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Fadlelmoula A, Catarino SO, Minas G, Carvalho V. A Review of Machine Learning Methods Recently Applied to FTIR Spectroscopy Data for the Analysis of Human Blood Cells. MICROMACHINES 2023; 14:1145. [PMID: 37374730 DOI: 10.3390/mi14061145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/23/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023]
Abstract
Machine learning (ML) is a broad term encompassing several methods that allow us to learn from data. These methods may permit large real-world databases to be more rapidly translated to applications to inform patient-provider decision-making. This paper presents a review of articles that discuss the use of Fourier transform infrared (FTIR) spectroscopy and ML for human blood analysis between the years 2019-2023. The literature review was conducted to identify published research of employed ML linked with FTIR for distinction between pathological and healthy human blood cells. The articles' search strategy was implemented and studies meeting the eligibility criteria were evaluated. Relevant data related to the study design, statistical methods, and strengths and limitations were identified. A total of 39 publications in the last 5 years (2019-2023) were identified and evaluated for this review. Diverse methods, statistical packages, and approaches were used across the identified studies. The most common methods included support vector machine (SVM) and principal component analysis (PCA) approaches. Most studies applied internal validation and employed more than one algorithm, while only four studies applied one ML algorithm to the data. A wide variety of approaches, algorithms, statistical software, and validation strategies were employed in the application of ML methods. There is a need to ensure that multiple ML approaches are used, the model selection strategy is clearly defined, and both internal and external validation are necessary to be sure that the discrimination of human blood cells is being made with the highest efficient evidence.
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Affiliation(s)
- Ahmed Fadlelmoula
- Center for Microelectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- LABBELS-Associate Laboratory, 4800-058 Guimarães, Portugal
| | - Susana O Catarino
- Center for Microelectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- LABBELS-Associate Laboratory, 4800-058 Guimarães, Portugal
| | - Graça Minas
- Center for Microelectromechanical Systems (CMEMS-UMinho), Campus de Azurém, University of Minho, 4800-058 Guimarães, Portugal
- LABBELS-Associate Laboratory, 4800-058 Guimarães, Portugal
| | - Vítor Carvalho
- 2Ai, School of Technology, IPCA, 4750-810 Barcelos, Portugal
- Algoritmi Research Center/LASI, University of Minho, 4800-058 Guimarães, Portugal
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Pattern Recognition for Human Diseases Classification in Spectral Analysis. COMPUTATION 2022. [DOI: 10.3390/computation10060096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Pattern recognition is a multidisciplinary area that received more scientific attraction during this period of rapid technological innovation. Today, many real issues and scenarios require pattern recognition to aid in the faster resolution of complicated problems, particularly those that cannot be solved using traditional human heuristics. One common problem in pattern recognition is dealing with multidimensional data, which is prominent in studies involving spectral data such as ultraviolet-visible (UV/Vis), infrared (IR), and Raman spectroscopy data. UV/Vis, IR, and Raman spectroscopy are well-known spectroscopic methods that are used to determine the atomic or molecular structure of a sample in various fields. Typically, pattern recognition consists of two components: exploratory data analysis and classification method. Exploratory data analysis is an approach that involves detecting anomalies in data, extracting essential variables, and revealing the data’s underlying structure. On the other hand, classification methods are techniques or algorithms used to group samples into a predetermined category. This article discusses the fundamental assumptions, benefits, and limitations of some well-known pattern recognition algorithms including Principal Component Analysis (PCA), Kernel PCA, Successive Projection Algorithm (SPA), Genetic Algorithm (GA), Partial Least Square Regression (PLS-R), Linear Discriminant Analysis (LDA), K-Nearest Neighbors (KNN), Decision Tree (DT), Random Forest (RF), Support Vector Machine (SVM), Partial Least Square-Discriminant Analysis (PLS-DA) and Artificial Neural Network (ANN). The use of UV/Vis, IR, and Raman spectroscopy for disease classification is also highlighted. To conclude, many pattern recognition algorithms have the potential to overcome each of their distinct limits, and there is also the option of combining all of these algorithms to create an ensemble of methods.
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Xiao D, Le TTG, Doan TT, Le BT. Coal identification based on a deep network and reflectance spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 270:120859. [PMID: 35033804 DOI: 10.1016/j.saa.2022.120859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 12/16/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
The rapid identification of coal types in the field is an important task. This research combines spectroscopy with deep learning algorithms and proposes a method for quickly identifying coal types in the field. First, we collect field spectral data of various coals and preprocess the spectra. Then, a coal identification model that uses a convolutional neural network in combination with an extreme learning machine is proposed. The two-dimensional spectral features of coal are extracted through the convolutional neural network, and the extreme learning machine is used as a classifier to identify the features. To further improve the identification performance of the model, we use the whale optimization algorithm to optimize the parameters of the model. The experimental results show that the proposed method can quickly and accurately identify types of coal. It provides a low-cost, convenient, and effective method for the rapid identification of coal in the field.
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Affiliation(s)
- Dong Xiao
- College of Information Science and Engineering, Northeastern University, Shenyang 110819, China; Key Laboratory of Intelligent Diagnosis and Safety for Metallurgical Industry, Liaoning Province, Northeastern University, Shenyang 110819, China
| | - Thi Tra Giang Le
- Training Department, Institute of Science and Technology, Hoang Sam 100000, Ha Noi, Viet Nam
| | | | - Ba Tuan Le
- Control, Automation in Production and Improvement of Technology Institute (CAPITI), Hanoi, 100000, Viet Nam.
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Dauda WP, Abraham P, Glen E, Adetunji CO, Ghazanfar S, Ali S, Al-Zahrani M, Azameti MK, Alao SEL, Zarafi AB, Abraham MP, Musa H. Robust Profiling of Cytochrome P450s (P450ome) in Notable Aspergillus spp. Life (Basel) 2022; 12:life12030451. [PMID: 35330202 PMCID: PMC8955511 DOI: 10.3390/life12030451] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 02/03/2023] Open
Abstract
Cytochrome P450s (P450ome) constitute an extended superfamily group of heme-thiolate enzymes identified in all biological domains. P450omes play a critical role in the oxidation of steroids and fatty acids, xenobiotic degradation of hydrophobic compounds, biosynthesis of hormones, and primary and secondary metabolism in organisms. Aspergillus species are among the most economically important fungal organisms in human medicine, industry, and agriculture worldwide. Exploring insight on the genome-wide annotations of cytochrome P450s in Aspergillus species is necessary for their biosynthetic applications. In this present study, we report the identification of 306 cytochrome P450s and their robust profiling in eight notable Aspergillus species (A. carbonarius, A. clavatus, A. flavus, A. fumigatus, A. nidulans, A. niger, A. oryzae, and A. terreus). Based on the evolutionary relationship, the Aspergillus P450s families clustered into 15 clades, with clades V, I, and XIII recording higher percentages (17.3%, 15.00%, and 14.71%, respectively) of Cyp families. Cyps were classified into 120 families 64 clans, and their putative functions were also elucidated. P450s were predicted to be located in 13 subcellular components, but the endoplasm reticulum was the dominant location across the eight Aspergillus species. Cyps genes of Aspergillus species were associated with seven secondary metabolism-related gene clusters. Elucidating the genome-wide annotations of P450s enzymes in Aspergillus species will form vital potential biotechnological tools that could be harnessed for industrial, pharmaceutical, and agricultural use.
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Affiliation(s)
- Wadzani Palnam Dauda
- Crop Science Unit, Department of Agronomy, Federal University Gashua, Gashua P.M.B 1005, Yobe State, Nigeria
- Correspondence:
| | - Peter Abraham
- Department of Horticulture, Federal College of Horticulture, Dadin Kowa P.M.B 108, Gombe State, Nigeria; (P.A.); (M.P.A.)
| | - Elkanah Glen
- Department of Biochemistry, Federal University Lokoja, Lokoja P.M.B 1154, Kogi State, Nigeria;
| | - Charles Oluwaseun Adetunji
- Applied Microbiology, Biotechnology and Nanotechnology Laboratory, Department of Microbiology, Edo University Iyamho, Auchi P.M.B 04, Edo State, Nigeria;
| | - Shakira Ghazanfar
- National Agricultural Research Centre, National Institute of Genomics and Agriculture Biotechnology (NIGAB), Park Road, Islamabad 45500, Pakistan;
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad 38000, Pakistan;
- Department of Biological Sciences and Technology, China Medical University, Taichung 40402, Taiwan
| | - Majid Al-Zahrani
- Biological Science Department, College of Sciences and Art, King Abdulaziz University, Rabigh 80200, Saudi Arabia;
| | - Mawuli Kwamla Azameti
- Division of Molecular Biology and Biotechnology, Indian Agricultural Research Institute, New Delhi 110012, India;
| | - Sheik Emmanuel Laykay Alao
- Department of Crop Protection, Faculty of Agriculture, Ahmadu Bello University, Zaria 810107, Kaduna State, Nigeria; (S.E.L.A.); (A.B.Z.)
| | - Afiniki Bawa Zarafi
- Department of Crop Protection, Faculty of Agriculture, Ahmadu Bello University, Zaria 810107, Kaduna State, Nigeria; (S.E.L.A.); (A.B.Z.)
| | - Maryam Peter Abraham
- Department of Horticulture, Federal College of Horticulture, Dadin Kowa P.M.B 108, Gombe State, Nigeria; (P.A.); (M.P.A.)
| | - Hannatu Musa
- Department of Botany, Ahmadu Bello University, Zaria 810107, Kaduna State, Nigeria;
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Kamnev AA, Dyatlova YA, Kenzhegulov OA, Vladimirova AA, Mamchenkova PV, Tugarova AV. Fourier Transform Infrared (FTIR) Spectroscopic Analyses of Microbiological Samples and Biogenic Selenium Nanoparticles of Microbial Origin: Sample Preparation Effects. Molecules 2021; 26:1146. [PMID: 33669948 PMCID: PMC7924863 DOI: 10.3390/molecules26041146] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 02/14/2021] [Accepted: 02/18/2021] [Indexed: 12/17/2022] Open
Abstract
To demonstrate the importance of sample preparation used in Fourier transform infrared (FTIR) spectroscopy of microbiological materials, bacterial biomass samples with and without grinding and after different drying periods (1.5-23 h at 45 °C), as well as biogenic selenium nanoparticles (SeNPs; without washing and after one to three washing steps) were comparatively studied by transmission FTIR spectroscopy. For preparing bacterial biomass samples, Azospirillum brasilense Sp7 and A. baldaniorum Sp245 (earlier known as A. brasilense Sp245) were used. The SeNPs were obtained using A. brasilense Sp7 incubated with selenite. Grinding of the biomass samples was shown to result in slight downshifting of the bands related to cellular poly-3-hydroxybutyrate (PHB) present in the samples in small amounts (under ~10%), reflecting its partial crystallisation. Drying for 23 h was shown to give more reproducible FTIR spectra of bacterial samples. SeNPs were shown to contain capping layers of proteins, polysaccharides and lipids. The as-prepared SeNPs contained significant amounts of carboxylated components in their bioorganic capping, which appeared to be weakly bound and were largely removed after washing. Spectroscopic characteristics and changes induced by various sample preparation steps are discussed with regard to optimising sample treatment procedures for FTIR spectroscopic analyses of microbiological specimens.
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Affiliation(s)
- Alexander A. Kamnev
- Laboratory of Biochemistry, Institute of Biochemistry and Physiology of Plants and Microorganisms, Russian Academy of Sciences, 410049 Saratov, Russia; (Y.A.D.); (O.A.K.); (A.A.V.); (P.V.M.); (A.V.T.)
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