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Possible conflicts: a compilation technique for consistency-based diagnosis.

Consistency-based diagnosis is one of the most widely used approaches to model-based diagnosis within the artificial intelligence community. It is usually carried out through an iterative cycle of behavior prediction, conflict detection, candidate generation, and candidate refinement. In that process conflict detection has proven to be a nontrivial step from the theoretical point of view. For this reason, many approaches to consistency-based diagnosis have relied upon some kind of dependency-recording. These techniques have had different problems, specially when they were applied to diagnose dynamic systems. Recently, offline dependency compilation has established itself as a suitable alternative approach to online dependency-recording. In this paper we propose the possible conflict concept as a compilation technique for consistency-based diagnosis. Each possible conflict represents a subsystem within system description containing minimal analytical redundancy and being capable to become a conflict. Moreover, the whole set of possible conflicts can be computed offline with no model evaluation. Once we have formalized the possible conflict concept, we explain how possible conflicts can be used in the consistency-based diagnosis framework, and how this concept can be easily extended to diagnose dynamic systems. Finally, we analyze its relation to conflicts in the general diagnosis engine (GDE) framework and compare possible conflicts with other compilation techniques, especially with analytical redundancy relations (ARRs) obtained through structural analysis. Based on results from these comparisons we provide additional insights in the work carried out within the BRIDGE community to provide a common framework for model-based diagnosis for both artificial intelligence and control engineering approaches.

Algorithms↗

Nuclear medicine and mathematics.

The purpose of this review is not to present a comprehensive description of all the mathematical tools used in nuclear medicine, but to emphasize the importance of the mathematical method in nuclear medicine and to elucidate some of the mathematical concepts currently used. We can distinguish three different areas in which mathematical support has been offered to nuclear medicine: physiology, methodology and data processing. Nevertheless, the boundaries between these areas can be indistinct. It is impossible in a single article to give even an idea of the extent and complexity of the procedures currently used in nuclear medicine, such as image processing, reconstruction from projections and artificial intelligence. These disciplines do not belong to nuclear medicine: they are already branches of engineering, and my interest will reside simply in revealing a little of the elegance and the fantastic potential of these new "allies" of nuclear medicine. In this review the mathematics of physiological interpretation and methodology are considered together in the same section. General aspects of data-processing methods, including image processing and artificial intelligence, are briefly analysed. The mathematical tools that are most often used to assist the interpretation of biological phenomena in nuclear medicine are considered; these include convolution and deconvolution methods, Fourier analysis, factorial analysis and neural networking.

Artificial Intelligence↗

Anatomical reasoning in the informatics age: Principles, ontologies, and agendas.

Reasoning about anatomy shares historical scientific roots with formal logic and artificial intelligence. With advances in computer-based intelligent programming, high-level biological structural knowledge may be exploited directly for biomedical research, clinical tasks, and educational applications. We consider the special nature of anatomical domain knowledge, emphasizing the complex concepts and semantics that must be represented in the development of ontologies, formally structured databases of biological information. We review the evolution of the fundamental scientific principles of logic and artificial intelligence needed for building machines that can make use of anatomical knowledge. We look at methods for compiling ontologies and compare the structural designs of the Foundational Model of Anatomy and Open GALEN ontologies. We further consider issues related to mapping developing anatomy resources with other biological ontologies in genomics, proteomics, and physiology. Although early results are promising, considerable resources and continuing effort must be committed to completing and extending anatomical ontologies for the ultimate success of computer-based anatomical reasoning. Anat Rec (Part B: New Anat) 289B:72-84, 2006. (c) 2006 Wiley-Liss, Inc.

Artificial Intelligence↗

Inductive analysis methods applied on questionnaires.

The am of this study was to evaluate subjective aspects from questionnaires dealing with dental trauma by applying different computerized inductive techniques within the field of artificial intelligence to questionnaires consisting of descriptive variables and of questions reflecting functional, personal, and social effects of patients' oral situation following dental trauma. As the methodology used is new to many readers in odontologic sciences, a detailed description of both the processes and the terminology is given. Utilizing a neural network as a first step in an analysis of data showed if relations existed in the training set, but the network could not make the relations explicit, so other methods, inductive methods, had to be applied. Inductive methods have the potential constructing rules from a set of examples. The rules combined with domain knowledge can reveal relations between the variables. It can be concluded that the usage of methods based on artificial intelligence can greatly improve explanatory value and make knowledge in databases explicit.

Algorithms↗

Automated detection of immunofluorescently labeled cytomegalovirus-infected cells in isolated peripheral blood leukocytes using decision tree analysis.

BACKGROUND: Cytomegalovirus (CMV) infection continues to be a major problem for immunocompromised patients. Detection of viral antigens in leukocytes (antigenemia assay) is widely used for the diagnosis of CMV infection and for guiding antiviral therapy. The antigenemia technique, contingent upon the manual microscopic analysis of rare cells, is a laborious task that is subject to human error. In this study, we combine automated microscopy with artificial intelligence for reliable detection of fluorescently labeled CMV-infected cells. METHODS: Cytospin preparations of peripheral blood leukocytes were immunofluorescently labeled for the CMV lower matrix phosphoprotein (pp65) and scanned in the Rare Event Imaging System (REIS), a fully automated image cytometer. The REIS detected potential positive objects and digitally recorded 49 measured cellular features for each identified case. The measurement data of these objects were analyzed by the See5 decision tree (DT) algorithm to ascertain whether they were true-positive detections. RESULTS: The DT was built from the measurement data of 2,047 true- and 2,028 false-positive detections, collected from 32 patient samples. By designating misclassifications of false-negatives three times more costly, the 10-fold cross-validation sensitivity, specificity, and misclassification error of the assay was 94.3%, 56.2%, and 25%, respectively. The method was also validated using an independent test set of 21 patient samples, in which similar results were obtained. CONCLUSIONS: To our knowledge, this study represents the first attempt to improve the accuracy of rare event image cytometry through the implementation of artificial intelligence methodology. Results suggest that cost-sensitive decision tree analysis of digitally measured cellular features vastly improves the performance of rare event image cytometry.

Artificial Intelligence↗

Plasma proteomic pattern as biomarkers for ovarian cancer.

Early detection of ovarian cancer remains a challenge. Pathologic changes within an organ might be reflected in proteomic patterns in serum or plasma. The objective of this study was to identify new plasma biomarkers in ovarian cancer patients using mass spectrometry (MS) protein profiling and artificial intelligence. The study included 35 women with ovarian cancer and 30 age-matched disease-free controls. For plasma protein signature analysis, the protein chip array surface-enhanced laser desorption/ionization (SELDI) analysis was performed. The strong anion exchange (SAX) and weak cation exchange (WCX) chips were used for analysis. After a training analysis by SAX and WCX protein chips, learning algorithm and clustering analysis was performed to reach a discriminate pattern of protein signature. SELDI mass spectroscopy was highly reproducible in detecting ovarian tumor-specific protein profiles. Four specific protein peaks were identified in plasma of women with ovarian cancer, but not in controls, with relative molecular masses of 6190.48, 5147.06, 11522.6, and 11537.7 d. Two peaks, with Mr 5295.5 and 8780.48 d, were present in plasma of control but not in women with ovarian cancer. A sensitivity of 90-96.3% and specificity of 100% for this studied cases and controls were reached. This study clearly demonstrates that the combined technology of SELDI-MS and artificial intelligence is effective in distinguishing protein expression between normal and ovary cancer plasma. The identified gained and lost protein peaks in plasma may provide as candidate proteins to be used for the detection or monitoring ovarian cancer.

Adolescent↗

Real-world deployment of a fine-tuned pathology foundation model for lung cancer biomarker detection.

Artificial intelligence models using digital histopathology slides stained with hematoxylin and eosin offer promising, tissue-preserving diagnostic tools for patients with cancer. Despite their advantages, their clinical utility in real-world settings remains unproven. Assessing EGFR mutations in lung adenocarcinoma demands rapid, accurate and cost-effective tests that preserve tissue for genomic sequencing. PCR-based assays provide rapid results but with reduced accuracy compared with next-generation sequencing and require additional tissue. Computational biomarkers leveraging modern foundation models can address these limitations. Here we assembled a large international clinical dataset of digital lung adenocarcinoma slides (N = 8,461) to develop a computational EGFR biomarker. Our model fine-tunes an open-source foundation model, improving task-specific performance with out-of-center generalization and clinical-grade accuracy on primary and metastatic specimens (mean area under the curve: internal 0.847, external 0.870). To evaluate real-world clinical translation, we conducted a prospective silent trial of the biomarker on primary samples, achieving an area under the curve of 0.890. The artificial-intelligence-assisted workflow reduced the number of rapid molecular tests needed by up to 43% while maintaining the current clinical standard performance. Our retrospective and prospective analyses demonstrate the real-world clinical utility of a computational pathology biomarker.

Humans↗

Clinical applications of digital twin technology in In Vitro Fertilisation.

BACKGROUND: Digital twin technology, originating from aerospace and manufacturing industries, has emerged as a transformative tool in healthcare. In vitro fertilisation (IVF) faces persistent challenges including suboptimal embryo selection, unpredictable treatment outcomes, and limited personalisation of protocols. Despite advances in assisted reproductive technology, existing literature exhibits fragmentation: artificial intelligence applications in embryo selection, ovarian stimulation, and endometrial assessment have been developed independently without systematic integration into comprehensive treatment frameworks. Digital twin technology offers unprecedented opportunities to create virtual replicas of biological systems, enabling real-time monitoring, predictive modelling, and personalised treatment strategies. AIM: This narrative review aims to critically examine the current applications of digital twin technology in IVF, evaluate its potential benefits and limitations, synthesize existing evidence into an integrative conceptual model, and identify future directions for implementation in reproductive medicine. METHOD: A comprehensive narrative review was conducted using PubMed, Scopus, Web of Science, and IEEE Xplore databases. A narrative review approach was selected over systematic review to accommodate the heterogeneity of evidence types in this emerging field, including theoretical frameworks, simulation studies, and proof-of-concept implementations that would be excluded from systematic reviews. Search terms included "digital twin," "IVF," "in vitro fertilisation," "assisted reproductive technology," "embryo selection," and "predictive modelling." Studies published between 2015 and 2025 were included, focusing on original research articles, systematic reviews, and proof-of-concept studies describing digital twin applications in reproductive medicine. RESULTS: Digital twin technology in IVF demonstrates significant potential across multiple domains including embryo development simulation, ovarian response prediction, endometrial receptivity modelling, and personalised stimulation protocols. Current applications integrate artificial intelligence, machine learning algorithms, time-lapse imaging, and omics data to create comprehensive virtual models. Early evidence suggests improvements in embryo selection accuracy, ovarian response prediction, and treatment protocol optimization, though large-scale randomized controlled trials remain limited. Implementation challenges include data integration complexity, computational requirements, regulatory considerations, and validation requirements. CONCLUSION: Digital twin technology represents a paradigm shift in IVF practice, offering personalised, predictive, and precision medicine approaches. This review synthesizes existing evidence to propose an integrative conceptual model for digital twin implementation across the IVF treatment spectrum, identifies critical knowledge gaps, and establishes research priorities to advance clinical translation. Despite current limitations, continued advancement promises improved success rates and patient outcomes.

Humans↗

Community-driven advances in computational mass spectrometry: The perspective of EuBIC-MS members.

Advances in data acquisition, artificial intelligence, and integrative bioinformatics are driving the rapid evolution of computational mass spectrometry, and in turn, transforming modern proteomics, metabolomics, and lipidomics. These developments have greatly increased the scale and complexity of mass spectrometry data, underscoring the importance of evolving accurate, transparent, efficient and reproducible data processing workflows. Addressing these challenges requires collaborative innovation that brings together expertise in software engineering, statistics, and biology. The European Bioinformatics Community for Mass Spectrometry (EuBIC-MS), an initiative of the European Proteomics Association (EuPA), fosters a culture of open, community-driven development through its biennial Developers Meetings and Winter Schools. This commentary summarizes the scientific background and outcomes of the EuBIC-MS Developers Meeting 2025, which took place in Novacella, Italy. Three keynote presentations highlighted major frontiers in the field: deep proteome and phosphoproteome profiling, text mining for protein-protein interaction extraction, and scalable proteomics for AI-driven drug discovery. Seven community-selected hackathons addressed emerging challenges such as single-cell proteomics data analysis, FAIR metadata extraction, deep learning frameworks, R-Python interoperability, and DIA validation. Together, these efforts demonstrate the potential for scientific and technical innovation to arise from open collaboration, and highlight how community-driven initiatives can accelerate progress in computational mass spectrometry. SIGNIFICANCE: Modern proteomics increasingly depends on computational advances to translate complex, high-dimensional data into biological knowledge. The EuBIC-MS Developers Meeting 2025 exemplifies how community-driven collaboration can directly accelerate this process by bringing together experts from bioinformatics, statistics, and experimental proteomics to co-develop open, interoperable, and reproducible analytical tools. By fostering shared software frameworks, transparent benchmarking, and collaborative problem solving, the EuBIC-MS community helps ensure that technological innovation translates into reliable biological insights. This collaborative model strengthens the foundation for quantitative, system-level understanding of proteomes and establishes a sustainable path for integrating artificial intelligence and next-generation data acquisition into routine biological discovery. This commentary shows some current highlights in the field of computational mass spectrometry and community-based approaches undertaken during the most recent Developers Meeting to solve these challenges. The approaches discussed and initiated during the meeting - ranging from deep proteome profiling and phosphosite mapping to text mining, single-cell data analysis, and FAIR metadata extraction - address key bottlenecks that currently limit the biological interpretability and comparability of proteomics data.

Mass Spectrometry↗

Microcomputer data acquisition and control.

In medicine and biology there are many tasks that involve routine well defined procedures. These tasks are ideal candidates for computerized data acquisition and control. As the performance of microcomputers rapidly increases and cost continues to go down the temptation to automate the laboratory becomes great. To the novice computer user the choices of hardware and software are overwhelming and sadly most of the computer sales persons are not at all familiar with real-time applications. If you want to bill your patients you have hundreds of packaged systems to choose from; however, if you want to do real-time data acquisition the choices are very limited and confusing. The purpose of this chapter is to provide the novice computer user with the basics needed to set up a real-time data acquisition system with the common microcomputers. This chapter will cover the following issues necessary to establish a real time data acquisition and control system: Analysis of the research problem: Definition of the problem; Description of data and sampling requirements; Cost/benefit analysis. Choice of Microcomputer hardware and software: Choice of microprocessor and bus structure; Choice of operating system; Choice of layered software. Digital Data Acquisition: Parallel Data Transmission; Serial Data Transmission; Hardware and software available. Analog Data Acquisition: Description of amplitude and frequency characteristics of the input signals; Sampling theorem; Specification of the analog to digital converter; Hardware and software available; Interface to the microcomputer. Microcomputer Control: Analog output; Digital output; Closed-Loop Control. Microcomputer data acquisition and control in the 21st Century--What is in the future? High speed digital medical equipment networks; Medical decision making and artificial intelligence.

Artificial Intelligence↗

Decision support system for classification of epilepsies in childhood.

Diagnosis of epilepsy in childhood is often difficult as the symptoms are often atypical and the epilepsy syndromes are multiform. Methods from the domain of artificial intelligence give the opportunity to formalize medical knowledge and standardize various diagnostic procedures in specific domains of medicine. We developed a decision support system using artificial intelligence techniques for the classification and ultimately the diagnosis of epilepsies and epilepsy syndromes in children. The system incorporates knowledge from the International Classification of Epilepsies and Epileptic Syndromes. It was assessed using clinical data and the system's conclusions were compared with the diagnoses proposed by an experienced doctor. The system and the physician reached identical diagnoses in 85.2% of the cases. In an additional 8.2% of the cases, the system's diagnosis was similar to that of the physician, thus raising its overall success rate to 93.4%. The system can be helpful, especially for trainees, since it only needs to import the clinical and laboratory data. Decision making and differential diagnosis are then performed automatically.

Child↗

Microcomputer based differential diagnosis of dysmorphic syndromes.

Dysmorphic syndromes are characterized by associations of physical abnormalities depending in its diagnosis on the recognition of a particular pattern. Because of their multiplicity, the rarity of some of them, and the frequency of new reports, computerized data bases have proved useful as powerful tools assisting in the differential diagnosis. The role of artificial intelligence methods, in particular Expert Systems, as promising tools in helping physicians to perform a clinical diagnosis is underlined. Using a high level computer language presently used in the artificial intelligence field (Prolog), a microcomputer based system for the differential diagnosis of dysmorphic syndromes is described. Its capabilities and simplicity of use, derived from an efficient and attractive computer interface, are underlined. The need of performance assessment by evaluating its accuracy and usefulness before its introduction into genetic clinical practice is stressed. Finally, for the completeness of the knowledge base, the need of cooperation between international centers is emphasized.

Congenital Abnormalities↗

Simulating physiology and methods for therapeutic evaluation with emphasis on hypertension.

Improvements in therapy are aimed at better diagnosis and more effective treatment. The use of computer simulation has the potential to improve therapy in both ways. Computational methods have been used extensively in diagnosis, for interpreting MRI results, CAT scans and the development of treatments in the study of biochemical structure. The present review examines how simulation may be used to play a more fundamental role in therapeutic treatment often referred to as In Silico Biology. Simulation of cells, organs and systems, such as pulmonary and cardiovascular, can be used in clinical practice to improve diagnosis. Initially these developments will probably have to be refined before being used in general practice. However, when these simulations are linked with artificial intelligence techniques containing experimental databases then very powerful tools will result. The use of simulation in the design and development of new drugs can both be cost and time effective. Again, artificial intelligence techniques are likely to play an important role in evaluating patient risk factors and unwanted side effects.

Antihypertensive Agents↗

Computer-assisted decision making in medicine.

This article reviews the strengths and limitations of five major paradigms of medical computer-assisted decision making (CADM): (1) clinical algorithms, (2) statistical analysis of collections of patient data, (3) mathematical models of physical processes, (4) decision analysis, and (5) symbolic reasoning or artificial intelligence (AI). No one technique is best for all applications, and there is recent promising work which combines two or more established techniques. We emphasize both the inherent power of symbolic reasoning and the promise of artificial intelligence and the other techniques to complement each other.

Computers↗

How AI-supported intelligent systems support infection prevention and control training in healthcare: A systematic review of educational functions and outcomes.

AIMS: Artificial intelligence (AI)-supported intelligent systems have been increasingly incorporated into infection prevention and control (IPC) education and training, primarily to support the monitoring of observable behaviors and the provision of feedback. However, existing evidence has focused largely on short-term compliance outcomes, with limited synthesis of the educational role of AI-supported intelligent systems in supporting sustained IPC competence. This systematic review examined how AI-supported intelligent systems have been designed and used to support IPC education and training, with a focus on system characteristics, educational functions, and reported outcomes. DESIGN: A systematic literature search was conducted across the PubMed/MEDLINE, Embase, Cochrane, and CINAHL databases. DATA SOURCES: A total of 18 studies met the inclusion criteria. Findings were qualitatively synthesized according to system design characteristics, educational functions, and outcome domains. REVIEW METHODS: Methodological quality was appraised using the Mixed Methods Appraisal Tool. RESULTS: Most AI-supported intelligent systems focused on hand hygiene and relied on fully automated monitoring systems to capture behaviors and provide performance feedback. Educational functions were predominantly limited to performance assessment, automated feedback, and reminders. Outcomes were mainly measured using compliance or performance metrics, whereas sustained behavioral change and decision quality were rarely assessed. CONCLUSIONS: AI-supported intelligent systems have been used primarily to reinforce short-term IPC performance and compliance. However, their current applications for supporting sustained competence over time remain limited. The findings of this review suggest that AI-supported intelligent systems may serve as maintenance-oriented educational support by extending learning beyond initial instruction through repeated practice and feedback. Future research should prioritize outcome measures that capture the durability of performance and decision-making processes to better align AI-supported intelligent systems used in IPC education and training with the educational demands of clinical practice.

Humans↗

Mapper: an intelligent restriction mapping tool.

MOTIVATION: To determine the most powerful artificial intelligence techniques for automated restriction mapping, and use them to create a powerful multiple-enzyme restriction mapping tool. RESULTS: The most effective search engine utilized model-driven exhaustive search and a form of binary logic pruning based on Pratt's separation theory. Additional experimentation led to the development of an input preprocessing module which significantly speeds up searches, and an output post-processing module which enables users to analyze large solution sets and reduce their apparent complexity. AVAILABILITY: An executable version of the resultant tool, Mapper, can be downloaded from our Web site (http://www.ai.eecs.uic.edu) by selecting the 'Software' option. CONTACT: nelson@eecs.uic.edu (http://www.ai.eecs.uic.edu/ñelson).

Algorithms↗

A user-friendly biological workstation.

Learning methods developed by artificial intelligence research teams are very efficient for biological sequences analysis but they need running on large computers accessed by terminals. These computers are interfaced with standard displays involving long and unpleasant alphanumerical data handling. The "biological work station" is a personal computer with a color graphic screen providing a user-friendly interface for the artificial intelligence learning programs running on large computers. It provides to biologist a graphical convenient tool for sequence analysis built with efficient man-machine communication methods such as multiwindows, icons and mouse selection. It allows the biologist to edit and display sequences in an efficient and natural way, showing off directly on color pictures the data and the results of learning programs.

Biology↗

Pulmonary perfusion patterns and pulmonary arterial pressure.

PURPOSE: To use artificial intelligence methods to determine whether quantitative parameters describing the perfusion image can be synthesized to make a reasonable estimate of the pulmonary arterial (PA) pressure measured at angiography. MATERIALS AND METHODS: Radionuclide perfusion images were obtained in 120 patients with normal chest radiographs who also underwent angiographic PA pressure measurement within 3 days of the radionuclide study. An artificial neural network (ANN) was constructed from several image parameters describing statistical and boundary characteristics of the perfusion images. With use of a leave-one-out cross-validation technique, this method was used to predict the PA systolic pressure in cases on which the ANN had not been trained. A Pearson correlation coefficient was determined between the predicted and measured PA systolic pressures. RESULTS: ANN predictions correlated with measured pulmonary systolic pressures (r = 0.846, P <.001). The accuracy of the predictions was not influenced by the presence of pulmonary embolism. None of the 51 patients with predicted PA pressures of less than 29 mm Hg had pulmonary hypertension at angiography. All 13 patients with predicted PA pressures greater than 48 mm Hg had pulmonary hypertension at angiography. CONCLUSION: Meaningful information regarding PA pressure can be derived from noninvasive radionuclide perfusion scanning. The use of image analysis in concert with artificial intelligence methods helps to reveal physiologic information not readily apparent at visual image inspection.

Adolescent↗