metrics focus on unique requirements in design and engineering, such as constraint satisfaction, functional performance, novelty, and conditioning. Throughout our discussion, we apply the metrics to models trained on simple-to-visualize 2-dimensional example problems. Finally, we evaluate four deep generative models on a bicycle frame design problem and structural topology generation problem. In particular, we showcase the use of proposed metrics to quantify performance target achievement, design novelty, and geometric constraints. We publicly release the code for the datasets, models, and metrics used throughout the paper at https://decode.mit.edu/projects/metrics/.

Bayesian methods for solving inverse problems are a powerful alternative to classical methods since the Bayesian approach offers the ability to quantify the uncertainty in the solution. In recent years, data-driven techniques for solving inverse problems have also been remarkably successful, due to their superior representation ability. In this work, we incorporate data-based models into a class of Langevin-based sampling algorithms for Bayesian inference in imaging inverse problems. In particular, we introduce NF-ULA (Normalizing Flow-based Unadjusted Langevin algorithm), which involves learning a normalizing flow (NF) as the image prior. We use NF to learn the prior because a tractable closed-form expression for the log prior enables the differentiation of it using autograd libraries. Our algorithm only requires a normalizing flow-based generative network, which can be pre-trained independently of the considered inverse problem and the forward operator. We perform theoretical analysis by investigating the well-posedness and non-asymptotic convergence of the resulting NF-ULA algorithm. The efficacy of the proposed NF-ULA algorithm is demonstrated in various image restoration problems such as image deblurring, image inpainting, and limited-angle X-ray computed tomography (CT) reconstruction. NF-ULA is found to perform better than competing methods for severely ill-posed inverse problems.

Topological Data Analysis (TDA) is a mathematical method using techniques from topology for the analysis of complex, multi-dimensional data that has been widely and successfully applied in several fields such as medicine, material science, biology, and others. This survey summarizes the state of the art of TDA in yet another application area: industrial manufacturing and production in the context of Industry 4.0. We perform a rigorous and reproducible literature search of applications of TDA on the setting of industrial production and manufacturing. The resulting works are clustered and analyzed based on their application area within the manufacturing process and their input data type. We highlight the key benefits of TDA and their tools in this area and describe its challenges, as well as future potential. Finally, we discuss which TDA methods are underutilized in (the specific area of) industry and the identified types of application, with the goal of prompting more research in this profitable area of application.

In recent years, deep learning has revolutionized natural language processing (NLP) by enabling the development of models that can learn complex representations of language data, leading to significant improvements in performance across a wide range of NLP tasks. Deep learning models for NLP typically use large amounts of data to train deep neural networks, allowing them to learn the patterns and relationships in language data. This is in contrast to traditional NLP approaches, which rely on hand-engineered features and rules to perform NLP tasks. The ability of deep neural networks to learn hierarchical representations of language data, handle variable-length input sequences, and perform well on large datasets makes them well-suited for NLP applications. Driven by the exponential growth of textual data and the increasing demand for condensed, coherent, and informative summaries, text summarization has been a critical research area in the field of NLP. Applying deep learning to text summarization refers to the use of deep neural networks to perform text summarization tasks. In this survey, we begin with a review of fashionable text summarization tasks in recent years, including extractive, abstractive, multi-document, and so on. Next, we discuss most deep learning-based models and their experimental results on these tasks. The paper also covers datasets and data representation for summarization tasks. Finally, we delve into the opportunities and challenges associated with summarization tasks and their corresponding methodologies, aiming to inspire future research efforts to advance the field further. A goal of our survey is to explain how these methods differ in their requirements as understanding them is essential for choosing a technique suited for a specific setting.

Recent global disruptions, such as the pandemic and geopolitical conflicts, have profoundly exposed vulnerabilities in traditional supply chains, requiring exploration of more resilient alternatives. Autonomous supply chains (ASCs) have emerged as a potential solution, offering increased visibility, flexibility, and resilience in turbulent trade environments. Despite discussions in industry and academia over several years, ASCs lack well-established theoretical foundations. This paper addresses this research gap by presenting a formal definition of ASC along with its defining characteristics and auxiliary concepts. We propose a layered conceptual framework called the MIISI model. An illustrative case study focusing on the meat supply chain demonstrates an initial ASC implementation based on this conceptual model. Additionally, we introduce a seven-level supply chain autonomy reference model, delineating a trajectory towards achieving a full supply chain autonomy. Recognising that this work represents an initial endeavour, we emphasise the need for continued exploration in this emerging domain. We anticipate that this work will stimulate further research, both theoretical and technical, and contribute to the continual evolution of ASCs.

Despite advances in artificial intelligence-enhanced trading methods, developing a profitable automated trading system remains challenging in the rapidly evolving cryptocurrency market. This study aims to address these challenges by developing a reinforcement learning-based automated trading system for five popular altcoins~(cryptocurrencies other than Bitcoin): Binance Coin, Ethereum, Litecoin, Ripple, and Tether. To this end, we present CausalReinforceNet, a framework framed as a decision support system. Designed as the foundational architecture of the trading system, the CausalReinforceNet framework enhances the capabilities of the reinforcement learning agent through causal analysis. Within this framework, we use Bayesian networks in the feature engineering process to identify the most relevant features with causal relationships that influence cryptocurrency price movements. Additionally, we incorporate probabilistic price direction signals from dynamic Bayesian networks to enhance our reinforcement learning agent's decision-making. Due to the high volatility of the cryptocurrency market, we design our framework to adopt a conservative approach that limits sell and buy position sizes to manage risk. We develop two agents using the CausalReinforceNet framework, each based on distinct reinforcement learning algorithms. The results indicate that our framework substantially surpasses the Buy-and-Hold benchmark strategy in profitability. Additionally, both agents generated notable returns on investment for Binance Coin and Ethereum.

Automatic Keyphrase Extraction involves identifying essential phrases in a document. These keyphrases are crucial in various tasks such as document classification, clustering, recommendation, indexing, searching, summarization, and text simplification. This paper introduces a platform that integrates keyphrase datasets and facilitates the evaluation of keyphrase extraction algorithms. The platform includes BibRank, an automatic keyphrase extraction algorithm that leverages a rich dataset obtained by parsing bibliographic data in BibTeX format. BibRank combines innovative weighting techniques with positional, statistical, and word co-occurrence information to extract keyphrases from documents. The platform proves valuable for researchers and developers seeking to enhance their keyphrase extraction algorithms and advance the field of natural language processing.