A Spatiotemporal Probabilistic Graphical Model Based on Adaptive Expectation-Maximization Attention for Individual Trajectory Reconstruction Considering Incomplete Observations.

Spatiotemporal information on individual trajectories in urban rail transit is important for operational strategy adjustment, personalized recommendation, and emergency command decision-making. However, due to the lack of journey observations, it is difficult to accurately infer unknown information from trajectories based only on AFC and AVL data. To address the problem, this paper proposes a spatiotemporal probabilistic graphical model based on adaptive expectation maximization attention (STPGM-AEMA) to achieve the reconstruction of individual trajectories. The approach consists of three steps: first, the potential train alternative set and the egress time alternative set of individuals are obtained through data mining and combinatorial enumeration. Then, global and local potential variables are introduced to construct a spatiotemporal probabilistic graphical model, provide the inference process for unknown events, and state information about individual trajectories. Further, considering the effect of missing data, an attention mechanism-enhanced expectation-maximization algorithm is proposed to achieve maximum likelihood estimation of individual trajectories. Finally, typical datasets of origin-destination pairs and actual individual trajectory tracking data are used to validate the effectiveness of the proposed method. The results show that the STPGM-AEMA method is more than 95% accurate in recovering missing information in the observed data, which is at least 15% more accurate than the traditional methods (i.e., PTAM-MLE and MPTAM-EM).

Estimating Distributions of Parameters in Nonlinear State Space Models with Replica Exchange Particle Marginal Metropolis-Hastings Method.

Extracting latent nonlinear dynamics from observed time-series data is important for understanding a dynamic system against the background of the observed data. A state space model is a probabilistic graphical model for time-series data, which describes the probabilistic dependence between latent variables at subsequent times and between latent variables and observations. Since, in many situations, the values of the parameters in the state space model are unknown, estimating the parameters from observations is an important task. The particle marginal Metropolis-Hastings (PMMH) method is a method for estimating the marginal posterior distribution of parameters obtained by marginalization over the distribution of latent variables in the state space model. Although, in principle, we can estimate the marginal posterior distribution of parameters by iterating this method infinitely, the estimated result depends on the initial values for a finite number of times in practice. In this paper, we propose a replica exchange particle marginal Metropolis-Hastings (REPMMH) method as a method to improve this problem by combining the PMMH method with the replica exchange method. By using the proposed method, we simultaneously realize a global search at a high temperature and a local fine search at a low temperature. We evaluate the proposed method using simulated data obtained from the Izhikevich neuron model and Lévy-driven stochastic volatility model, and we show that the proposed REPMMH method improves the problem of the initial value dependence in the PMMH method, and realizes efficient sampling of parameters in the state space models compared with existing methods.

Discovering Clinical Information Models Online to Promote Interoperability of Electronic Health Records: A Feasibility Study of OpenEHR.

BACKGROUND: Clinical information models (CIMs) enabling semantic interoperability are crucial for electronic health record (EHR) data use and reuse. Dual model methodology, which distinguishes the CIMs from the technical domain, could help enable the interoperability of EHRs at the knowledge level. How to help clinicians and domain experts discover CIMs from an open repository online to represent EHR data in a standard manner becomes important. OBJECTIVE: This study aimed to develop a retrieval method to identify CIMs online to represent EHR data. METHODS: We proposed a graphical retrieval method and validated its feasibility using an online CIM repository: openEHR Clinical Knowledge Manager (CKM). First, we represented CIMs (archetypes) using an extended Bayesian network. Then, an inference process was run in the network to discover relevant archetypes. In the evaluation, we defined three retrieval tasks (medication, laboratory test, and diagnosis) and compared our method with three typical retrieval methods (BM25F, simple Bayesian network, and CKM), using mean average precision (MAP), average precision (AP), and precision at 10 (P@10) as evaluation metrics. RESULTS: We downloaded all available archetypes from the CKM. Then, the graphical model was applied to represent the archetypes as a four-level clinical resources network. The network consisted of 5513 nodes, including 3982 data element nodes, 504 concept nodes, 504 duplicated concept nodes, and 523 archetype nodes, as well as 9867 edges. The results showed that our method achieved the best MAP (MAP=0.32), and the AP was almost equal across different retrieval tasks (AP=0.35, 0.31, and 0.30, respectively). In the diagnosis retrieval task, our method could successfully identify the models covering "diagnostic reports," "problem list," "patients background," "clinical decision," etc, as well as models that other retrieval methods could not find, such as "problems and diagnoses." CONCLUSIONS: The graphical retrieval method we propose is an effective approach to meet the uncertainty of finding CIMs. Our method can help clinicians and domain experts identify CIMs to represent EHR data in a standard manner, enabling EHR data to be exchangeable and interoperable.

Exploring complaints by female and male patients at Swedish hospitals using a probabilistic graphical model.

BACKGROUND: Patients' complaints have been highlighted as important for constructively improving healthcare services. In so doing, it may be important to identify disparities in experiences based on patients' demographics, such as sex. AIM: To explore hospital recorded complaints addressing potential sex differences and whether complaints were reported by the patient or a relative. METHODS: Quantitative study of all 835 closed patient complaints during 2013 at three mid-sized hospitals in Sweden. The complaints were categorisation based on perceived quality theory and analysed using a probabilistic graphical model. The findings were validated through qualitative interviews. FINDINGS: Female patients were more likely than male patients to report dissatisfaction with interpersonal issues, whereas male patients were more likely to report dissatisfaction with administration. If a complaint from a male patient had been reported by a relative, the matter was more likely to be interpersonal. Improvement suggestions were predominantly reported by staff. However, patients and relatives proved more likely than staff to report improvement suggestions when dissatisfied with interpersonal matters. CONCLUSION: Using a Bayesian network, this article suggests that complaints in health care should be more holistically understood and the factors should be viewed as interconnected. This article addresses complaints as an important source of identifying not only perceived healthcare deficiencies and sex disparities, but also improvement suggestions.

A Dual-Field Sensing Scheme for a Guidance System for the Blind.

An electronic guidance system is very helpful in improving blind people's perceptions in a local environment. In our previous work "Lin, Q.; Han, Y. A Context-Aware-Based Audio Guidance System for Blind People Using a Multimodal Profile Model. Sensors 2014, 14, 18670-18700", a context-aware guidance system using a combination of a laser scanner and a camera was proposed. By using a near-field graphical model, the proposed system could interpret a near-field scene in very high resolution. In this paper, our work is extended by adding a far-field graphical model. The integration of the near-field and the far-field models constitutes a dual-field sensing scheme. In the near-field range, reliable inference of the ground and object status is obtained by fusing range data and image data using the near-field graphical model. In the far-field range, which only the camera can cover, the far-field graphical model is proposed to interpret far-field image data based on appearance and spatial prototypes built using the near-field interpreted data. The dual-field sensing scheme provides a solution for the guidance systems to optimise their scene interpretation capability using simple sensor configurations. Experiments under various local conditions were conducted to show the efficiency of the proposed scheme in improving blind people's perceptions in urban environments.

Salient and Non-Salient Fiducial Detection using a Probabilistic Graphical Model.

Deformable shape detection is an important problem in computer vision and pattern recognition. However, standard detectors are typically limited to locating only a few salient landmarks such as landmarks near edges or areas of high contrast, often conveying insufficient shape information. This paper presents a novel statistical pattern recognition approach to locate a dense set of salient and non-salient landmarks in images of a deformable object. We explore the fact that several object classes exhibit a homogeneous structure such that each landmark position provides some information about the position of the other landmarks. In our model, the relationship between all pairs of landmarks is naturally encoded as a probabilistic graph. Dense landmark detections are then obtained with a new sampling algorithm that, given a set of candidate detections, selects the most likely positions as to maximize the probability of the graph. Our experimental results demonstrate accurate, dense landmark detections within and across different databases.

Modelling-based joint embedding of histology and genomics using canonical correlation analysis for breast cancer survival prediction.

Traditional approaches to predicting breast cancer patients' survival outcomes were based on clinical subgroups, the PAM50 genes, or the histological tissue's evaluation. With the growth of multi-modality datasets capturing diverse information (such as genomics, histology, radiology and clinical data) about the same cancer, information can be integrated using advanced tools and have improved survival prediction. These methods implicitly exploit the key observation that different modalities originate from the same cancer source and jointly provide a complete picture of the cancer. In this work, we investigate the benefits of explicitly modelling multi-modality data as originating from the same cancer under a probabilistic framework. Specifically, we consider histology and genomics as two modalities originating from the same breast cancer under a probabilistic graphical model (PGM). We construct maximum likelihood estimates of the PGM parameters based on canonical correlation analysis (CCA) and then infer the underlying properties of the cancer patient, such as survival. Equivalently, we construct CCA-based joint embeddings of the two modalities and input them to a learnable predictor. Real-world properties of sparsity and graph-structures are captured in the penalized variants of CCA (pCCA) and are better suited for cancer applications. For generating richer multi-dimensional embeddings with pCCA, we introduce two novel embedding schemes that encourage orthogonality to generate more informative embeddings. The efficacy of our proposed prediction pipeline is first demonstrated via low prediction errors of the hidden variable and the generation of informative embeddings on simulated data. When applied to breast cancer histology and RNA-sequencing expression data from The Cancer Genome Atlas (TCGA), our model can provide survival predictions with average concordance-indices of up to 68.32% along with interpretability. We also illustrate how the pCCA embeddings can be used for survival analysis through Kaplan-Meier curves.

Effective diagnosis of sepsis in critically ill children using probabilistic graphical model.

Background: Probabilistic graphical model, a rich graphical framework in modelling associations between variables in complex domains, can be utilized to aid clinical diagnosis. However, its application in pediatric sepsis remains limited. This study aims to explore the utility of probabilistic graphical models in pediatric sepsis in the pediatric intensive care unit. Methods: We conducted a retrospective study on children using the first 24-hour clinical data of the intensive care unit admission from the Pediatric Intensive Care Dataset, 2010-2019. A probabilistic graphical model method, Tree Augmented Naive Bayes, was used to build diagnosis models using combinations of four categories: vital signs, clinical symptoms, laboratory, and microbiological tests. Variables were reviewed and selected by clinicians. Sepsis cases were identified with the discharged diagnosis of sepsis or suspected infection with the systemic inflammatory response syndrome. Performance was measured by the average sensitivity, specificity, accuracy, and area under the curve of ten-fold cross-validations. Results: We extracted 3,014 admissions [median age of 1.13 (interquartile range: 0.15-4.30) years old]. There were 134 (4.4%) and 2,880 (95.6%) sepsis and non-sepsis patients, respectively. All diagnosis models had high accuracy (0.92-0.96), specificity (0.95-0.99), and area under the curve (0.77-0.87). Sensitivity varied with different combinations of variables. The model that combined all four categories yielded the best performance [accuracy: 0.93 (95% confidence interval (CI): 0.916-0.936); sensitivity: 0.46 (95% CI: 0.376-0.550), specificity: 0.95 (95% CI: 0.940-0.956), area under the curve: 0.87 (95% CI: 0.826-0.906)]. Microbiological tests had low sensitivity (<0.10) with high incidence of negative results (67.2%). Conclusions: We demonstrated that the probabilistic graphical model is a feasible diagnostic tool for pediatric sepsis. Future studies using different datasets should be conducted to assess its utility to aid clinicians in the diagnosis of sepsis.

Graph algorithms for predicting subcellular localization at the pathway level

Protein subcellular localization is an important factor in normal cellular processes and disease. While many protein localization resources treat it as static, protein localization is dynamic and heavily influenced by biological context. Biological pathways are graphs that represent a specific biological context and can be inferred from large-scale data. We develop graph algorithms to predict the localization of all interactions in a biological pathway as an edge-labeling task. We compare a variety of models including graph neural networks, probabilistic graphical models, and discriminative classifiers for predicting localization annotations from curated pathway databases. We also perform a case study where we construct biological pathways and predict localizations of human fibroblasts undergoing viral infection. Pathway localization prediction is a promising approach for integrating publicly available localization data into the analysis of large-scale biological data.

Exploiting noise as a resource for computation and learning in spiking neural networks.

Networks of spiking neurons underpin the extraordinary information-processing capabilities of the brain and have become pillar models in neuromorphic artificial intelligence. Despite extensive research on spiking neural networks (SNNs), most studies are established on deterministic models, overlooking the inherent non-deterministic, noisy nature of neural computations. This study introduces the noisy SNN (NSNN) and the noise-driven learning (NDL) rule by incorporating noisy neuronal dynamics to exploit the computational advantages of noisy neural processing. The NSNN provides a theoretical framework that yields scalable, flexible, and reliable computation and learning. We demonstrate that this framework leads to spiking neural models with competitive performance, improved robustness against challenging perturbations compared with deterministic SNNs, and better reproducing probabilistic computation in neural coding. Generally, this study offers a powerful and easy-to-use tool for machine learning, neuromorphic intelligence practitioners, and computational neuroscience researchers.

Bayesian network analysis reveals the interplay of intracranial aneurysm rupture risk factors.

Clinical decision making regarding the treatment of unruptured intracranial aneurysms (IA) benefits from a better understanding of the interplay of IA rupture risk factors. Probabilistic graphical models can capture and graphically display potentially causal relationships in a mechanistic model. In this study, Bayesian networks (BN) were used to estimate IA rupture risk factors influences. From 1248 IA patient records, a retrospective, single-cohort, patient-level data set with 9 phenotypic rupture risk factors (n=790 complete entries) was extracted. Prior knowledge together with score-based structure learning algorithms estimated rupture risk factor interactions. Two approaches, discrete and mixed-data additive BN, were implemented and compared. The corresponding graphs were learned using non-parametric bootstrapping and Markov chain Monte Carlo, respectively. The BN models were compared to standard descriptive and regression analysis methods. Correlation and regression analyses showed significant associations between IA rupture status and patient's sex, familial history of IA, age at IA diagnosis, IA location, IA size and IA multiplicity. BN models confirmed the findings from standard analysis methods. More precisely, they directly associated IA rupture with familial history of IA, IA size and IA location in a discrete framework. Additive model formulation, enabling mixed-data, found that IA rupture was directly influenced by patient age at diagnosis besides additional mutual influences of the risk factors. This study establishes a data-driven methodology for mechanistic disease modelling of IA rupture and shows the potential to direct clinical decision-making in IA treatment, allowing personalised prediction.

Probabilistic graphical model for the evaluation of the emotional and dramatic personality disorders.

Personality disorders are psychological ailments with a major negative impact on patients, their families, and society in general, especially those of the dramatic and emotional type. Despite all the research, there is still no consensus on the best way to assess and treat them. Traditional assessment of personality disorders has focused on a limited number of psychological constructs or behaviors using structured interviews and questionnaires, without an integrated and holistic approach. We present a novel methodology for the study and assessment of personality disorders consisting in the development of a Bayesian network, whose parameters have been obtained by the Delphi method of consensus from a group of experts in the diagnosis and treatment of personality disorders. The result is a probabilistic graphical model that represents the psychological variables related to the personality disorders along with their relations and conditional probabilities, which allow identifying the symptoms with the highest diagnostic potential. This model can be used, among other applications, as a decision support system for the assessment and treatment of personality disorders of the dramatic or emotional cluster. In this paper, we discuss the need to validate this model in the clinical population along with its strengths and limitations.

A data-driven Bayesian network for probabilistic crash risk assessment of individual driver with traffic violation and crash records.

In recent years, individual drivers' crash risk assessments have received much attention for identifying high-risk drivers. To this end, we propose a probabilistic assessment method of crash risks with a reproducible long-term dataset (i.e., traffic violations, license, and crash records). In developing this method, we used 7.75 million violations and crashes of 5.5 million individual drivers in Seoul, South Korea, from June 2013 to June 2017 (four years). The stochastic process of the Bayesian network (BN), whose structure is optimized by tabu-search, successfully evaluates individual drivers' crash and violation probability. In addition, the cluster analysis classifies drivers into five distinctive groups according to their estimated violation and crash probabilities. As a result, this study found that the estimated average crash rate within a cluster converges with the actual crash rate by the proposed framework without privacy issues. We also confirm that violation records and expected crash probability are strongly correlated, and there is a direct relationship between a driver's previous violations and crash record and the future at-fault crash. The proposed assessment method is valuable in developing proactive driver education programs and safety countermeasures, including adjusting the penalty system and developing user-based insurance by recognizing dangerous drivers and identifying their properties.

Intersection two-vehicle crash scenario specification for automated vehicle safety evaluation using sequence analysis and Bayesian networks.

This paper introduces a test scenario specification procedure using crash sequence analysis and Bayesian network modeling. Intersection two-vehicle crash data was obtained from the 2016-2018 National Highway Traffic Safety Administration (NHTSA) Crash Report Sampling System (CRSS) database. Vehicles involved in the crashes are specifically renumbered based on their initial positions and trajectories. Crash sequences are encoded to include detailed pre-crash events and concise collision events. Based on sequence patterns, the crashes are characterized as 55 types. A Bayesian network model is developed to depict the interrelationships among crash sequence types, crash outcomes, human factors, and environmental conditions. Scenarios are specified by querying the Bayesian network's conditional probability table. Distributions of operational design domain (ODD) attributes (e.g., driver behavior, weather, lighting condition, intersection geometry, traffic control device) are specified based on conditions of sequence types. Also, distribution of sequence types is specified on specific crash outcomes or combinations of ODD attributes.

Toward an idiomatic framework for cognitive robotics.

Inspired by the "cognitive hourglass" model presented by the researchers behind the cognitive architecture called Sigma, we propose a framework for developing cognitive architectures for cognitive robotics. The main purpose of the proposed framework is to ease development of cognitive architectures by encouraging cooperation and re-use of existing results. This is done by proposing a framework dividing development of cognitive architectures into a series of layers that can be considered partly in isolation, some of which directly relate to other research fields. Finally, we introduce and review some topics essential for the proposed framework. We also outline a set of applications.

SPIN reveals genome-wide landscape of nuclear compartmentalization.

We report SPIN, an integrative computational method to reveal genome-wide intranuclear chromosome positioning and nuclear compartmentalization relative to multiple nuclear structures, which are pivotal for modulating genome function. As a proof-of-principle, we use SPIN to integrate nuclear compartment mapping (TSA-seq and DamID) and chromatin interaction data (Hi-C) from K562 cells to identify 10 spatial compartmentalization states genome-wide relative to nuclear speckles, lamina, and putative associations with nucleoli. These SPIN states show novel patterns of genome spatial organization and their relation to other 3D genome features and genome function (transcription and replication timing). SPIN provides critical insights into nuclear spatial and functional compartmentalization.

CACTUS: integrating clonal architecture with genomic clustering and transcriptome profiling of single tumor cells.

BACKGROUND: Drawing genotype-to-phenotype maps in tumors is of paramount importance for understanding tumor heterogeneity. Assignment of single cells to their tumor clones of origin can be approached by matching the genotypes of the clones to the mutations found in RNA sequencing of the cells. The confidence of the cell-to-clone mapping can be increased by accounting for additional measurements. Follicular lymphoma, a malignancy of mature B cells that continuously acquire mutations in parallel in the exome and in B cell receptor loci, presents a unique opportunity to join exome-derived mutations with B cell receptor sequences as independent sources of evidence for clonal evolution. METHODS: Here, we propose CACTUS, a probabilistic model that leverages the information from an independent genomic clustering of cells and exploits the scarce single cell RNA sequencing data to map single cells to given imperfect genotypes of tumor clones. RESULTS: We apply CACTUS to two follicular lymphoma patient samples, integrating three measurements: whole exome, single-cell RNA, and B cell receptor sequencing. CACTUS outperforms a predecessor model by confidently assigning cells and B cell receptor-based clusters to the tumor clones. CONCLUSIONS: The integration of independent measurements increases model certainty and is the key to improving model performance in the challenging task of charting the genotype-to-phenotype maps in tumors. CACTUS opens the avenue to study the functional implications of tumor heterogeneity, and origins of resistance to targeted therapies. CACTUS is written in R and source code, along with all supporting files, are available on GitHub ( https://github.com/LUMC/CACTUS ).

Graphical-model framework for automated annotation of cell identities in dense cellular images.

Although identifying cell names in dense image stacks is critical in analyzing functional whole-brain data enabling comparison across experiments, unbiased identification is very difficult, and relies heavily on researchers' experiences. Here, we present a probabilistic-graphical-model framework, CRF_ID, based on Conditional Random Fields, for unbiased and automated cell identification. CRF_ID focuses on maximizing intrinsic similarity between shapes. Compared to existing methods, CRF_ID achieves higher accuracy on simulated and ground-truth experimental datasets, and better robustness against challenging noise conditions common in experimental data. CRF_ID can further boost accuracy by building atlases from annotated data in highly computationally efficient manner, and by easily adding new features (e.g. from new strains). We demonstrate cell annotation in Caenorhabditis elegans images across strains, animal orientations, and tasks including gene-expression localization, multi-cellular and whole-brain functional imaging experiments. Together, these successes demonstrate that unbiased cell annotation can facilitate biological discovery, and this approach may be valuable to annotation tasks for other systems.

Incorporating structured assumptions with probabilistic graphical models in fMRI data analysis.

With the wide adoption of functional magnetic resonance imaging (fMRI) by cognitive neuroscience researchers, large volumes of brain imaging data have been accumulated in recent years. Aggregating these data to derive scientific insights often faces the challenge that fMRI data are high-dimensional, heterogeneous across people, and noisy. These challenges demand the development of computational tools that are tailored both for the neuroscience questions and for the properties of the data. We review a few recently developed algorithms in various domains of fMRI research: fMRI in naturalistic tasks, analyzing full-brain functional connectivity, pattern classification, inferring representational similarity and modeling structured residuals. These algorithms all tackle the challenges in fMRI similarly: they start by making clear statements of assumptions about neural data and existing domain knowledge, incorporate those assumptions and domain knowledge into probabilistic graphical models, and use those models to estimate properties of interest or latent structures in the data. Such approaches can avoid erroneous findings, reduce the impact of noise, better utilize known properties of the data, and better aggregate data across groups of subjects. With these successful cases, we advocate wider adoption of explicit model construction in cognitive neuroscience. Although we focus on fMRI, the principle illustrated here is generally applicable to brain data of other modalities.

Probabilistic Multigraph Modeling for Improving the Quality of Crowdsourced Affective Data.

We proposed a probabilistic approach to joint modeling of participants' reliability and humans' regularity in crowdsourced affective studies. Reliability measures how likely a subject will respond to a question seriously; and regularity measures how often a human will agree with other seriously-entered responses coming from a targeted population. Crowdsourcing-based studies or experiments, which rely on human self-reported affect, pose additional challenges as compared with typical crowdsourcing studies that attempt to acquire concrete non-affective labels of objects. The reliability of participants has been massively pursued for typical non-affective crowdsourcing studies, whereas the regularity of humans in an affective experiment in its own right has not been thoroughly considered. It has been often observed that different individuals exhibit different feelings on the same test question, which does not have a sole correct response in the first place. High reliability of responses from one individual thus cannot conclusively result in high consensus across individuals. Instead, globally testing consensus of a population is of interest to investigators. Built upon the agreement multigraph among tasks and workers, our probabilistic model differentiates subject regularity from population reliability. We demonstrate the method's effectiveness for in-depth robust analysis of large-scale crowdsourced affective data, including emotion and aesthetic assessments collected by presenting visual stimuli to human subjects.