Knowledge Engineering in Chemistry: From Expert Systems to Agents of Creation.

Passing knowledge from human to human is a natural process that has continued since the beginning of humankind. Over the past few decades, we have witnessed that knowledge is no longer passed only between humans but also from humans to machines. The latter form of knowledge transfer represents a cornerstone in artificial intelligence (AI) and lays the foundation for knowledge engineering (KE). In order to pass knowledge to machines, humans need to structure, formalize, and make knowledge machine-readable. Subsequently, humans also need to develop software that emulates their decision-making process. In order to engineer chemical knowledge, chemists are often required to challenge their understanding of chemistry and thinking processes, which may help improve the structure of chemical knowledge.Knowledge engineering in chemistry dates from the development of expert systems that emulated the thinking process of analytical and organic chemists. Since then, many different expert systems employing rather limited knowledge bases have been developed, solving problems in retrosynthesis, analytical chemistry, chemical risk assessment, etc. However, toward the end of the 20th century, the AI winters slowed down the development of expert systems for chemistry. At the same time, the increasing complexity of chemical research, alongside the limitations of the available computing tools, made it difficult for many chemistry expert systems to keep pace.In the past two decades, the semantic web, the popularization of object-oriented programming, and the increase in computational power have revitalized knowledge engineering. Knowledge formalization through ontologies has become commonplace, triggering the subsequent development of knowledge graphs and cognitive software agents. These tools enable the possibility of interoperability, enabling the representation of more complex systems, inference capabilities, and the synthesis of new knowledge.This Account introduces the history, the core principles of KE, and its applications within the broad realm of chemical research and engineering. In this regard, we first discuss how chemical knowledge is formalized and how a chemist's cognition can be emulated with the help of reasoning algorithms. Following this, we discuss various applications of knowledge graph and agent technology used to solve problems in chemistry related to molecular engineering, chemical mechanisms, multiscale modeling, automation of calculations and experiments, and chemist-machine interactions. These developments are discussed in the context of a universal and dynamic knowledge ecosystem, referred to as The World Avatar (TWA).

An expert-based system to predict population survival rate from health data.

Timely detection and understanding of causes for population decline are essential for effective wildlife management and conservation. Assessing trends in population size has been the standard approach, but we propose that monitoring population health could prove more effective. We collated data from 7 bottlenose dolphin (Tursiops truncatus) populations in the southeastern United States to develop a method for estimating survival probability based on a suite of health measures identified by experts as indices for inflammatory, metabolic, pulmonary, and neuroendocrine systems. We used logistic regression to implement the veterinary expert system for outcome prediction (VESOP) within a Bayesian analysis framework. We fitted parameters with records from 5 of the sites that had a robust network of responders to marine mammal strandings and frequent photographic identification surveys that documented definitive survival outcomes. We also conducted capture-mark-recapture (CMR) analyses of photographic identification data to obtain separate estimates of population survival rates for comparison with VESOP survival estimates. The VESOP analyses showed that multiple measures of health, particularly markers of inflammation, were predictive of 1- and 2-year individual survival. The highest mortality risk 1 year following health assessment related to low alkaline phosphatase (odds ratio [OR] = 10.2 [95% CI: 3.41-26.8]), whereas 2-year mortality was most influenced by elevated globulin (OR = 9.60 [95% CI: 3.88-22.4]); both are markers of inflammation. The VESOP model predicted population-level survival rates that correlated with estimated survival rates from CMR analyses for the same populations (1-year Pearson's r = 0.99, p = 1.52 × 10-5 ; 2-year r = 0.94, p = 0.001). Although our proposed approach will not detect acute mortality threats that are largely independent of animal health, such as harmful algal blooms, it can be used to detect chronic health conditions that increase mortality risk. Random sampling of the population is important and advancement in remote sampling methods could facilitate more random selection of subjects, obtainment of larger sample sizes, and extension of the approach to other wildlife species.

Un sistema basado en conocimiento experto para predecir la tasa de supervivencia a partir de datos de salud Resumen La detección y el entendimiento oportunos de la declinación poblacional son esenciales para que el manejo y la conservación de fauna tengan efectividad. La evaluación de las tendencias en el tamaño poblacional ha sido la estrategia estándar, pero proponemos que el monitoreo de la salud poblacional podría ser más efectivo. Recopilamos datos de siete poblaciones de delfines (Tursiops truncatus) en el sureste de Estados Unidos para desarrollar un método de estimación de la probabilidad de supervivencia con base en un conjunto de medidas sanitarias identificadas por expertos como índices para los sistemas inflamatorio, metabólico, pulmonar y neuroendocrino. Usamos la regresión logística para implementar el sistema de expertos veterinarios para la predicción de resultados (SEVPR) en un análisis bayesiano. Ajustamos los parámetros con los registros de cinco sitios que contaban con una buena red de respondientes a los varamientos de mamíferos marinos y censos de identificación fotográfica (foto-ID) que documentaron los resultados de supervivencia definitivos. También realizamos análisis de marcaje-recaptura (MR) en los datos de identificación fotográfica para obtener estimados separados de las tasas de supervivencia poblacional para compararlos con los estimados del SEVPR. Los análisis del SEVPR mostraron que varias medidas sanitarias, particularmente los marcadores de inflamación son buenos predictores de la supervivencia individual para uno y dos años. El riesgo de mortalidad más alto un año después de la valoración sanitaria se relacionó con una fosfatasa alcalina baja (cociente de probabilidades de 10.2 [95% CI 3.41-26.8]), mientras que la mortalidad a los dos años estuvo más influenciada por una globulina elevada (9.60 [95% CI 3.88-22.4]); ambas son marcadores de la inflamación. El modelo del SEVPR predijo las tasas de supervivencia a nivel poblacional en correlación con las tasas estimadas de supervivencia de los análisis de MR para las mismas poblaciones (Pearson de un año r = 0.99, p = 1.52e-05; dos años r = 0.94, p = 0.001). Aunque nuestra propuesta no detecta las amenazas agudas de mortalidad que en su mayoría son independientes de la salud animal, como la proliferación de algas nocivas, puede usarse para detectar las condiciones crónicas de salud que incrementan el riesgo de mortalidad. Es importante el muestreo aleatorio de la población y los avances en los métodos de muestreo remoto podrían facilitar una selección más aleatoria de los sujetos, la obtención de muestras de mayor tamaño y la expansión de la estrategia a otras especies de fauna.

Designing, validation and evaluation of the expert system of "Healthy Menopause" and assessing its effect on the management of menopause symptoms: an exploratory mixed method study protocol.

BACKGROUND: Menopause is a period of women's life that has the especial physical, psychological and social challenges. So provision of an effective, practical and affordable way for meeting women's related needs is important. In addition, women should be able to incorporate such programs into their daily work. Considering the dearth of suitable services in this regard, this study will be conducted with the aim of designing, validating and evaluating the "Healthy Menopause" expert system on the management of menopausal symptoms. METHODS/DESIGN: A mixed methods exploratory design will be used to conduct this study in 3 phases. The first phase is a qualitative conventional content analysis study with purposes of exploring the women's experience of menopausal symptoms and extracting their needs, and collecting data about their expectations from a healthy menopause expert system.. The purposive sampling (In his phase data will be gathered through interviewing menopaused women aged 40 to 60 years old and other persons that have rich information in this regard and will be continued until data saturation. The second phase includes designing a healthy menopause expert system in this stage, the needs will be extracted from the qualitative findings along with a comprehensive literature review. The extracted needs will be again confirmed by the participants. Then, through a participatory approach (Participatory Design) using nominal group or Delphi technique the experts' opinion about the priority needs of menopaused women and related solutions will be explored based on the categories of identified needs. Such findings will be used to design a healthy menopause expert system at this stage. The third phase of study is a quantitative research in which the evaluation of the healthy menopause expert system will be done through a randomized controlled clinical trial with the aim of determining the effect of the healthy menopause expert system on the management of menopause symptoms by menopausal women themselves. DISCUSSION: This is the first study that uses a mixed method approach for designing, validating and evaluating of the expert system "Healthy Menopause". This study will fill the research gap in the field of improving menopausal symptoms and designing a healthy menopause expert system based on the needs of the large group of menopause women. We hope that by applying this expert system, the menopausal women be empowered to management and improving their health with an easy and affordable manner.

Menopause is a period of women's life that has the especial physical, psychological and social challenges. So provision of an effective, easy for use and affordable way for managing related problems and meeting related needs is important. Menopause is a period of women's life that has physical, psychological and social consequences. It is important to identify methods that are effective, practical and affordable. New technologies can increase women's ability to access educational information. This is the first study for designing, validating and evaluating of the expert system "Healthy Menopause". A mixed methods exploratory design will be used to conduct this study in 3 phases. The first phase (qualitative): The conventional content analysis method will be used. The second phase: Designing a healthy menopause expert system: It is based on the codes of women's challenges from the first phase, along with conducting interviews and literature review. The participatory approach (Participatory Design) through nominal group or if needed, Delphi method based on the categories of needs and solutions by considering the opinions of the participants, available experts related to this issue will be listed. It should be used to design a healthy menopause expert system at this stage. The third phase (quantitative): The evaluation of the healthy menopause expert system will be a randomized clinical trial that determine the effect of the healthy menopause expert system on the management of menopause symptoms. In the present study an expert system (ES) will be designed that can be installed on mobile phones and computers. This tool is not only educational but also interactively helps to adapt to continuous changes, so by asking questions about menopause the system will respond as if an expert (midwife or gynecologist) is giving advice.

Scoring systems, expert assessment, and identification of risk factors for the emergence of delirium in paediatric patients: Prospective cohort study.

INTRODUCTION: Emergence delirium (ED) is a transient irritative and dissociative state that arises after the cessation of anaesthesia in patients who do not respond to calming measures. There are many risk factors for ED, but the exact cause and underlying mechanism have not been determined because the definition of ED is still unclear in consensus. This study aims to determine ED incidence, identify ED risk factors and external validation of Watcha, Cravero and expert assessment to Pediatric Anesthesia Emergence Delirium (PAED) scoring system in ED prediction. MATERIALS AND METHODS: This study is a prospective cohort study on 79 paediatrics who underwent elective surgery with general anaesthesia. Parameter measures include the incidence of ED, ED risk factors, and the relationship between PAED, Watcha, Cravero score and expert assessment. The ED risk factor was analysed using univariate and multivariate analysis. The relationship between PAED, Watcha, Cravero score, and expert assessment was determined using Receiver Operating Characteristic (ROC) curve analysis. RESULTS: The incidence of ED was 22.8%. All parameters examined in this study showed p < 0.05. Watcha's scoring correlates with the PAED scoring and shows the highest discrimination ability with AUC 0.741 and p < 0.05. CONCLUSION: The incidence of ED in paediatrics is relatively high. Compared to others, Watcha score are more reliable for ED prediction. However, some demographic and perioperative factors are not the risk factor of ED.

Computer-aided diagnosis of primary membranous nephropathy using expert system.

BACKGROUND: The diagnosis of primary membranous nephropathy (PMN) often depends on invasive renal biopsy, and the diagnosis based on clinical manifestations and target antigens may not be completely reliable as it could be affected by uncertain factors. Moreover, different experts could even have different diagnosis results due to their different experiences, which could further impact the reliability of the diagnosis. Therefore, how to properly integrate the knowledge of different experts to provide more reliable and comprehensive PMN diagnosis has become an urgent issue. METHODS: This paper develops a belief rule-based system for PMN diagnosis. The belief rule base is constructed based on the knowledge of the experts, with 9 biochemical indicators selected as the input variables. The belief rule-based system is developed of three layers: (1) input layer; (2) belief rule base layer; and (3) output layer, where 9 biochemical indicators are selected as the input variables and the diagnosis result is provided as the conclusion. The belief rule base layer is constructed based on the knowledge of the experts. The final validation was held with gold pattern clinical cases, i.e., with known and clinically confirmed diagnoses. RESULTS: 134 patients are used in this study, and the proposed method is defined by its sensitivity, specificity, accuracy and area under curve (AUC), which are 98.0%, 96.9%, 97.8% and 0.93, respectively. The results of this study present a novel and effective way for PMN diagnosis without the requirement of renal biopsy. CONCLUSIONS: Through analysis of the diagnosis results and comparisons with other methods, it can be concluded that the developed system could help diagnose PMN based on biochemical indicators with relatively high accuracy.

Therapy-based expert system on function and postural stability after anterior cruciate ligament reconstruction: a pilot study.

PURPOSE: Wii Fit exergames have been less commonly used for the rehabilitation of athletes after Anterior Cruciate Ligament Reconstruction (ACLR). This study aims to investigate the effects of an expert system using Wii Fit exergames compared to conventional rehabilitation following ACLR. A forward-chaining rule-based expert system was developed which proposed a rehabilitation program that included the number and type of exercise in terms of difficulty and ease and the duration of each exercise in a progressive manner according to the patient's physical condition. MATERIALS AND METHODS: Twenty eligible athletes aged 20-30 who underwent ACLR were enrolled in this study and randomly assigned to two groups; and received 12 sessions of either Wii Fit exergames as Wii group (n = 10) or conventional rehabilitation as CL group (n = 10). RESULTS: The main outcomes consisted of pain (Visual Analogue Scale (VAS)), knee effusion, knee flexion range (KFR), thigh girth (TG), single-leg hop for distance (SLHD), and for time (SLHT), static and dynamic balance tests. Both groups had considerable improvement in all outcomes, also there were significantly differences between Wii and CL groups as follows; VAS (P < 0.001), knee effusion (P < 0.001), TG (P = 0.001), KFR (P = 0.012), static balance in stable position (P < 0.001) and in unstable position (P = 0.001), dynamic balance in the anterior (P < 0.001), posteromedial (P < 0.001), posterolateral (P = 0.004) directions, symmetry index of SLHD (P < 0.001) and symmetry index of SLHT (P = 0.013). CONCLUSIONS: The findings showed that using Wii Fit exergames in post-ACLR patients reduced pain and effusion while also improving function and balance significantly. Iranian Registry of Clinical Trials registration number is IRCT20191013045090N1, and the registration date is 03-03-2020.

Expert-augmented machine learning.

Machine learning is proving invaluable across disciplines. However, its success is often limited by the quality and quantity of available data, while its adoption is limited by the level of trust afforded by given models. Human vs. machine performance is commonly compared empirically to decide whether a certain task should be performed by a computer or an expert. In reality, the optimal learning strategy may involve combining the complementary strengths of humans and machines. Here, we present expert-augmented machine learning (EAML), an automated method that guides the extraction of expert knowledge and its integration into machine-learned models. We used a large dataset of intensive-care patient data to derive 126 decision rules that predict hospital mortality. Using an online platform, we asked 15 clinicians to assess the relative risk of the subpopulation defined by each rule compared to the total sample. We compared the clinician-assessed risk to the empirical risk and found that, while clinicians agreed with the data in most cases, there were notable exceptions where they overestimated or underestimated the true risk. Studying the rules with greatest disagreement, we identified problems with the training data, including one miscoded variable and one hidden confounder. Filtering the rules based on the extent of disagreement between clinician-assessed risk and empirical risk, we improved performance on out-of-sample data and were able to train with less data. EAML provides a platform for automated creation of problem-specific priors, which help build robust and dependable machine-learning models in critical applications.

Proposal of neural network model for neurocognitive rehabilitation and its comparison with fuzzy expert system model.

This article focuses on the development of algorithms for a smart neurorehabilitation system, whose core is made up of artificial neural networks. The authors of the article have proposed a completely unique transfer of ACE-R results to the CHC model. This unique approach allows for the saturation of the CHC model domains according to modified ACE-R factor analysis. The outputs of the proposed algorithm thus enable the automatic creation of a personalized and optimized neurorehabilitation plan for individual patients to train their cognitive functions. A set of tasks in 6 levels of difficulty (level 1 to level 6) was designed for each of the nine CHC model domains. For each patient, the results of the ACE-R screening helped deter-mine the specific CHC domains to be rehabilitated, as well as the initial gaming level for rehabilitation in each domain. The proposed artificial neural network algorithm was adapted to real data from 703 patients. Experimental outputs were compared to the outputs of the initially designed fuzzy expert system, which was trained on the same real data, and all outputs from both systems were statistically evaluated against expert conclusions that were available. It is evident from the conducted experimental study that the smart neurorehabilitation system using artificial neural networks achieved significantly better results than the neurorehabilitation system whose core is a fuzzy expert system. Both algorithms are implemented into a comprehensive neurorehabilitation portal (Eddie), which was supported by a research project from the Technology Agency of the Czech Republic.

Updating the Dermal Sensitisation Thresholds using an expanded dataset and an in silico expert system.

The Dermal Sensitisation Thresholds (DST) are Thresholds of Toxicological Concern, which can be used to justify exposure-based waiving when conducting a skin sensitisation risk assessment. This study aimed to update the published DST values by expanding the size of the Local Lymph Node Assay dataset upon which they are based, whilst assigning chemical reactivity using an in silico expert system (Derek Nexus). The potency values within the expanded dataset fitted a similar gamma distribution to that observed for the original dataset. Derek Nexus was used to classify the sensitisation activity of the 1152 chemicals in the expanded dataset and to predict which chemicals belonged to a High Potency Category (HPC). This two-step classification led to three updated thresholds: a non-reactive DST of 710 µg/cm2 (based on 79 sensitisers), a reactive (non-HPC) DST of 73 µg/cm2 (based on 331 sensitisers) and an HPC DST of 1.0 µg/cm2 (based on 146 sensitisers). Despite the dataset containing twice as many sensitisers, these values are similar to the previously published thresholds, highlighting their robustness and increasing confidence in their use. By classifying reactivity in silico the updated DSTs can be applied within a skin sensitisation risk assessment in a reproducible, scalable and accessible manner.

The Nature-Based Solutions Case-Based System: A hybrid expert system.

Deriving knowledge and learning from past experiences is essential for the successful adoption of Nature-Based Solutions (NBS) as novel integrative solutions that involve many uncertainties. Past experiences in implementing NBS have been collected in a number of repositories; however, it is a major challenge to derive knowledge from the huge amount of information provided by these repositories. This calls for information systems that can facilitate the knowledge extraction process. This paper introduces the NBS Case-Based System (NBS-CBS), an expert system that uses a hybrid architecture to derive information and recommendations from an NBS experience repository. The NBS-CBS combines a 'black-box' artificial neural networks model with a 'white-box' case-based reasoning model to deliver an intelligent, adaptive, and explainable system. Experts have tested this system to assess its functionality and accuracy. Accordingly, the NBS-CBS appears to provide inspirational recommendations and information for the NBS planning and design process.

Nutrient expert system optimizes fertilizer management to improve potato productivity and tuber quality.

BACKGROUND: Improving potato productivity and quality plays an important role in enhancing global food security and human health. However, inappropriate fertilizer management negatively affects potato growth and tuber development, especially in developing countries where there are large numbers of smallholders without modern soil testing equipment. Nutrient Expert (NE), a new and convenient fertilization decision system, was evaluated in the present study by conducting four site-years field experiments in Northeast China, aiming to determine its effectiveness and applicability for potato production relative to local farmers' practice (FP) and fertilizer recommendation based on soil testing (ST). RESULTS: The excessive fertilization at planting promoted seedling growth for potato plants in FP. Nevertheless, superior plant growth and tuber development were observed in NE at the middle and later growing stages, by optimizing fertilizer input and implementing split fertilization. Overall, compared to FP, the NE system increased total and marketable tuber yields by 12-15% and 16-26%, respectively, at the same time as obtaining 19-31% higher net returns and enhanced fertilizer use efficiencies. Moreover, NE improved tuber quality by increasing the contents of starch, soluble protein and vitamin C and decreasing reducing sugar content relative to FP, as well as increasing starch yields by 23-52%. The ST method also showed comprehensive improvements in potato performances compared to FP, although it did not show any advantages compared to NE system. CONCLUSION: The NE system improved potato productivity and tuber quality by optimizing fertilization management, which is an effective and promising alternative to the ST method for potato production in China and other developing countries. © 2021 Society of Chemical Industry.

Pharmacotechnical Evaluation by SeDeM Expert System to Develop Orodispersible Tablets.

Sediment delivery model (SeDeM) system is innovative tool to correlate micromeritic properties of powders with compressibility. It involves computation of indices which facilitate direct compressibility of solids and enable corrective measures through particle engineering. Study had multiple objectives, viz, (i) to enhance solubility of BCS class II, nevirapine using solid dispersions; (ii) SeDeM analyses of excipients and solid dispersions to analyze direct compressibility; and (iii) prepare orodispersible tablets (ODT). Solid dispersions were prepared by solvent evaporation. Superdisintegrants and solid dispersions were analyzed for primary indices of dimension, compressibility, flowability, stability, and disgregability derived from micromeritic properties. Radar diagrams were constructed to provide visual clues to deficient properties for direct compressibility. ODTs were prepared using excipients which passed criteria for direct compressibility and evaluated for tablet properties. Solid dispersions with Eudragit S100 revealed 6 to 10 fold increase in solubility in various dissolution media including biorelevant media in comparison with plain drug. Solubility was found to be pH dependent. SeDeM analyses facilitated identification of superdisintegrants and excipients with unfavorable compressibility. Radar diagrams provided a clear pictorial evidence of lacunae in powder properties. Based on SeDeM results, tablets were formulated by direct compression using crosspovidone, croscarmellose sodium, and mannitol. All batches showed 40% release in first minute in simulated salivary fluid.

[Intelligent fault diagnosis expert system for multi-parameter monitor based on fault tree].

Aiming at the dilemma of expensive and difficult maintenance, lack of technical data and insufficient maintenance force for modern medical equipment, an intelligent fault diagnosis expert system of multi-parameter monitor based on fault tree was proposed in this study. Firstly, the fault tree of multi-parameter monitor was established and analyzed qualitatively and quantitatively, then based on the analysis results of fault tree, the expert system knowledge base and inference engine were constructed and the overall framework of the system was determined, finally the intelligent fault diagnosis expert system for multi-parameter monitor was developed by using the page hypertext preprocessor (PHP) language, with an accuracy rate of 80% in fault diagnosis. The results showed that technology fusion on the basis of fault tree and expert system can effectively realize intelligent fault diagnosis of multi-parameter monitors and provide troubleshooting suggestions, which can not only provide experience accumulation for fault diagnosis of multi-parameter monitors, but also provide a new idea and technical support for fault diagnosis of medical equipment.

Your Path to Transplant: A randomized controlled trial of a tailored expert system intervention to increase knowledge, attitudes, and pursuit of kidney transplant.

Individually tailoring education over time may help more patients, especially racial/ethnic minorities, get waitlisted and pursue deceased and living donor kidney transplant (DDKT and LDKT, respectively). We enrolled 802 patients pursuing transplant evaluation at the University of California, Los Angeles Transplant Program into a randomized education trial. We compared the effectiveness of Your Path to Transplant (YPT), an individually tailored coaching and education program delivered at 4 time points, with standard of care (SOC) education on improving readiness to pursue DDKT and LDKT, transplant knowledge, taking 15 small transplant-related actions, and pursuing transplant (waitlisting or LDKT rates) over 8 months. Survey outcomes were collected prior to evaluation and at 4 and 8 months. Time to waitlisting or LDKT was assessed with at least 18 months of follow-up. At 8 months, compared to SOC, the YPT group demonstrated increased LDKT readiness (47% vs 33%, P = .003) and transplant knowledge (effect size [ES] = 0.41, P < .001). Transplant pursuit was higher in the YPT group (hazard ratio: 1.44, 95% confidence interval: 1.15-1.79, P = .002). A focused, coordinated education effort can improve transplant-seeking behaviors and waitlisting rates. ClinicalTrials.gov registration: NCT02181114.

Performance of Fully Automated Antimicrobial Disk Diffusion Susceptibility Testing Using Copan WASP Colibri Coupled to the Radian In-Line Carousel and Expert System.

The purpose of the present study was to assess the agreement at the categorical level between the Vitek 2 system and the Colibri coupled to the Radian under real routine laboratory conditions. The 675 nonduplicate clinical strains included in this study (249 Enterobacterales isolates, 198 Pseudomonas aeruginosa, 107 Staphylococcus aureus, 78 coagulase-negative staphylococci, 38 Enterococcus faecalis, and 5 Enterococcus faecium) were isolated from nonconsecutive clinical samples referred to our laboratory between June and November 2020. In addition, 43 carbapenemase-producing Enterobacterales (CPE) formerly identified and stored in our laboratory were added to the panel, for a total of 718 strains. The overall categorical agreements between the two compared methods were 99.3% (4,350/4,380; 95% CI 99% to 99.5%); 98.6% (2,147/2,178; 95% CI 98.0% to 99.0%); 99.4% (1,839/1,850; 95% CI 98.9% to 99.7%); and 99.4% (342/344; 95% CI 97.9% to 99.8%) for Enterobacterales, P. aeruginosa, Staphylococcus spp., and Enterococcus spp., respectively. The most important cause of the very major errors encountered on the Vitek 2 for P. aeruginosa (62%, 13/21) was related to the presence of heteroresistant populations. Among the 43 CPE included in this study, one OXA-48-like, and one OXA-181-like were missed by the Vitek 2, even by rigorously applying the CPE screening cutoffs defined by EUCAST. The Colibri coupled to the Radian provide a fully automated solution for antimicrobial disk diffusion susceptibility testing with an accuracy that is equal to or better than that of the Vitek 2 system.

Where to search top-K biomedical ontologies?

MOTIVATION: Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. RESULT: We have implemented seven comparable Information Retrieval ranking algorithms to search through ontologies and compared them against four search engines for ontologies. Free-text queries have been performed, the outcomes have been judged by experts and the ranking algorithms and search engines have been evaluated against the expert-based ground truth (GT). In addition, we propose a probabilistic GT that is developed automatically to provide deeper insights and confidence to the expert-based GT as well as evaluating a broader range of search queries. CONCLUSION: The main outcome of this work is the identification of key search factors for biomedical ontologies together with search requirements and a set of recommendations that will help biomedical experts and ontology engineers to select the best-suited retrieval mechanism in their search scenarios. We expect that this evaluation will allow researchers and practitioners to apply the current search techniques more reliably and that it will help them to select the right solution for their daily work. AVAILABILITY: The source code (of seven ranking algorithms), ground truths and experimental results are available at https://github.com/danielapoliveira/bioont-search-benchmark.

Artificial intelligence in drug combination therapy.

Currently, the development of medicines for complex diseases requires the development of combination drug therapies. It is necessary because in many cases, one drug cannot target all necessary points of intervention. For example, in cancer therapy, a physician often meets a patient having a genomic profile including more than five molecular aberrations. Drug combination therapy has been an area of interest for a while, for example the classical work of Loewe devoted to the synergism of drugs was published in 1928-and it is still used in calculations for optimal drug combinations. More recently, over the past several years, there has been an explosion in the available information related to the properties of drugs and the biomedical parameters of patients. For the drugs, hundreds of 2D and 3D molecular descriptors for medicines are now available, while for patients, large data sets related to genetic/proteomic and metabolomics profiles of the patients are now available, as well as the more traditional data relating to the histology, history of treatments, pretreatment state of the organism, etc. Moreover, during disease progression, the genetic profile can change. Thus, the ability to optimize drug combinations for each patient is rapidly moving beyond the comprehension and capabilities of an individual physician. This is the reason, that biomedical informatics methods have been developed and one of the more promising directions in this field is the application of artificial intelligence (AI). In this review, we discuss several AI methods that have been successfully implemented in several instances of combination drug therapy from HIV, hypertension, infectious diseases to cancer. The data clearly show that the combination of rule-based expert systems with machine learning algorithms may be promising direction in this field.

Expert Characteristics: Implications for Expert Systems.

While expert systems are artificial intelligence (AI) agents, they share many common characteristics with human experts. As technology progresses, such systems are not just able to make simple decisions following "simplistic" linear logical protocols; they "behave" as real experts in at least two ways: by demonstrating superb decision-making skills and by conforming to the social norms for expertise, i.e., they "feel" as human experts. A review of the common characteristics of human experts may have important implications for the direction of the development for such systems. Implications for bioinformatics and future research (especially concerning the accompanying concept of "expert generalist") are also discussed.

A systematic review of the applications of Expert Systems (ES) and machine learning (ML) in clinical urology.

BACKGROUND: Testing a hypothesis for 'factors-outcome effect' is a common quest, but standard statistical regression analysis tools are rendered ineffective by data contaminated with too many noisy variables. Expert Systems (ES) can provide an alternative methodology in analysing data to identify variables with the highest correlation to the outcome. By applying their effective machine learning (ML) abilities, significant research time and costs can be saved. The study aims to systematically review the applications of ES in urological research and their methodological models for effective multi-variate analysis. Their domains, development and validity will be identified. METHODS: The PRISMA methodology was applied to formulate an effective method for data gathering and analysis. This study search included seven most relevant information sources: WEB OF SCIENCE, EMBASE, BIOSIS CITATION INDEX, SCOPUS, PUBMED, Google Scholar and MEDLINE. Eligible articles were included if they applied one of the known ML models for a clear urological research question involving multivariate analysis. Only articles with pertinent research methods in ES models were included. The analysed data included the system model, applications, input/output variables, target user, validation, and outcomes. Both ML models and the variable analysis were comparatively reported for each system. RESULTS: The search identified n = 1087 articles from all databases and n = 712 were eligible for examination against inclusion criteria. A total of 168 systems were finally included and systematically analysed demonstrating a recent increase in uptake of ES in academic urology in particular artificial neural networks with 31 systems. Most of the systems were applied in urological oncology (prostate cancer = 15, bladder cancer = 13) where diagnostic, prognostic and survival predictor markers were investigated. Due to the heterogeneity of models and their statistical tests, a meta-analysis was not feasible. CONCLUSION: ES utility offers an effective ML potential and their applications in research have demonstrated a valid model for multi-variate analysis. The complexity of their development can challenge their uptake in urological clinics whilst the limitation of the statistical tools in this domain has created a gap for further research studies. Integration of computer scientists in academic units has promoted the use of ES in clinical urological research.

Deceptive Online Content Detection Using Only Message Characteristics and a Machine Learning Trained Expert System.

This paper considers the use of a post metadata-based approach to identifying intentionally deceptive online content. It presents the use of an inherently explainable artificial intelligence technique, which utilizes machine learning to train an expert system, for this purpose. It considers the role of three factors (textual context, speaker background, and emotion) in fake news detection analysis and evaluates the efficacy of using key factors, but not the inherently subjective processing of post text itself, to identify deceptive online content. This paper presents initial work on a potential deceptive content detection tool and also, through the networks that it presents for this purpose, considers the interrelationships of factors that can be used to determine whether a post is deceptive content or not and their comparative importance.