Building a knowledge base for colorectal cancer patient care using formal concept analysis.

BACKGROUND: Colorectal cancer (CRC) is a heterogeneous disease with different responses to targeted therapies due to various factors, and the treatment effect differs significantly between individuals. Personalize medical treatment (PMT) is a method that takes individual patient characteristics into consideration, making it the most effective way to deal with this issue. Patient similarity and clustering analysis is an important aspect of PMT. This paper describes how to build a knowledge base using formal concept analysis (FCA), which clusters patients based on their similarity and preserves the relations between clusters in hierarchical structural form. METHODS: Prognostic factors (attributes) of 2442 CRC patients, including patient age, cancer cell differentiation, lymphatic invasion and metastasis stages were used to build a formal context in FCA. A concept was defined as a set of patients with their shared attributes. The formal context was formed based on the similarity scores between each concept identified from the dataset, which can be used as a knowledge base. RESULTS: A hierarchical knowledge base was constructed along with the clinical records of the diagnosed CRC patients. For each new patient, a similarity score to each existing concept in the knowledge base can be retrieved with different similarity calculations. The ranked similarity scores that are associated with the concepts can offer references for treatment plans. CONCLUSIONS: Patients that share the same concept indicates the potential similar effect from same clinical procedures or treatments. In conjunction with a clinician's ability to undergo flexible analyses and apply appropriate judgement, the knowledge base allows faster and more effective decisions to be made for patient treatment and care.

A theoretical model of health management using data-driven decision-making: the future of precision medicine and health.

BACKGROUND: The burden of chronic and societal diseases is affected by many risk factors that can change over time. The minimalisation of disease-associated risk factors may contribute to long-term health. Therefore, new data-driven health management should be used in clinical decision-making in order to minimise future individual risks of disease and adverse health effects. METHODS: We aimed to develop a health trajectories (HT) management methodology based on electronic health records (EHR) and analysing overlapping groups of patients who share a similar risk of developing a particular disease or experiencing specific adverse health effects. Formal concept analysis (FCA) was applied to identify and visualise overlapping patient groups, as well as for decision-making. To demonstrate its capabilities, the theoretical model presented uses genuine data from a local total knee arthroplasty (TKA) register (a total of 1885 patients) and shows the influence of step by step changes in five lifestyle factors (BMI, smoking, activity, sports and long-distance walking) on the risk of early reoperation after TKA. RESULTS: The theoretical model of HT management demonstrates the potential of using EHR data to make data-driven recommendations to support both patients' and physicians' decision-making. The model example developed from the TKA register acts as a clinical decision-making tool, built to show surgeons and patients the likelihood of early reoperation after TKA and how the likelihood changes when factors are modified. The presented data-driven tool suits an individualised approach to health management because it quantifies the impact of various combinations of factors on the early reoperation rate after TKA and shows alternative combinations of factors that may change the reoperation risk. CONCLUSION: This theoretical model introduces future HT management as an understandable way of conceiving patients' futures with a view to positively (or negatively) changing their behaviour. The model's ability to influence beneficial health care decision-making to improve patient outcomes should be proved using various real-world data from EHR datasets.

Identification of missing concepts in biomedical terminologies using sequence-based formal concept analysis.

BACKGROUND: As biomedical knowledge is rapidly evolving, concept enrichment of biomedical terminologies is an active research area involving automatic identification of missing or new concepts. Previously, we prototyped a lexical-based formal concept analysis (FCA) approach in which concepts were derived by intersecting bags of words, to identify potentially missing concepts in the National Cancer Institute (NCI) Thesaurus. However, this prototype did not handle concept naming and positioning. In this paper, we introduce a sequenced-based FCA approach to identify potentially missing concepts, supporting concept naming and positioning. METHODS: We consider the concept name sequences as FCA attributes to construct the formal context. The concept-forming process is performed by computing the longest common substrings of concept name sequences. After new concepts are formalized, we further predict their potential positions in the original hierarchy by identifying their supertypes and subtypes from original concepts. Automated validation via external terminologies in the Unified Medical Language System (UMLS) and biomedical literature in PubMed is performed to evaluate the effectiveness of our approach. RESULTS: We applied our sequenced-based FCA approach to all the sub-hierarchies under Disease or Disorder in the NCI Thesaurus (19.08d version) and five sub-hierarchies under Clinical Finding and Procedure in the SNOMED CT (US Edition, March 2020 release). In total, 1397 potentially missing concepts were identified in the NCI Thesaurus and 7223 in the SNOMED CT. For NCI Thesaurus, 85 potentially missing concepts were found in external terminologies and 315 of the remaining 1312 appeared in biomedical literature. For SNOMED CT, 576 were found in external terminologies and 1159 out of the remaining 6647 were found in biomedical literature. CONCLUSION: Our sequence-based FCA approach has shown the promise for identifying potentially missing concepts in biomedical terminologies.

Multi-View Data Analysis Techniques for Monitoring Smart Building Systems.

In smart buildings, many different systems work in coordination to accomplish their tasks. In this process, the sensors associated with these systems collect large amounts of data generated in a streaming fashion, which is prone to concept drift. Such data are heterogeneous due to the wide range of sensors collecting information about different characteristics of the monitored systems. All these make the monitoring task very challenging. Traditional clustering algorithms are not well equipped to address the mentioned challenges. In this work, we study the use of MV Multi-Instance Clustering algorithm for multi-view analysis and mining of smart building systems' sensor data. It is demonstrated how this algorithm can be used to perform contextual as well as integrated analysis of the systems. Various scenarios in which the algorithm can be used to analyze the data generated by the systems of a smart building are examined and discussed in this study. In addition, it is also shown how the extracted knowledge can be visualized to detect trends in the systems' behavior and how it can aid domain experts in the systems' maintenance. In the experiments conducted, the proposed approach was able to successfully detect the deviating behaviors known to have previously occurred and was also able to identify some new deviations during the monitored period. Based on the results obtained from the experiments, it can be concluded that the proposed algorithm has the ability to be used for monitoring, analysis, and detecting deviating behaviors of the systems in a smart building domain.

Formalizing and enriching phenotype signatures using Boolean networks.

In order to predict the behavior of a biological system, one common approach is to perform a simulation on a dynamic model. Boolean networks allow to analyze the qualitative aspects of the model by identifying its steady states and attractors. Each of them, when possible, is associated with a phenotype which conveys a biological interpretation. Phenotypes are characterized by their signatures, provided by domain experts. The number of steady states tends to increase with the network size and the number of simulation conditions, which makes the biological interpretation difficult. As a first step, we explore the use of Formal Concept Analysis as a symbolic bi-clustering technics to classify and sort the steady states of a Boolean network according to biological signatures based on the hierarchy of the roles the network components play in the phenotypes. FCA generates a lattice structure describing the dependencies between proteins in the signature and steady-states of the Boolean network. We use this lattice (i) to enrich the biological signatures according to the dependencies carried by the network dynamics, (ii) to identify variants to the phenotypes and (iii) to characterize hybrid phenotypes. We applied our approach on a T helper lymphocyte (Th) differentiation network with a set of signatures corresponding to the sub-types of Th. Our method generated the same classification as a manual analysis performed by experts in the field, and was also able to work under extended simulation conditions. This led to the identification and prediction of a new hybrid sub-type later confirmed by the literature.

Interactive knowledge discovery and data mining on genomic expression data with numeric formal concept analysis.

BACKGROUND: Gene Expression Data (GED) analysis poses a great challenge to the scientific community that can be framed into the Knowledge Discovery in Databases (KDD) and Data Mining (DM) paradigm. Biclustering has emerged as the machine learning method of choice to solve this task, but its unsupervised nature makes result assessment problematic. This is often addressed by means of Gene Set Enrichment Analysis (GSEA). RESULTS: We put forward a framework in which GED analysis is understood as an Exploratory Data Analysis (EDA) process where we provide support for continuous human interaction with data aiming at improving the step of hypothesis abduction and assessment. We focus on the adaptation to human cognition of data interpretation and visualization of the output of EDA. First, we give a proper theoretical background to bi-clustering using Lattice Theory and provide a set of analysis tools revolving around [Formula: see text]-Formal Concept Analysis ([Formula: see text]-FCA), a lattice-theoretic unsupervised learning technique for real-valued matrices. By using different kinds of cost structures to quantify expression we obtain different sequences of hierarchical bi-clusterings for gene under- and over-expression using thresholds. Consequently, we provide a method with interleaved analysis steps and visualization devices so that the sequences of lattices for a particular experiment summarize the researcher's vision of the data. This also allows us to define measures of persistence and robustness of biclusters to assess them. Second, the resulting biclusters are used to index external omics databases-for instance, Gene Ontology (GO)-thus offering a new way of accessing publicly available resources. This provides different flavors of gene set enrichment against which to assess the biclusters, by obtaining their p-values according to the terminology of those resources. We illustrate the exploration procedure on a real data example confirming results previously published. CONCLUSIONS: The GED analysis problem gets transformed into the exploration of a sequence of lattices enabling the visualization of the hierarchical structure of the biclusters with a certain degree of granularity. The ability of FCA-based bi-clustering methods to index external databases such as GO allows us to obtain a quality measure of the biclusters, to observe the evolution of a gene throughout the different biclusters it appears in, to look for relevant biclusters-by observing their genes and what their persistence is-to infer, for instance, hypotheses on their function.

Non-redundant implicational base of formal context with constraints using SAT.

An implicational base is knowledge extracted from a formal context. The implicational base of a formal context consists of attribute implications which are sound, complete, and non-redundant regarding to the formal context. Non-redundant means that each attribute implication in the implication base cannot be inferred from the others. However, sometimes some attribute implications in the implication base can be inferred from the others together with a prior knowledge. Regarding knowledge discovery, such attribute implications should be not considered as new knowledge and ignored from the implicational base. In other words, such attribute implications are redundant based on prior knowledge. One sort of prior knowledge is a set of constraints that restricts some attributes in data. In formal context, constraints restrict some attributes of objects in the formal context. This article proposes a method to generate non-redundant implication base of a formal context with some constraints which restricting the formal context. In this case, non-redundant implicational base means that the implicational base does not contain all attribute implications which can be inferred from the others together with information of the constraints. This article also proposes a formulation to check the redundant attribute implications and encoding the problem into satisfiability (SAT) problem such that the problem can be solved by SAT Solver, a software which can solve a SAT problem. After implementation, an experiment shows that the proposed method is able to check the redundant attribute implication and generates a non-redundant implicational base of formal context with constraints.

Revealing the hierarchical structure of microbial communities.

Measuring the dynamics of microbial communities results in high-dimensional measurements of taxa abundances over time and space, which is difficult to analyze due to complex changes in taxonomic compositions. This paper presents a new method to investigate and visualize the intrinsic hierarchical community structure implied by the measurements. The basic idea is to identify significant intersection sets, which can be seen as sub-communities making up the measured communities. Using the subset relationship, the intersection sets together with the measurements form a hierarchical structure visualized as a Hasse diagram. Chemical organization theory (COT) is used to relate the hierarchy of the sets of taxa to potential taxa interactions and to their potential dynamical persistence. The approach is demonstrated on a data set of community data obtained from bacterial 16S rRNA gene sequencing for samples collected monthly from four groundwater wells over a nearly 3-year period (n = 114) along a hillslope area. The significance of the hierarchies derived from the data is evaluated by showing that they significantly deviate from a random model. Furthermore, it is demonstrated how the hierarchy is related to temporal and spatial factors; and how the idea of a core microbiome can be extended to a set of interrelated core microbiomes. Together the results suggest that the approach can support developing models of taxa interactions in the future.

Factor diagnosis and governance strategies of ship oil spill accidents based on formal concept analysis.

Ship oil spill accidents have a prolonged duration, complex consequences, challenging cleaning and repairing efforts, and pose a significant threat to the environment, economy, and society. Eliminating irrelevant information and identifying key factors using traditional methods is challenging due to the complexity of the causes of ship oil spill accidents. To address this, this article sorts out the accident databases of the International Tanker Owners Pollution Federation (ITOPF) and eight national maritime administration agencies, and innovatively constructs a formal concept analysis (FCA) model based on reports of 100-plus ship oil spill accidents. The model results prove that improper operation, less complete ship equipment, large tonnage, and poor navigation conditions are the key factors. The different causal rules of oil spills in collision/contact, grounding, fire/explosion, and foundering are further compared and analyzed. Finally, corresponding improvement measures are put forward for the key factors of oil spills and different causal rules.

Interval association of remote sensing ecological index in China based on concept lattice.

The correlation coefficient can calculate paired correlations among different ecological indicators as a whole, but it cannot calculate the specific interval association and the correlation among multiple indicators. This paper proposed an interval association (IA) method of the remote sensing ecological index (RSEI), based on the concept lattice and frequent closed itemset. In the IA method, the ecosystem was viewed as a complex system with a hierarchical structure, and the association among multiple indicators was calculated using the information granulation of RSEI. The interval association support degree (IASD) could measure the association clustering strength of these IA concepts. Calculation of MODIS data compiled by Google Earth Engine (GEE) showed that the IA concepts of RSEI in China were primarily composed of selected middle indicator intervals in 2017. The overall eco-environmental condition in China was general when assessed through IA. The spatial distribution of the remote sensing eco-environment in China displayed strong spatial association clustering. Furthermore, the IA of RSEI focused on the first few concepts with high IASD values.

Applying Formal Concept Analysis for the Recognition of Infant Mortality Patterns.

Infant mortality (IM), an index that corresponds to the number of deaths among children up to one year, is an important social indicator of a region. It generally reflects the conditions of socioeconomic development - in addition, the access and quality of resources available for maternal and child health care. Monitoring its magnitude, thus, can help in the definition of public policies for its confrontation. The main causes of IM can be also associated with biological, behavioral, and public health issues. In this work, implication and association rules based on Formal Concept Analysis are used to recognize patterns in births occurring in the state of Amapá (located in the Brazilian Amazon), where the index of infant mortality is more severe.

Defining factors in hospital admissions during COVID-19 using LSTM-FCA explainable model.

Outbreaks of the COVID-19 pandemic caused by the SARS-CoV-2 infection that started in Wuhan, China, have quickly spread worldwide. The current situation has contributed to a dynamic rate of hospital admissions. Global efforts by Artificial Intelligence (AI) and Machine Learning (ML) communities to develop solutions to assist COVID-19-related research have escalated ever since. However, despite overwhelming efforts from the AI and ML community, many machine learning-based AI systems have been designed as black boxes. This paper proposes a model that utilizes Formal Concept Analysis (FCA) to explain a machine learning technique called Long-short Term Memory (LSTM) on a dataset of hospital admissions due to COVID-19 in the United Kingdom. This paper intends to increase the transparency of decision-making in the era of ML by using the proposed LSTM-FCA explainable model. Both LSTM and FCA are able to evaluate the data and explain the model to make the results more understandable and interpretable. The results and discussions are helpful and may lead to new research to optimize the use of ML in various real-world applications and to contain the disease.

Covid-19 sentiments in smart cities: The role of technology anxiety before and during the pandemic.

The spread of Covid-19 profoundly changed citizens' daily lives due to the introduction of new modes of work and access to services based on smart technologies. Although the relevance of new technologies as strategic levers for crisis resolution has been widely debated before the pandemic, especially in the smart cities' context, how individuals have agreed to include the technological changes dictated by the pandemic in their daily interactions remains an open question. This paper aims at detecting citizens' sentiment toward technology before and after the emergence of the Covid-19 pandemic using Fuzzy Formal Concept Analysis (FFCA) to analyze a large corpus of tweets. Specifically, citizens' attitudes in five cities (Berlin, Dublin, London, Milan, and Madrid) were explored to extract and classify the key topics related to the degree of confidence, familiarity and approval of new technologies. The results shed light on the complex technology acceptance process and help managers identify the potential negative effects of smart technologies. In this way, the study enhances scholars' and practitioners' understanding of the strategies for enabling the use of technology within smart cities to manage the transformations introduced by the health emergency and guide citizens' behaviour.

A rational strategy to support approved COVID-19 vaccines prioritization.

The World Health Organization (WHO) proposed a set of criteria to be considered for the prioritization of COVID-19 candidate vaccines for further development of phase II/III clinical trials, thinking in a target audience that includes vaccine scientists, product developers, manufacturers, regulators, and funding agencies. In this paper, a knowledge-based or rational strategy is employed to perform a prioritization matrix of approved COVID-19 vaccines: BBIBP-CorV, JANSSEN, CORONAVAC, SPUTNIK V, MODERNA, PFIZER, and VAXZEVRIA, based on those proposed criteria by WHO, related to safety, efficacy, stability, implementation, and availability. We found that JANSSEN vaccine is the one with the highest score in the present study, but our analysis suggests that the WHO criteria could be more useful if they are considered separately, taking into account the social, demographic and economic characteristics of each country.

A Lexical-based Formal Concept Analysis Method to Identify Missing Concepts in the NCI Thesaurus.

Biomedical terminologies have been increasingly used in modern biomedical research and applications to facilitate data management and ensure semantic interoperability. As part of the evolution process, new concepts are regularly added to biomedical terminologies in response to the evolving domain knowledge and emerging applications. Most existing concept enrichment methods suggest new concepts via directly importing knowledge from external sources. In this paper, we introduced a lexical method based on formal concept analysis (FCA) to identify potentially missing concepts in a given terminology by leveraging its intrinsic knowledge - concept names. We first construct the FCA formal context based on the lexical features of concepts. Then we perform multistage intersection to formalize new concepts and detect potentially missing concepts. We applied our method to the Disease or Disorder sub-hierarchy in the National Cancer Institute (NCI) Thesaurus (19.08d version) and identified a total of 8,983 potentially missing concepts. As a preliminary evaluation of our method to validate the potentially missing concepts, we further checked whether they were included in any external source terminology in the Unified Medical Language System (UMLS). The result showed that 592 out of 8,937 potentially missing concepts were found in the UMLS.

Investigating the Association between Motor Function, Neuroinflammation, and Recording Metrics in the Performance of Intracortical Microelectrode Implanted in Motor Cortex.

Long-term reliability of intracortical microelectrodes remains a challenge for increased acceptance and deployment. There are conflicting reports comparing measurements associated with recording quality with postmortem histology, in attempts to better understand failure of intracortical microelectrodes (IMEs). Our group has recently introduced the assessment of motor behavior tasks as another metric to evaluate the effects of IME implantation. We hypothesized that adding the third dimension to our analysis, functional behavior testing, could provide substantial insight on the health of the tissue, success of surgery/implantation, and the long-term performance of the implanted device. Here we present our novel analysis scheme including: (1) the use of numerical formal concept analysis (nFCA) and (2) a regression analysis utilizing modern model/variable selection. The analyses found complimentary relationships between the variables. The histological variables for glial cell activation had associations between each other, as well as the neuronal density around the electrode interface. The neuronal density had associations to the electrophysiological recordings and some of the motor behavior metrics analyzed. The novel analyses presented herein describe a valuable tool that can be utilized to assess and understand relationships between diverse variables being investigated. These models can be applied to a wide range of ongoing investigations utilizing various devices and therapeutics.

Learning recommendation with formal concept analysis for intelligent tutoring system.

The aim of this research was to develop a learning recommendation component in an intelligent tutoring system (ITS) that dynamically predicts and adapts to a learner's style. In order to develop a proper ITS, we present an improved knowledge base supporting adaptive learning, which can be achieved by a suitable knowledge construction. This process is illustrated by implementing a web-based online tutor system. In addition, our knowledge structure provides adaptive presentation and personalized learning with the proposed adaptive algorithm, to retrieve content according to individual learner characteristics. To demonstrate the proposed adaptive algorithm, pre-test and post-test were used to evaluate suggestion accuracy of the course in a class for adapting to a learner's style. In addition, pre- and post-testing were also used with students in a real teaching/learning environment to evaluate the performance of the proposed model. The results show that the proposed system can be used to help students or learners achieve improved learning.

Analysis of Trajectories of Care After Bariatric Surgery Using Data Mining Method and Health Administrative Information Systems.

CONTEXT: The 30-day readmission rate after bariatric surgery is considered an important metric of the quality of hospital care. However, readmission rate beyond 30 days is rarely reported and does not provide any information about trajectories of care which would be of great interest for healthcare planning. The aim of this study was to analyze trajectories of care during the first year after bariatric surgery on a nationwide basis using data mining methods. METHOD: This was a retrospective descriptive study on the trajectories of care within the first year after bariatric surgery. Data were extracted from a national administrative claims database (the PMSI database) and trajectories were defined as principal diagnosis of successive readmissions. Formal Concept Analysis was performed to find common concepts of trajectories of care. RESULTS: We included for analysis 198,389 bariatric procedures performed on 196,323 patients. Twelve main concepts were selected. About one third of patients (32.4%) were readmitted in the first year after surgery. Most common trajectories were as follows: regular follow-up (14.9%), cholelithiasis (2.2%), abdominal pain (1.9%), and abdominal sepsis (1.3%). Important differences were found in trajectories among different bariatric procedures: 1.8% of gastric banding patients had pregnancy-related events (delivery or medical abortion), while we observed a readmission rate for abdominal sepsis in 2.7% and 5.1% of patients operated of gastric bypass and sleeve gastrectomy respectively. CONCLUSION: Administrative claim data can be analyzed through Formal Concept Analysis in order to classify trajectories of care. This approach permits to quantify expected postoperative complications and to identify unexpected events.

The interplay between QSAR/QSPR studies and partial order ranking and formal concept analyses.

The often observed scarcity of physical-chemical and well as toxicological data hampers the assessment of potentially hazardous chemicals released to the environment. In such cases Quantitative Structure-Activity Relationships/Quantitative Structure-Property Relationships (QSAR/QSPR) constitute an obvious alternative for rapidly, effectively and inexpensively generatng missing experimental values. However, typically further treatment of the data appears necessary, e.g., to elucidate the possible relations between the single compounds as well as implications and associations between the various parameters used for the combined characterization of the compounds under investigation. In the present paper the application of QSAR/QSPR in combination with Partial Order Ranking (POR) methodologies will be reviewed and new aspects using Formal Concept Analysis (FCA) will be introduced. Where POR constitutes an attractive method for, e.g., prioritizing a series of chemical substances based on a simultaneous inclusion of a range of parameters, FCA gives important information on the implications associations between the parameters. The combined approach thus constitutes an attractive method to a preliminary assessment of the impact on environmental and human health by primary pollutants or possibly by a primary pollutant well as a possible suite of transformation subsequent products that may be both persistent in and bioaccumulating and toxic. The present review focus on the environmental - and human health impact by residuals of the rocket fuel 1,1-dimethylhydrazine (heptyl) and its transformation products as an illustrative example.

Matching biomedical ontologies based on formal concept analysis.

BACKGROUND: The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. METHODS: We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. RESULTS: Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign demonstrates the effectiveness of FCA-Map and its competitiveness with the top-ranked systems. FCA-Map can achieve a better balance between precision and recall for large-scale domain ontologies through constructing multiple FCA structures, whereas it performs unsatisfactorily for smaller-sized ontologies with less lexical and semantic expressions. CONCLUSIONS: Compared with other FCA-based OM systems, the study in this paper is more comprehensive as an attempt to push the envelope of the Formal Concept Analysis formalism in ontology matching tasks. Five types of formal contexts are constructed incrementally, and their derived concept lattices are used to cluster the commonalities among classes at lexical and structural level, respectively. Experiments on large, real-world domain ontologies show promising results and reveal the power of FCA.