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We apply logic-based machine learning techniques to facilitate cellular engineering and drive biological discovery, based on comprehensive databases of metabolic processes called genome-scale metabolic network models (GEMs). Predicted host behaviours are not always correctly described by GEMs. Learning the intricate genetic interactions within GEMs presents computational and empirical challenges. To address these, we describe a novel approach called Boolean Matrix Logic Programming (BMLP) by leveraging boolean matrices to evaluate large logic programs. We introduce a new system, $BMLP_{active}$, which efficiently explores the genomic hypothesis space by guiding informative experimentation through active learning. In contrast to sub-symbolic methods, $BMLP_{active}$ encodes a state-of-the-art GEM of a widely accepted bacterial host in an interpretable and logical representation using datalog logic programs. Notably, $BMLP_{active}$ can successfully learn the interaction between a gene pair with fewer training examples than random experimentation, overcoming the increase in experimental design space. $BMLP_{active}$ enables rapid optimisation of metabolic models and offers a realistic approach to a self-driving lab for microbial engineering., Comment: arXiv admin note: substantial text overlap with arXiv:2405.06724

Class imbalance refers to the significant difference in the number of samples from different classes within a dataset, making it challenging to identify minority class samples correctly. This issue is prevalent in real-world classification tasks, such as software defect prediction, medical diagnosis, and fraud detection. The synthetic minority oversampling technique (SMOTE) is widely used to address class imbalance issue, which is based on interpolation between randomly selected minority class samples and their neighbors. However, traditional SMOTE and most of its variants only interpolate between existing samples, which may be affected by noise samples in some cases and synthesize samples that lack diversity. To overcome these shortcomings, this paper proposes the Minimum Enclosing Ball SMOTE (MEB-SMOTE) method from a geometry perspective. Specifically, MEB is innovatively introduced into the oversampling method to construct a representative point. Then, high-quality samples are synthesized by interpolation between this representative point and the existing samples. The rationale behind constructing a representative point is discussed, demonstrating that the center of MEB is more suitable as the representative point. To exhibit the superiority of MEB-SMOTE, experiments are conducted on 15 real-world imbalanced datasets. The results indicate that MEB-SMOTE can effectively improve the classification performance on imbalanced datasets.

The Yang-Lee edge singularity is an intriguing critical phenomenon characterized by nonunitary field theory. However, its experimental realization for interacting many-body systems remains elusive. We show that Yang-Lee edge singularities, regarded as many-body exceptional points, can be observed using both the self-normal and the associated-biorthogonal Loschmidt echoes, leveraging the advantages of nonunitary dynamics in non-Hermitian systems. The Loschmidt echoes are demonstrated to display unitary dynamics in the $\mathcal{PT}$-symmetric regime but exhibit nonunitary dynamics in the $\mathcal{PT}$ symmetry-broken regime, leading to a sharp change near an exceptional point. We hereby identify exceptional points in both the non-Hermitian transverse field Ising model and the Yang-Lee model, and determine the critical exponent that is consistent with nonunitary conformal field theory. This work provides a direct observation of Yang-Lee edge singularities in non-Hermitian many-body systems arising from nonunitary dynamics., Comment: 6 pages, 4 figures and 1 table

Parameter extraction of photovoltaic (PV) models is crucial for the planning, optimization, and control of PV systems. Although some methods using meta-heuristic algorithms have been proposed to determine these parameters, the robustness of solutions obtained by these methods faces great challenges when the complexity of the PV model increases. The unstable results will affect the reliable operation and maintenance strategies of PV systems. In response to this challenge, an improved RIME algorithm with enhanced exploration and exploitation is proposed for robust and accurate parameter identification for various PV models. Specifically, the differential evolution mutation operator is integrated in the exploration phase to enhance the population diversity. Meanwhile, a new exploitation strategy incorporating randomization and neighborhood strategies simultaneously is developed to maintain the balance of exploitation width and depth. The improved RIME algorithm is applied to estimate the optimal parameters of the single-diode model (SDM), double-diode model (DDM), and triple-diode model (TDM) combined with the Lambert-W function for three PV cell and module types including RTC France, Photo Watt-PWP 201 and S75. According to the statistical analysis in 100 runs, the TEIMRE achieves more accurate and robust parameter estimations than other techniques to various PV models in varying environmental conditions. All of our source codes are publicly available at https://github.com/dirge1/TERIME.

Uncertainty reduction is vital for improving system reliability and reducing risks. To identify the best target for uncertainty reduction, uncertainty importance measure is commonly used to prioritize the significance of input variable uncertainties. Then, designers will take steps to reduce the uncertainties of variables with high importance. However, for variables with minimal uncertainty, the cost of controlling their uncertainties can be unacceptable. Therefore, uncertainty magnitude should also be considered in developing uncertainty reduction strategies. Although variance-based methods have been developed for this purpose, they are dependent on statistical moments and have limitations when dealing with highly-skewed distributions that are commonly encountered in practical applications. Motivated by this problem, we propose a new uncertainty importance measure based on cumulative residual entropy. The proposed measure is moment-independent based on the cumulative distribution function, which can handle the highly-skewed distributions properly. Numerical implementations for estimating the proposed measure are devised and verified. A real-world engineering case considering highly-skewed distributions is introduced to show the procedure of developing uncertainty reduction strategies considering uncertainty magnitude and corresponding cost. The results demonstrate that the proposed measure can present a different uncertainty reduction recommendation compared to the variance-based approach because of its moment-independent characteristic.

Global sensitivity analysis (GSA) can provide rich information for controlling output uncertainty. In practical applications, segmented models are commonly used to describe an abrupt model change. For segmented models, the complicated uncertainty propagation during the transition region may lead to different importance rankings of different GSA methods. If an unsuitable GSA method is applied, misleading results will be obtained, resulting in suboptimal or even wrong decisions. In this paper, four GSA indices, i.e., Sobol index, mutual information, delta index and PAWN index, are applied for a segmented fire spread model (Dry Eucalypt). The results show that four GSA indices give different importance rankings during the transition region since segmented characteristics affect different GSA indices in different ways. We suggest that analysts should rely on the results of different GSA indices according to their practical purpose, especially when making decisions for segmented models during the transition region.

Recent attention to relational knowledge bases has sparked a demand for understanding how relations change between entities. Petri nets can represent knowledge structure and dynamically simulate interactions between entities, and thus they are well suited for achieving this goal. However, logic programs struggle to deal with extensive Petri nets due to the limitations of high-level symbol manipulations. To address this challenge, we introduce a novel approach called Boolean Matrix Logic Programming (BMLP), utilising boolean matrices as an alternative computation mechanism for Prolog to evaluate logic programs. Within this framework, we propose two novel BMLP algorithms for simulating a class of Petri nets known as elementary nets. This is done by transforming elementary nets into logically equivalent datalog programs. We demonstrate empirically that BMLP algorithms can evaluate these programs 40 times faster than tabled B-Prolog, SWI-Prolog, XSB-Prolog and Clingo. Our work enables the efficient simulation of elementary nets using Prolog, expanding the scope of analysis, learning and verification of complex systems with logic programming techniques., Comment: arXiv admin note: text overlap with arXiv:2405.06724

Techniques to autonomously drive research have been prominent in Computational Scientific Discovery, while Synthetic Biology is a field of science that focuses on designing and constructing new biological systems for useful purposes. Here we seek to apply logic-based machine learning techniques to facilitate cellular engineering and drive biological discovery. Comprehensive databases of metabolic processes called genome-scale metabolic network models (GEMs) are often used to evaluate cellular engineering strategies to optimise target compound production. However, predicted host behaviours are not always correctly described by GEMs, often due to errors in the models. The task of learning the intricate genetic interactions within GEMs presents computational and empirical challenges. To address these, we describe a novel approach called Boolean Matrix Logic Programming (BMLP) by leveraging boolean matrices to evaluate large logic programs. We introduce a new system, $BMLP_{active}$, which efficiently explores the genomic hypothesis space by guiding informative experimentation through active learning. In contrast to sub-symbolic methods, $BMLP_{active}$ encodes a state-of-the-art GEM of a widely accepted bacterial host in an interpretable and logical representation using datalog logic programs. Notably, $BMLP_{active}$ can successfully learn the interaction between a gene pair with fewer training examples than random experimentation, overcoming the increase in experimental design space. $BMLP_{active}$ enables rapid optimisation of metabolic models to reliably engineer biological systems for producing useful compounds. It offers a realistic approach to creating a self-driving lab for microbial engineering.

Accelerated degradation testing (ADT) is an effective way to evaluate the lifetime and reliability of highly reliable products. Markovian stochastic processes are usually applied to describe the degradation process. However, the degradation processes of some products are non-Markovian due to the interaction with environments. Besides, owing to the differences in materials and manufacturing processes, products from the same population exhibit diverse degradation paths. Motivated by this issue, an ADT model with memory effects and unit-to-unit variability (UtUV) is proposed in this article. The memory effect in the degradation process is captured by the fractional Brownian motion (FBM) and the UtUV is considered in the acceleration model. Then, the lifetime and reliability under the normal operating condition are presented. To give an accurate estimation of the memory effect, a statistical inference method is devised based on the expectation maximization (EM) algorithm. The effectiveness of the proposed method is verified by a simulation case and a microwave case. It is shown that the estimation of the memory effect obtained by the EM algorithm is much more accurate than the traditional method. Moreover, without considering UtUV in the ADT model, the estimation of the memory effect can be highly biased. The proposed ADT model is superior in both deterministic degradation trend predictions and degradation boundary quantification compared to existing models.

An important application of Synthetic Biology is the engineering of the host cell system to yield useful products. However, an increase in the scale of the host system leads to huge design space and requires a large number of validation trials with high experimental costs. A comprehensible machine learning approach that efficiently explores the hypothesis space and guides experimental design is urgently needed for the Design-Build-Test-Learn (DBTL) cycle of the host cell system. We introduce a novel machine learning framework ILP-iML1515 based on Inductive Logic Programming (ILP) that performs abductive logical reasoning and actively learns from training examples. In contrast to numerical models, ILP-iML1515 is built on comprehensible logical representations of a genome-scale metabolic model and can update the model by learning new logical structures from auxotrophic mutant trials. The ILP-iML1515 framework 1) allows high-throughput simulations and 2) actively selects experiments that reduce the experimental cost of learning gene functions in comparison to randomly selected experiments., Comment: Invited presentation for AAAI Spring Symposium Series 2023 on Computational Scientific Discovery