Algorithms

28 pages, 2896 KiB

Open AccessArticle

Qualitative Perturbation Analysis and Machine Learning: Elucidating Bacterial Optimization of Tryptophan Production

by Miguel Angel Ramos-Valdovinos, Prisciluis Caheri Salas-Navarrete, Gerardo R. Amores, Ana Lilia Hernández-Orihuela and Agustino Martínez-Antonio

Algorithms 2024, 17(7), 282; https://doi.org/10.3390/a17070282 (registering DOI) - 27 Jun 2024

Abstract

L-tryptophan is an essential amino acid widely used in the pharmaceutical and feed industries. Enhancing its production in microorganisms necessitates activating and inactivating specific genes to direct more resources toward its synthesis. In this study, we developed a classification model based on Qualitative [...] Read more.

L-tryptophan is an essential amino acid widely used in the pharmaceutical and feed industries. Enhancing its production in microorganisms necessitates activating and inactivating specific genes to direct more resources toward its synthesis. In this study, we developed a classification model based on Qualitative Perturbation Analysis and Machine Learning (QPAML). The model uses pFBA to obtain optimal reactions for tryptophan production and FSEOF to introduce perturbations on fluxes of the optima reactions while registering all changes over the iML1515a Genome-Scale Metabolic Network model. The altered reaction fluxes and their relationship with tryptophan and biomass production are translated to qualitative variables classified with GBDT. In the end, groups of enzymatic reactions are predicted to be deleted, overexpressed, or attenuated for tryptophan and 30 other metabolites in E. coli with a 92.34% F1-Score. The QPAML model can integrate diverse data types, promising improved predictions and the discovery of complex patterns in microbial metabolic engineering. It has broad potential applications and offers valuable insights for optimizing microbial production in biotechnology. Full article

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23 pages, 1378 KiB

Open AccessArticle

Optimizing Automated Brain Extraction for Moderate to Severe Traumatic Brain Injury Patients: The Role of Intensity Normalization and Bias-Field Correction

by Patrick Carbone, Celina Alba, Alexis Bennett, Kseniia Kriukova and Dominique Duncan

Algorithms 2024, 17(7), 281; https://doi.org/10.3390/a17070281 - 27 Jun 2024

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Abstract

Accurate brain extraction is crucial for the validity of MRI analyses, particularly in the context of traumatic brain injury (TBI), where conventional automated methods frequently fall short. This study investigates the interplay between intensity normalization, bias-field correction (also called intensity inhomogeneity correction), and [...] Read more.

Accurate brain extraction is crucial for the validity of MRI analyses, particularly in the context of traumatic brain injury (TBI), where conventional automated methods frequently fall short. This study investigates the interplay between intensity normalization, bias-field correction (also called intensity inhomogeneity correction), and automated brain extraction in MRIs of individuals with TBI. We analyzed 125 T1-weighted Magnetization-Prepared Rapid Gradient-Echo (T1-MPRAGE) and 72 T2-weighted Fluid-Attenuated Inversion Recovery (T2-FLAIR) MRI sequences from a cohort of 143 patients with moderate to severe TBI. Our study combined 14 different intensity processing procedures, each using a configuration of N3 inhomogeneity correction, Z-score normalization, KDE-based normalization, or WhiteStripe intensity normalization, with 10 different configurations of the Brain Extraction Tool (BET) and the Optimized Brain Extraction Tool (optiBET). Our results demonstrate that optiBET with N3 inhomogeneity correction produces the most accurate brain extractions, specifically with one iteration of N3 for T1-MPRAGE and four iterations for T2-FLAIR, and pipelines incorporating N3 inhomogeneity correction significantly improved the accuracy of BET as well. Conversely, intensity normalization demonstrated a complex relationship with brain extraction, with effects varying by the normalization algorithm and BET parameter configuration combination. This study elucidates the interactions between intensity processing and the accuracy of brain extraction. Understanding these relationships is essential to the effective and efficient preprocessing of TBI MRI data, laying the groundwork for the development of robust preprocessing pipelines optimized for multi-site TBI MRI data. Full article

(This article belongs to the Special Issue Algorithms for Computer Aided Diagnosis)

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17 pages, 8135 KiB

Open AccessArticle

LungVision: X-ray Imagery Classification for On-Edge Diagnosis Applications

by Raghad Aldamani, Diaa Addeen Abuhani and Tamer Shanableh

Algorithms 2024, 17(7), 280; https://doi.org/10.3390/a17070280 - 27 Jun 2024

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Abstract

This study presents a comprehensive analysis of utilizing TensorFlow Lite on mobile phones for the on-edge medical diagnosis of lung diseases. This paper focuses on the technical deployment of various deep learning architectures to classify nine respiratory system diseases using X-ray imagery. We [...] Read more.

This study presents a comprehensive analysis of utilizing TensorFlow Lite on mobile phones for the on-edge medical diagnosis of lung diseases. This paper focuses on the technical deployment of various deep learning architectures to classify nine respiratory system diseases using X-ray imagery. We propose a simple deep learning architecture that experiments with six different convolutional neural networks. Various quantization techniques are employed to convert the classification models into TensorFlow Lite, including post-classification quantization with floating point 16 bit representation, integer quantization with representative data, and quantization-aware training. This results in a total of 18 models suitable for on-edge deployment for the classification of lung diseases. We then examine the generated models in terms of model size reduction, accuracy, and inference time. Our findings indicate that the quantization-aware training approach demonstrates superior optimization results, achieving an average model size reduction of 75.59%. Among many CNNs, MobileNetV2 exhibited the highest performance-to-size ratio, with an average accuracy loss of 4.1% across all models using the quantization-aware training approach. In terms of inference time, TensorFlow Lite with integer quantization emerged as the most efficient technique, with an average improvement of 1.4 s over other conversion approaches. Our best model, which used EfficientNetB2, achieved an F1-Score of approximately 98.58%, surpassing state-of-the-art performance on the X-ray lung diseases dataset in terms of accuracy, specificity, and sensitivity. The model experienced an F1 loss of around 1% using quantization-aware optimization. The study culminated in the development of a consumer-ready app, with TensorFlow Lite models tailored to mobile devices. Full article

(This article belongs to the Special Issue Machine Learning in Medical Signal and Image Processing (2nd Edition))

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7 pages, 290 KiB

Open AccessBrief Report

A Short Note on Physics-Guided GAN to Learn Physical Models without Gradients

by Kazuo Yonekura

Algorithms 2024, 17(7), 279; https://doi.org/10.3390/a17070279 - 26 Jun 2024

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Abstract

This study briefly describes the concept of guided training of deep neural networks (DNNs) to learn physically reasonable solutions. The proposed method does not need the gradients of the physical equations, although the conventional physics-informed models need the gradients. DNNs are widely used [...] Read more.

This study briefly describes the concept of guided training of deep neural networks (DNNs) to learn physically reasonable solutions. The proposed method does not need the gradients of the physical equations, although the conventional physics-informed models need the gradients. DNNs are widely used to predict phenomena in physics and mechanics. One of the issues with DNNs is that their output does not always satisfy physical equations. One approach to consider with physical equations is adding a residual of the equations into the loss function; this is called physics-informed neural network (PINN). One feature of PINNs is that the physical equations and corresponding residuals must be implemented as part of a neural network model. In addition, the residual does not always converge to a small value. The proposed model is a physics-guided generative adversarial network (PG-GAN) that uses a GAN architecture, in which physical equations are used to judge whether the neural network’s output is consistent with physics. The proposed method was applied to a simple problem to assess its potential usability. Full article

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18 pages, 1674 KiB

Open AccessArticle

Domain-Specific Few-Shot Table Prompt Question Answering via Contrastive Exemplar Selection

by Tianjin Mo, Qiao Xiao, Hongyi Zhang, Ren Li and Yunsong Wu

Algorithms 2024, 17(7), 278; https://doi.org/10.3390/a17070278 - 26 Jun 2024

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Abstract

As a crucial task in natural language processing, table question answering has garnered significant attention from both the academic and industrial communities. It enables intelligent querying and question answering over structured data by translating natural language into corresponding SQL statements. Recently, there have [...] Read more.

As a crucial task in natural language processing, table question answering has garnered significant attention from both the academic and industrial communities. It enables intelligent querying and question answering over structured data by translating natural language into corresponding SQL statements. Recently, there have been notable advancements in the general domain table question answering task, achieved through prompt learning with large language models. However, in specific domains, where tables often have a higher number of columns and questions tend to be more complex, large language models are prone to generating invalid SQL or NoSQL statements. To address the above issue, this paper proposes a novel few-shot table prompt question answering approach. Specifically, we design a prompt template construction strategy for structured SQL generation. It utilizes prompt templates to restructure the input for each test data and standardizes the model output, which can enhance the integrity and validity of generated SQL. Furthermore, this paper introduces a contrastive exemplar selection approach based on the question patterns and formats in domain-specific contexts. This enables the model to quickly retrieve the relevant exemplars and learn characteristics about given question. Experimental results on the two datasets in the domains of electric energy and structural inspection show that the proposed approach outperforms the baseline models across all comparison settings. Full article

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21 pages, 1092 KiB

Open AccessArticle

Algorithmic Implementation of Visually Guided Interceptive Actions: Harmonic Ratios and Stimulation Invariants

by Wangdo Kim, Duarte Araujo, MooYoung Choi, Albert Vette and Eunice Ortiz

Algorithms 2024, 17(7), 277; https://doi.org/10.3390/a17070277 - 24 Jun 2024

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Abstract

This research presents a novel algorithmic implementation to improve the analysis of visually controlled interception and accompanying motor action through the computational application of harmonic ratios and stimulation invariants. Unlike traditional models that focus mainly on psychological aspects, our approach integrates the relevant [...] Read more.

This research presents a novel algorithmic implementation to improve the analysis of visually controlled interception and accompanying motor action through the computational application of harmonic ratios and stimulation invariants. Unlike traditional models that focus mainly on psychological aspects, our approach integrates the relevant constructs into a practical mathematical framework. This allows for dynamic prediction of interception points with improved accuracy and real-time perception–action capabilities, essential for applications in neurorehabilitation and virtual reality. Our methodology uses stimulation invariants as key parameters within a mathematical model to quantitatively predict and improve interception outcomes. The results demonstrate the superior performance of our algorithms over conventional methods, confirming their potential for advancing robotic vision systems and adaptive virtual environments. By translating complex theories of visual perception into algorithmic solutions, this study provides innovative ways to improve motion perception and interactive systems. This study aims to articulate the complex interplay of geometry, perception, and technology in understanding and utilizing cross ratios at infinity, emphasizing their practical applications in virtual and augmented reality settings. Full article

(This article belongs to the Special Issue Algorithms for Virtual and Augmented Environments)

21 pages, 20486 KiB

Open AccessArticle

AFE-YOLOv8: A Novel Object Detection Model for Unmanned Aerial Vehicle Scenes with Adaptive Feature Enhancement

by Shijie Wang, Zekun Zhang, Qingqing Chao and Teng Yu

Algorithms 2024, 17(7), 276; https://doi.org/10.3390/a17070276 - 24 Jun 2024

Viewed by 275

Abstract

Object detection in unmanned aerial vehicle (UAV) scenes is a challenging task due to the varying scales and complexities of targets. To address this, we propose a novel object detection model, AFE-YOLOv8, which integrates three innovative modules: the Multi-scale Nonlinear Fusion Module (MNFM), [...] Read more.

Object detection in unmanned aerial vehicle (UAV) scenes is a challenging task due to the varying scales and complexities of targets. To address this, we propose a novel object detection model, AFE-YOLOv8, which integrates three innovative modules: the Multi-scale Nonlinear Fusion Module (MNFM), the Adaptive Feature Enhancement Module (AFEM), and the Receptive Field Expansion Module (RFEM). The MNFM introduces nonlinear mapping by exploiting the property that deformable convolution can dynamically adjust the shape of the convolution kernel according to the shape of the target, and it effectively enhances the feature extraction capability of the backbone network by integrating multi-scale feature maps from different mapping branches. Meanwhile, the AFEM introduces an adaptive fusion factor, and through the fusion factor, it adaptively integrates the small-target features contained in the feature maps of different detection branches into the small-target detection branch, thus enhancing the expression of the small-target features contained in the feature maps of the small-target detection branch. Furthermore, the RFEM expands the receptive field of the feature maps of the large- and medium-scale target detection branches through stacked convolution, so as to make the model’s receptive field cover the whole target, and thereby learn more rich and comprehensive features of the target. The experimental results demonstrate the superior performance of the proposed model compared to the baseline in detecting objects of various scales. On the VisDrone dataset, the proposed model achieves a 4.5% enhancement in mean average precision (mAP) and a 5.45% improvement in average precision at an IOU threshold of 0.5 (AP50). Additionally, ablation experiments conducted on the challenging DOTA dataset showcase the model’s robustness and generalization capabilities. Full article

(This article belongs to the Collection Feature Papers on Artificial Intelligence Algorithms and Their Applications)

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18 pages, 382 KiB

Open AccessArticle

Supervised Dynamic Correlated Topic Model for Classifying Categorical Time Series

by Namitha Pais, Nalini Ravishanker and Sanguthevar Rajasekaran

Algorithms 2024, 17(7), 275; https://doi.org/10.3390/a17070275 - 22 Jun 2024

Viewed by 259

Abstract

In this paper, we describe the supervised dynamic correlated topic model (sDCTM) for classifying categorical time series. This model extends the correlated topic model used for analyzing textual documents to a supervised framework that features dynamic modeling of latent topics. sDCTM treats each [...] Read more.

In this paper, we describe the supervised dynamic correlated topic model (sDCTM) for classifying categorical time series. This model extends the correlated topic model used for analyzing textual documents to a supervised framework that features dynamic modeling of latent topics. sDCTM treats each time series as a document and each categorical value in the time series as a word in the document. We assume that the observed time series is generated by an underlying latent stochastic process. We develop a state-space framework to model the dynamic evolution of the latent process, i.e., the hidden thematic structure of the time series. Our model provides a Bayesian supervised learning (classification) framework using a variational Kalman filter EM algorithm. The E-step and M-step, respectively, approximate the posterior distribution of the latent variables and estimate the model parameters. The fitted model is then used for the classification of new time series and for information retrieval that is useful for practitioners. We assess our method using simulated data. As an illustration to real data, we apply our method to promoter sequence identification data to classify E. coli DNA sub-sequences by uncovering hidden patterns or motifs that can serve as markers for promoter presence. Full article

(This article belongs to the Special Issue Hybrid Intelligent Algorithms)

21 pages, 4962 KiB

Open AccessArticle

Multi-Criteria Decision Support System for Automatically Selecting Photovoltaic Sets to Maximise Micro Solar Generation

by Guilherme Zanlorenzi, Anderson Luis Szejka and Osiris Canciglieri Junior

Algorithms 2024, 17(7), 274; https://doi.org/10.3390/a17070274 - 22 Jun 2024

Viewed by 299

Abstract

Technological advancements have improved solar energy generation and reduced the cost of installing photovoltaic (PV) systems. However, challenges such as low energy-conversion efficiency and the unpredictability of electricity generation due to shading or climate conditions persist. Despite decreasing costs, access to solar energy [...] Read more.

Technological advancements have improved solar energy generation and reduced the cost of installing photovoltaic (PV) systems. However, challenges such as low energy-conversion efficiency and the unpredictability of electricity generation due to shading or climate conditions persist. Despite decreasing costs, access to solar energy generation technologies remains limited. This paper proposes a multi-criteria decision support system (MCDSS) for selecting the most suitable PV set (comprising PV modules, inverters, and batteries) for microgrid installations. The MCDSS employs two multi-criteria decision-making methods (MCDM) for analysis and decision-making: AHP and TOPSIS. The system was tested in two case studies: Barreiras, with a global efficiency of 14.4% and an internal rate of return (IRR) of 56.0%, and Curitiba, with a worldwide efficiency of 14.8% and an IRR of 52.0%. The research provided a framework for assessing and selecting PV sets based on efficiency, cost, and return on investment. Methodologically, it integrates multiple MCDM techniques, demonstrating their applicability in renewable energy. Managerially, it offers a practical tool for decision-makers in the energy sector to enhance the feasibility and attractiveness of microgeneration projects. This research highlights the potential of MCDSS to improve the efficiency and accessibility of solar energy generation. Full article

(This article belongs to the Special Issue Scheduling Theory and Algorithms for Sustainable Manufacturing)

23 pages, 687 KiB

Open AccessArticle

Verification of Control System Runtime Using an Executable Semantic Model

by Jan Sadolewski and Bartosz Trybus

Algorithms 2024, 17(7), 273; https://doi.org/10.3390/a17070273 - 22 Jun 2024

Viewed by 211

Abstract

The paper outlines a methodology for validating the accuracy of a control system’s runtime implementation. The runtime takes the form of a virtual machine executing portable code compliant with IEC 61131-3 standards. A formal model, comprising denotational semantics equations, has been devised to [...] Read more.

The paper outlines a methodology for validating the accuracy of a control system’s runtime implementation. The runtime takes the form of a virtual machine executing portable code compliant with IEC 61131-3 standards. A formal model, comprising denotational semantics equations, has been devised to specify machine instruction decoding and operations, including arithmetic functions across various data types, arrays, and subprogram calls. The model also encompasses exception-handling mechanisms for runtime errors, such as division by zero and invalid array index access. This denotational model is translated into executable form using the functional F

^{♯}

language. Verification involves comparing the actual implementation of the virtual machine against this executable model. Any disparities between the model and implementation indicate deviations from the specification. Implemented within the CPDev engineering environment, this approach ensures consistent and predictable control program execution across different target platforms. Full article

(This article belongs to the Special Issue Algorithms for Network Systems and Applications)

13 pages, 1585 KiB

Open AccessArticle

An Improved Adam’s Algorithm for Stomach Image Classification

by Haijing Sun, Hao Yu, Yichuan Shao, Jiantao Wang, Lei Xing, Le Zhang and Qian Zhao

Algorithms 2024, 17(7), 272; https://doi.org/10.3390/a17070272 - 21 Jun 2024

Viewed by 243

Abstract

Current stomach disease detection and diagnosis is challenged by data complexity and high dimensionality and requires effective deep learning algorithms to improve diagnostic accuracy. To address this challenge, in this paper, an improved strategy based on the Adam algorithm is proposed, which aims [...] Read more.

Current stomach disease detection and diagnosis is challenged by data complexity and high dimensionality and requires effective deep learning algorithms to improve diagnostic accuracy. To address this challenge, in this paper, an improved strategy based on the Adam algorithm is proposed, which aims to alleviate the influence of local optimal solutions, overfitting, and slow convergence rates by controlling the restart strategy and the gradient norm joint clipping technique. This improved algorithm is abbreviated as the CG-Adam algorithm. The control restart strategy performs a restart operation by periodically checking the number of steps and once the number of steps reaches a preset restart period. After the restart is completed, the algorithm will restart the optimization process. It helps the algorithm avoid falling into the local optimum and maintain convergence stability. Meanwhile, gradient norm joint clipping combines both gradient clipping and norm clipping techniques, which can avoid gradient explosion and gradient vanishing problems and help accelerate the convergence of the optimization process by restricting the gradient and norm to a suitable range. In order to verify the effectiveness of the CG-Adam algorithm, experimental validation is carried out on the MNIST, CIFAR10, and Stomach datasets and compared with the Adam algorithm as well as the current popular optimization algorithms. The experimental results demonstrate that the improved algorithm proposed in this paper achieves an accuracy of 98.59%, 70.7%, and 73.2% on the MNIST, CIFAR10, and Stomach datasets, respectively, surpassing the Adam algorithm. The experimental results not only prove the significant effect of the CG-Adam algorithm in accelerating the model convergence and improving generalization performance but also demonstrate its wide potential and practical application value in the field of medical image recognition. Full article

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Algorithms, Volume 17, Issue 7 (July 2024) – 11 articles

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