1
|
Khatibi SMH, Ali J. Harnessing the power of machine learning for crop improvement and sustainable production. FRONTIERS IN PLANT SCIENCE 2024; 15:1417912. [PMID: 39188546 PMCID: PMC11346375 DOI: 10.3389/fpls.2024.1417912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/15/2024] [Indexed: 08/28/2024]
Abstract
Crop improvement and production domains encounter large amounts of expanding data with multi-layer complexity that forces researchers to use machine-learning approaches to establish predictive and informative models to understand the sophisticated mechanisms underlying these processes. All machine-learning approaches aim to fit models to target data; nevertheless, it should be noted that a wide range of specialized methods might initially appear confusing. The principal objective of this study is to offer researchers an explicit introduction to some of the essential machine-learning approaches and their applications, comprising the most modern and utilized methods that have gained widespread adoption in crop improvement or similar domains. This article explicitly explains how different machine-learning methods could be applied for given agricultural data, highlights newly emerging techniques for machine-learning users, and lays out technical strategies for agri/crop research practitioners and researchers.
Collapse
Affiliation(s)
| | - Jauhar Ali
- Rice Breeding Platform, International Rice Research Institute, Los Baños, Laguna, Philippines
| |
Collapse
|
2
|
van Diest PJ, Flach RN, van Dooijeweert C, Makineli S, Breimer GE, Stathonikos N, Pham P, Nguyen TQ, Veta M. Pros and cons of artificial intelligence implementation in diagnostic pathology. Histopathology 2024; 84:924-934. [PMID: 38433288 DOI: 10.1111/his.15153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/29/2023] [Accepted: 01/19/2024] [Indexed: 03/05/2024]
Abstract
The rapid introduction of digital pathology has greatly facilitated development of artificial intelligence (AI) models in pathology that have shown great promise in assisting morphological diagnostics and quantitation of therapeutic targets. We are now at a tipping point where companies have started to bring algorithms to the market, and questions arise whether the pathology community is ready to implement AI in routine workflow. However, concerns also arise about the use of AI in pathology. This article reviews the pros and cons of introducing AI in diagnostic pathology.
Collapse
Affiliation(s)
- Paul J van Diest
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Rachel N Flach
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Oncological Urology, University Medical Center Utrecht, Utrecht, the Netherlands
| | | | - Seher Makineli
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Surgical Oncology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Gerben E Breimer
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Nikolas Stathonikos
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Paul Pham
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Tri Q Nguyen
- Department of Pathology, University Medical Center Utrecht, Utrecht, the Netherlands
| | - Mitko Veta
- Department of Oncological Urology, University Medical Center Utrecht, Utrecht, the Netherlands
- Department of Biomedical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
| |
Collapse
|
3
|
Vandenberk B, Chew DS, Prasana D, Gupta S, Exner DV. Successes and challenges of artificial intelligence in cardiology. Front Digit Health 2023; 5:1201392. [PMID: 37448836 PMCID: PMC10336354 DOI: 10.3389/fdgth.2023.1201392] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 06/19/2023] [Indexed: 07/15/2023] Open
Abstract
In the past decades there has been a substantial evolution in data management and data processing techniques. New data architectures made analysis of big data feasible, healthcare is orienting towards personalized medicine with digital health initiatives, and artificial intelligence (AI) is becoming of increasing importance. Despite being a trendy research topic, only very few applications reach the stage where they are implemented in clinical practice. This review provides an overview of current methodologies and identifies clinical and organizational challenges for AI in healthcare.
Collapse
Affiliation(s)
- Bert Vandenberk
- Department of Cardiac Sciences, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
- Department of Cardiovascular Sciences, KU Leuven, Leuven, Belgium
| | - Derek S. Chew
- Department of Cardiac Sciences, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Dinesh Prasana
- Intelense Inc., Markham, ON, Canada
- IOT/AI- Caliber Interconnect Pvt Ltd., Coimbatore, India
| | | | - Derek V. Exner
- Department of Cardiac Sciences, Libin Cardiovascular Institute, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
4
|
Sinonquel P, Schilirò A, Verstockt B, Vermeire S, Bisschops R. Evaluating the potential of artificial intelligence in ulcerative colitis. Expert Rev Gastroenterol Hepatol 2023; 17:145-153. [PMID: 36610437 DOI: 10.1080/17474124.2023.2166928] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
INTRODUCTION Diagnosis and therapeutic management in ulcerative colitis (UC) relies on a combination of endoscopic and histological scorings which are difficult to objectively quantify. Artificial intelligence (AI) might overcome the current issues of inter-observer variability, repetitive need for biopsies and estimation of disease activity medicine currently encourages. AREAS COVERED With this narrative literature review we aim to provide a clear and critical overview of the recent evolutions in the field of AI and UC, based on a literature search performed on Pubmed, Embase and Cochrane Library. The major focus of this review is the use of AI for endoscopic assessment of disease activity and the correlation with histology and long-term outcome. Moreover, we elucidate on the more recent developments in the field of AI as support in histological disease assessment, surveillance, therapy monitoring and natural language processing. EXPERT OPINION UC management is evolving with AI impacting nearly every aspect of it. The immediate future influence of AI in UC management will be focussed on the collection, extraction and organization of particular clinical information. Expect is the transformation toward a real-time standardized, reproducible, objective and high-reliable disease grading, especially in endoscopy, histology and eventually radiology applications for UC.
Collapse
Affiliation(s)
- Pieter Sinonquel
- Department of Gastroenterology and Hepatology, UZ Leuven, Leuven, Belgium.,Department of Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | | | - Bram Verstockt
- Department of Gastroenterology and Hepatology, UZ Leuven, Leuven, Belgium.,Department of Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Séverine Vermeire
- Department of Gastroenterology and Hepatology, UZ Leuven, Leuven, Belgium.,Department of Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| | - Raf Bisschops
- Department of Gastroenterology and Hepatology, UZ Leuven, Leuven, Belgium.,Department of Translational Research in Gastrointestinal Disorders (TARGID), KU Leuven, Leuven, Belgium
| |
Collapse
|
5
|
Stafford IS, Gosink MM, Mossotto E, Ennis S, Hauben M. A Systematic Review of Artificial Intelligence and Machine Learning Applications to Inflammatory Bowel Disease, with Practical Guidelines for Interpretation. Inflamm Bowel Dis 2022; 28:1573-1583. [PMID: 35699597 PMCID: PMC9527612 DOI: 10.1093/ibd/izac115] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Indexed: 12/15/2022]
Abstract
BACKGROUND Inflammatory bowel disease (IBD) is a gastrointestinal chronic disease with an unpredictable disease course. Computational methods such as machine learning (ML) have the potential to stratify IBD patients for the provision of individualized care. The use of ML methods for IBD was surveyed, with an additional focus on how the field has changed over time. METHODS On May 6, 2021, a systematic review was conducted through a search of MEDLINE and Embase databases, with the search structure ("machine learning" OR "artificial intelligence") AND ("Crohn* Disease" OR "Ulcerative Colitis" OR "Inflammatory Bowel Disease"). Exclusion criteria included studies not written in English, no human patient data, publication before 2001, studies that were not peer reviewed, nonautoimmune disease comorbidity research, and record types that were not primary research. RESULTS Seventy-eight (of 409) records met the inclusion criteria. Random forest methods were most prevalent, and there was an increase in neural networks, mainly applied to imaging data sets. The main applications of ML to clinical tasks were diagnosis (18 of 78), disease course (22 of 78), and disease severity (16 of 78). The median sample size was 263. Clinical and microbiome-related data sets were most popular. Five percent of studies used an external data set after training and testing for additional model validation. DISCUSSION Availability of longitudinal and deep phenotyping data could lead to better modeling. Machine learning pipelines that consider imbalanced data and that feature selection only on training data will generate more generalizable models. Machine learning models are increasingly being applied to more complex clinical tasks for specific phenotypes, indicating progress towards personalized medicine for IBD.
Collapse
Affiliation(s)
- Imogen S Stafford
- Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
- Institute for Life Sciences, University Of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research, University HospitalSouthampton, Southampton, UK
| | | | - Enrico Mossotto
- Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Sarah Ennis
- Human Genetics and Genomic Medicine, University of Southampton, Southampton, UK
| | - Manfred Hauben
- Pfizer Inc, New York, NY, USA
- NYU Langone Health, Department of Medicine, New York, NY, USA
| |
Collapse
|
6
|
Pareek A, Lungren MP, Halabi SS. The requirements for performing artificial-intelligence-related research and model development. Pediatr Radiol 2022; 52:2094-2100. [PMID: 35996023 DOI: 10.1007/s00247-022-05483-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 07/06/2022] [Accepted: 08/09/2022] [Indexed: 11/25/2022]
Abstract
Artificial intelligence research in health care has undergone tremendous growth in the last several years thanks to the explosion of digital health care data and systems that can leverage large amounts of data to learn patterns that can be applied to clinical tasks. In addition, given broad acceleration in machine learning across industries like transportation, media and commerce, there has been a significant growth in demand for machine-learning practitioners such as engineers and data scientists, who have skill sets that can be applied to health care use cases but who simultaneously lack important health care domain expertise. The purpose of this paper is to discuss the requirements of building an artificial-intelligence research enterprise including the research team, technical software/hardware, and procurement and curation of health care data.
Collapse
Affiliation(s)
- Anuj Pareek
- Stanford AIMI Center, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, USA.
| | - Matthew P Lungren
- Stanford AIMI Center, Stanford University, 1701 Page Mill Road, Palo Alto, CA, 94304, USA
| | - Safwan S Halabi
- Department of Medical Imaging, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| |
Collapse
|
7
|
Yang CB, Kim SH, Lim YJ. Preparation of image databases for artificial intelligence algorithm development in gastrointestinal endoscopy. Clin Endosc 2022; 55:594-604. [PMID: 35636749 PMCID: PMC9539300 DOI: 10.5946/ce.2021.229] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 03/07/2022] [Indexed: 12/09/2022] Open
Abstract
Over the past decade, technological advances in deep learning have led to the introduction of artificial intelligence (AI) in medical imaging. The most commonly used structure in image recognition is the convolutional neural network, which mimics the action of the human visual cortex. The applications of AI in gastrointestinal endoscopy are diverse. Computer-aided diagnosis has achieved remarkable outcomes with recent improvements in machine-learning techniques and advances in computer performance. Despite some hurdles, the implementation of AI-assisted clinical practice is expected to aid endoscopists in real-time decision-making. In this summary, we reviewed state-of-the-art AI in the field of gastrointestinal endoscopy and offered a practical guide for building a learning image dataset for algorithm development.
Collapse
Affiliation(s)
- Chang Bong Yang
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Korea
| | - Sang Hoon Kim
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Korea
| | - Yun Jeong Lim
- Department of Internal Medicine, Dongguk University Ilsan Hospital, Dongguk University College of Medicine, Goyang, Korea
| |
Collapse
|