Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches

Metabolic Fluxes Using Deep Learning Based on Enzyme Variations: Application to Glycolysis in Entamoeba histolytica

Metabolic pathway modeling, essential for understanding organism metabolism, is pivotal in predicting genetic mutation effects, drug design, and biofuel development. Enhancing these modeling techniques is crucial for achieving greater prediction accuracy and reliability. However, the limited experimental data or the complexity of the pathway makes it challenging for researchers to predict phenotypes. Deep learning (DL) is known to perform better than other Machine Learning (ML) approaches if the right conditions are met (i.e., a large database and good choice of parameters). Here, we use a knowledge-based model to massively generate synthetic data and extend a small initial dataset of experimental values. The main objective is to assess if DL can perform at least as well as other ML approaches in flux prediction, using 68,950 instances. Two processing methods are used to generate DL models: cross-validation and repeated holdout evaluation. DL models predict the metabolic fluxes with high precision and slightly outperform the best-known ML approach (the Cubist model) with a lower RMSE (≤0.01) in both cases. They also outperform the PLS model (RMSE ≥ 30). This study is the first to use DL to predict the overall flux of a metabolic pathway only from variations of enzyme concentrations.

Harnessing Interactional Sensory Genes for Rationally Reprogramming Chaotic Metabolism

Rationally controlling cellular metabolism is of great importance but challenging owing to its highly complex and chaotic nature. Natural existing sensory proteins like histidine kinases (HKs) are understood as "sensitive nodes" of biological networks that can trigger disruptive metabolic reprogramming (MRP) upon perceiving environmental fluctuation. Here, the "sensitive node" genes were adopted to devise a global MRP platform consisting of a CRISPR interference-mediated dual-gene combinational knockdown toolbox and survivorship-based metabolic interaction decoding algorithm. The platform allows users to decode the interfering effects of n × n gene pairs while only requiring the synthesis of n pairs of primers. A total of 35 HK genes and 24 glycine metabolic genes were selected as the targets to determine the effectiveness of our platform in a Vibrio sp. FA2. The platform was applied to decode the interfering impact of HKs on antibiotic resistance in strain FA2. A pattern of combined knockdown of HK genes (sasA_8 and 04288) was demonstrated to be capable of reducing antibiotic resistance of Vibrio by 108-fold. Patterns of combined knockdown of glycine pathway genes (e.g., gcvT and ltaE) and several HK genes (e.g., cpxA and btsS) were also revealed to increase glycine production. Our platform may enable an efficient and rational approach for global MRP based on the elucidation of high-order gene interactions. A web-based 1-stop service (https://smrp.sjtu.edu.cn) is also provided to simplify the implementation of this smart strategy in a broad range of cells.

Dendrite Net: A White-Box Module for Classification, Regression, and System Identification

The simulation of biological dendrite computations is vital for the development of artificial intelligence (AI). This article presents a basic machine-learning (ML) algorithm, called Dendrite Net or DD, just like the support vector machine (SVM) or multilayer perceptron (MLP). DD's main concept is that the algorithm can recognize this class after learning, if the output's logical expression contains the corresponding class's logical relationship among inputs (and \ or \ not). Experiments and main results: DD, a white-box ML algorithm, showed excellent system identification performance for the black-box system. Second, it was verified by nine real-world applications that DD brought better generalization capability relative to the MLP architecture that imitated neurons' cell body (Cell body Net) for regression. Third, by MNIST and FASHION-MNIST datasets, it was verified that DD showed higher testing accuracy under greater training loss than the cell body net for classification. The number of modules can effectively adjust DD's logical expression capacity, which avoids overfitting and makes it easy to get a model with outstanding generalization capability. Finally, repeated experiments in MATLAB and PyTorch (Python) demonstrated that DD was faster than Cell body Net both in epoch and forwardpropagation. The main contribution of this article is the basic ML algorithm (DD) with a white-box attribute, controllable precision for better generalization capability, and lower computational complexity. Not only can DD be used for generalized engineering, but DD has vast development potential as a module for deep learning. DD code is available at https://github.com/liugang1234567/Gang-neuron.

Non-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model

The use of machine learning (ML) in life sciences has gained wide interest over the past years, as it speeds up the development of high performing models. Important modeling tools in biology have proven their worth for pathway design, such as mechanistic models and metabolic networks, as they allow better understanding of mechanisms involved in the functioning of organisms. However, little has been done on the use of ML to model metabolic pathways, and the degree of non-linearity associated with them is not clear. Here, we report the construction of different metabolic pathways with several linear and non-linear ML models. Different types of data are used; they lead to the prediction of important biological data, such as pathway flux and final product concentration. A comparison reveals that the data features impact model performance and highlight the effectiveness of non-linear models (e.g., QRF: RMSE = 0.021 nmol·min-1 and R2 = 1 vs. Bayesian GLM: RMSE = 1.379 nmol·min-1 R2 = 0.823). It turns out that the greater the degree of non-linearity of the pathway, the better suited a non-linear model will be. Therefore, a decision-making support for pathway modeling is established. These findings generally support the hypothesis that non-linear aspects predominate within the metabolic pathways. This must be taken into account when devising possible applications of these pathways for the identification of biomarkers of diseases (e.g., infections, cancer, neurodegenerative diseases) or the optimization of industrial production processes.

ASAS-NANP symposium: mathematical modeling in animal nutrition: limitations and potential next steps for modeling and modelers in the animal sciences

The field of animal science, and especially animal nutrition, relies heavily on modeling to accomplish its day-to-day objectives. New data streams ("big data") and the exponential increase in computing power have allowed the appearance of "new" modeling methodologies, under the umbrella of artificial intelligence (AI). However, many of these modeling methodologies have been around for decades. According to Gartner, technological innovation follows five distinct phases: technology trigger, peak of inflated expectations, trough of disillusionment, slope of enlightenment, and plateau of productivity. The appearance of AI certainly elicited much hype within agriculture leading to overpromised plug-and-play solutions in a field heavily dependent on custom solutions. The threat of failure can become real when advertising a disruptive innovation as sustainable. This does not mean that we need to abandon AI models. What is most necessary is to demystify the field and place a lesser emphasis on the technology and more on business application. As AI becomes increasingly more powerful and applications start to diverge, new research fields are introduced, and opportunities arise to combine "old" and "new" modeling technologies into hybrids. However, sustainable application is still many years away, and companies and universities alike do well to remain at the forefront. This requires investment in hardware, software, and analytical talent. It also requires a strong connection to the outside world to test, that which does, and does not work in practice and a close view of when the field of agriculture is ready to take its next big steps. Other research fields, such as engineering and automotive, have shown that the application power of AI can be far reaching but only if a realistic view of models as whole is maintained. In this review, we share our view on the current and future limitations of modeling and potential next steps for modelers in the animal sciences. First, we discuss the inherent dependencies and limitations of modeling as a human process. Then, we highlight how models, fueled by AI, can play an enhanced sustainable role in the animal sciences ecosystem. Lastly, we provide recommendations for future animal scientists on how to support themselves, the farmers, and their field, considering the opportunities and challenges the technological innovation brings.

Modeling and Optimization of a Molecular Biocontroller for the Regulation of Complex Metabolic Pathways

Achieving optimal production in microbial cell factories, robustness against changing intracellular and environmental perturbations requires the dynamic feedback regulation of the pathway of interest. Here, we consider a merging metabolic pathway motif, which appears in a wide range of metabolic engineering applications, including the production of phenylpropanoids among others. We present an approach to use a realistic model that accounts for in vivo implementation and then propose a methodology based on multiobjective optimization for the optimal tuning of the gene circuit parts composing the biomolecular controller and biosensor devices for a dynamic regulation strategy. We show how this approach can deal with the trade-offs between the performance of the regulated pathway, robustness to perturbations, and stability of the feedback loop. Using realistic models, our results suggest that the strategies for fine-tuning the trade-offs among performance, robustness, and stability in dynamic pathway regulation are complex. It is not always possible to infer them by simple inspection. This renders the use of the multiobjective optimization methodology valuable and necessary.

EEGG: An Analytic Brain-computer Interface Algorithm

OBJECTIVE

Modeling the brain as a white box is vital for investigating the brain. However, the physical properties of the human brain are unclear. Therefore, BCI algorithms using EEG signals are generally a data-driven approach and generate a black- or gray-box model. This paper presents the first EEG-based BCI algorithm (EEG-BCI using Gang neurons, EEGG) decomposing the brain into some simple components with physical meaning and integrating recognition and analysis of brain activity.

APPROACH

Independent and interactive components of neurons or brain regions can fully describe the brain. This paper constructed a relation frame based on the independent and interactive compositions for intention recognition and analysis using a novel dendrite module of Gang neurons. A total of 4,906 EEG data of left- and right-hand motor imagery(MI) from 26 subjects were obtained from GigaDB. Firstly, this paper explored EEGG's classification performance by cross-subject accuracy. Secondly, this paper transformed the trained EEGG model into a relation spectrum expressing independent and interactive components of brain regions. Then, the relation spectrum was verified using the known ERD/ERS phenomenon. Finally, this paper explored the previously unreachable further BCI-based analysis of the brain.

MAIN RESULTS

(1) EEGG was more robust than typical "CSP+" algorithms for the low-quality data. (2) The relation spectrum showed the known ERD/ERS phenomenon. (3) Interestingly, EEGG showed that interactive components between brain regions suppressed ERD/ERS effects on classification. This means that generating fine hand intention needs more centralized activation in the brain.

SIGNIFICANCE

EEGG decomposed the biological EEG-intention system of this paper into the relation spectrum inheriting the Taylor series (in analogy with the data-driven but human-readable Fourier transform and frequency spectrum), which offers a novel frame for analysis of the brain.

A perspective on embracing emerging technologies research for organizational behavior

Purpose

Emerging technologies are capable of enhancing organizational- and individual-level outcomes. The organizational behavior (OB) field is beginning to pursue opportunities for researching emerging technologies. This study aims to describe a framework consisting of white, black and grey boxes to demonstrate the tight coupling of phenomena and paradigms in the field and discusses deconstructing OB’s white box to encourage data-driven phenomena to coexist in the spatial framework.

Design/methodology/approach

A scoping literature review was conducted to offer a preliminary assessment of technology-oriented research currently occurring in OB.

Findings

The literature search revealed two findings. First, the number of published papers on emerging technologies in top management journals has been increasing at a steady pace. Second, various theoretical perspectives at the micro- and macro- organizational level have been used so far for conducting technology-oriented research.

Originality/value

By conducting a scoping review of emerging technologies research in OB literature, this paper reveals a conceptual black box relating to technology-oriented research. The essay advocates for loosening OB’s tightly coupled white box to incorporate emerging technologies both as a phenomenon and as data analytical techniques.