Different Levels Of Granularity Research Articles

Desiderata for discoverability and FAIR adoption of health data hubs

BackgroundThe future European Health Research and Innovation Cloud (HRIC), as fundamental part of the European Health Data Space (EHDS), will promote the secondary use of data and the capabilities to push the boundaries of health research within an ethical and legally compliant framework that reinforces the trust of patients and citizens. ObjectiveThis study aimed to analyse health data management mechanisms in Europe to determine their alignment with FAIR principles and data discovery generating best.practices for new data hubs joining the HRIC ecosystem. In this line, the compliance of health data hubs with FAIR principles and data discovery were assessed, and a set of best practices for health data hubs was concluded. MethodsA survey was conducted in January 2022, involving 99 representative health data hubs from multiple countries, and 42 responses were obtained in June 2022. Stratification methods were employed to cover different levels of granularity. The survey data was analysed to assess compliance with FAIR and data discovery principles. The study started with a general analysis of survey responses, followed by the creation of specific profiles based on three categories: organization type, function, and level of data aggregation. ResultsThe study produced specific best practices for data hubs regarding the adoption of FAIR principles and data discoverability. It also provided an overview of the survey study and specific profiles derived from category analysis, considering different types of data hubs. ConclusionsThe study concluded that a significant number of health data hubs in Europe did not fully comply with FAIR and data discovery principles. However, the study identified specific best practices that can guide new data hubs in adhering to these principles. The study highlighted the importance of aligning health data management mechanisms with FAIR principles to enhance interoperability and reusability in the future HRIC.

Unlocking the promise of process mining: shaping perceptions and impact in the public sector

PurposeWorldwide challenges impose public organizations to rethink their processes and satisfactorily meet citizens’ needs. Process mining (PM) techniques enable organizations to objectively analyse and improve their processes, by providing higher process transparency and efficiency. However, extant literature on PM applications in the public sector reveals there is still limited evidence on the opportunities and challenges perceived from PM introduction in the public sector, and on PM potential to enhance public sector digital transformation: this study aims to fill these gaps.Design/methodology/approachBased on Business Process Management and digital innovation fields of research, we administered a questionnaire to a sample of Italian civil servants working in different public organizations to investigate their perceptions of PM opportunities and challenges and the extent to which it can support public sector digital transformation. A three-level analysis was conducted to inspect findings with different levels of granularity, and results were analysed both descriptively and quantitatively.FindingsWe found a positive attitude towards PM introduction in the public sector, and perceived opportunities and challenges related to both the technical and the social systems. The triangulation between close-ended and open-ended questions suggests that PM could be the missing link between public sector digitalization and digital transformation. These findings can be used by policymakers to develop the best strategies to introduce PM into public organizations and support its adoption, and by researchers to further explore PM role in public sector digital transformation.Originality/valueDespite PM claiming to push digital transformation, it is not clear if it is also true for public sector organizations. This paper addresses this gap and it is among the first attempts to explore PM from civil servants’ viewpoint to investigate their perceptions of PM opportunities and challenges, as well as the variables that influence these perceptions.

A novel metric for assessing structural complexity of data warehouse requirements models

Metrics can be used to evaluate the overall structural complexity of the data warehouse (DW) and assess its quality in the early phases of design and development. The requirements data model plays a crucial role in developing a quality-based DW. Several researchers have assessed the quality of the requirements data model using the requirements metrics based on the agent-goal-decision-information (AGDI) model, both formally and empirically. However, no assessment has been implemented on the structural complexities of the requirements data model based on goal, decision, and information hierarchies. Considering this, the study proposes a novel structural complexity metric to assess the overall complexity of the requirements data model at different phases (information, decision and organisation) and to analyze the links between the different levels of granularity in these models. The proposed metric is formally validated by applying the measurement theory-based Briand’s framework for complexity measure (i.e., one of the five notions of measurements in Software Engineering) by confirming that the proposed metric is valid and defined correctly under certain mathematical properties. As a result, we conclude that the proposed structural complexity metric is accurately defined and effectively valid. We also provide a detailed comparison of various requirements metrics commonly used in similar contexts to contextualize our proposed metric within the broader landscape of existing methodologies. Additionally, we have included comprehensive guidelines and practical examples for applying the proposed structural complexity metric in DW development scenarios to enhance its utility among practitioners. The proposed metric can be utilized to ensure the accuracy of the requirements model, thereby improving the overall quality of DW.

Multi-granularity tooth analysis via YOLO-based object detection models for effective tooth detection and classification

Accurate detection and classification of teeth is the first step in dental disease diagnosis. However, the same class of tooth exhibits significant variations in surface appearance. Moreover, the complex geometrical structure poses challenges in learning discriminative features among the different tooth classes. Due to these complex features, tooth classification is one of the challenging research domains in deep learning. To address the aforementioned issues, the presented study proposes discriminative local feature extraction at different granular levels using YOLO models. However, this necessitates a granular intra-oral image dataset. To facilitate this requirement, a dataset at three granular levels (two, four, and seven teeth classes) is developed. YOLOv5, YOLOv6, and YOLOv7 models were trained using 2,790 images. The results indicate superior performance of YOLOv6 for two-class classification problems. The model generated a mean average precision (mAP) value of 94%. However, as the granularity level is increased, the performance of YOLO models decreases. For, four and seven-class classification problems, the highest mAP value of 87% and 79% was achieved by YOLOv5 respectively. The results indicate that different levels of granularity play an important role in tooth detection and classification. The YOLO’s performance gradually decreased as the granularity decreased especially at the finest granular level.

A Bayesian Approach to Uncertainty in Word Embedding Bias Estimation

Abstract Multiple measures, such as WEAT or MAC, attempt to quantify the magnitude of bias present in word embeddings in terms of a single-number metric. However, such metrics and the related statistical significance calculations rely on treating pre-averaged data as individual data points and utilizing bootstrapping techniques with low sample sizes. We show that similar results can be easily obtained using such methods even if the data are generated by a null model lacking the intended bias. Consequently, we argue that this approach generates false confidence. To address this issue, we propose a Bayesian alternative: hierarchical Bayesian modeling, which enables a more uncertainty-sensitive inspection of bias in word embeddings at different levels of granularity. To showcase our method, we apply it to Religion, Gender, and Race word lists from the original research, together with our control neutral word lists. We deploy the method using Google, GloVe, and Reddit embeddings. Further, we utilize our approach to evaluate a debiasing technique applied to the Reddit word embedding. Our findings reveal a more complex landscape than suggested by the proponents of single-number metrics. The datasets and source code for the paper are publicly available.1

The SCOPE framework - implementing ideals of responsible research assessment.

Research and researchers are heavily evaluated, and over the past decade it has become widely acknowledged that the consequences of evaluating the research enterprise and particularly individual researchers are considerable. This has resulted in the publishing of several guidelines and principles to support moving towards more responsible research assessment (RRA). To ensure that research evaluation is meaningful, responsible, and effective the International Network of Research Management Societies (INORMS) Research Evaluation Group created the SCOPE framework enabling evaluators to deliver on existing principles of RRA. SCOPE bridges the gap between principles and their implementation by providing a structured five-stage framework by which evaluations can be designed and implemented, as well as evaluated. SCOPE is a step-by-step process designed to help plan, design, and conduct research evaluations as well as check effectiveness of existing evaluations. In this article, four case studies are presented to show how SCOPE has been used in practice to provide value-based research evaluation. This article situates SCOPE within the international work towards more meaningful and robust research evaluation practices and shows through the four case studies how it can be used by different organisations to develop evaluations at different levels of granularity and in different settings. The article demonstrates that the SCOPE framework is rooted firmly in the existing literature. In addition, it is argued that it does not simply translate existing principles of RRA into practice, but provides additional considerations not always addressed in existing RRA principles and practices thus playing a specific role in the delivery of RRA. Furthermore, the use cases show the value of SCOPE across a range of settings, including different institutional types, sizes, and missions.

Development of a recommendation system and data analysis in personalized medicine: an approach towards healthy vascular ageing.

Understanding early vascular ageing has become crucial for preventing adverse cardiovascular events. To this respect, recent AI-based risk clustering models offer early detection strategies focused on healthy populations, yet their complexity limits clinical use. This work introduces a novel recommendation system embedded in a web app to assess and mitigate early vascular ageing risk, leading patients towards improved cardiovascular health. This system employs a methodology that calculates distances within multidimensional spaces and integrates cost functions to obtain personalized optimisation of recommendations. It also incorporates a classification system for determining the intensity levels of the clinical interventions. The recommendation system showed high efficiency in identifying and visualizing individuals at high risk of early vascular ageing among healthy patients. Additionally, the system corroborated its consistency and reliability in generating personalized recommendations among different levels of granularity, emphasizing its focus on moderate or low-intensity recommendations, which could improve patient adherence to the intervention. This tool might significantly aid healthcare professionals in their daily analysis, improving the prevention and management of cardiovascular diseases.

A collostructional approach to Japanese noun-modifying clause construction use and acquisition: a learner corpus study

Abstract Japanese features a general noun-modifying clause construction (NMCC) with a more versatile range of semantic and pragmatic interpretations than equivalent constructions in other languages. Motivated by the learning challenge NMCCs pose to Japanese as a foreign language (JFL) learners, this article examines speech data from the International Corpus of Japanese as a Second Language (I-JAS) to compare learner use of NMCCs against a large L1 Japanese corpus. Instances of the construction from both corpora were analyzed to identify high-frequency part-of-speech categories and subcategories in the modifying clause predicate and head noun slots. A simple collexeme analysis was then employed to identify strongly attracted and repelled lexical items among those identified in realizations of the construction. Taken together, findings from these analyses revealed an important connection between the semantic weight of head nouns in NMCCs and the idiomaticity of the construction, with learner productions demonstrating a tendency toward heavy head nouns. This study lays the groundwork for future research seeking to explore the NMCC at different levels of granularity and to improve its treatment in JFL pedagogical materials.

Block-Level Goal Recognition Design

Existing works on goal recognition design (GRD) consider the underlying domain as a classical planning domain and apply modifications to the domain to minimize the worst case distinctiveness. In this paper, we propose replacing existing modifications with blocks, which group several closely related modifications together such that a block can modify a region in a search space with respect to some design constraints. Moreover, there could be blocks within blocks such that the design space becomes hierarchical for modifications at different levels of granularity. We present 1) a new version of pruned-reduce, a successful pruning rule for GRD, for block-level GRD, and 2) a new pruning rule for pruning some branches in both hierarchical and non-hierarchical design space. Our experiments show that searching in hierarchical design spaces greatly speeds up the redesign process.

Imputation of plasma lipid species to facilitate integration of lipidomic datasets

Recent advancements in plasma lipidomic profiling methodology have significantly increased specificity and accuracy of lipid measurements. This evolution, driven by improved chromatographic and mass spectrometric resolution of newer platforms, has made it challenging to align datasets created at different times, or on different platforms. Here we present a framework for harmonising such plasma lipidomic datasets with different levels of granularity in their lipid measurements. Our method utilises elastic-net prediction models, constructed from high-resolution lipidomics reference datasets, to predict unmeasured lipid species in lower-resolution studies. The approach involves (1) constructing composite lipid measures in the reference dataset that map to less resolved lipids in the target dataset, (2) addressing discrepancies between aligned lipid species, (3) generating prediction models, (4) assessing their transferability into the targe dataset, and (5) evaluating their prediction accuracy. To demonstrate our approach, we used the AusDiab population-based cohort (747 lipid species) as the reference to impute unmeasured lipid species into the LIPID study (342 lipid species). Furthermore, we compared measured and imputed lipids in terms of parameter estimation and predictive performance, and validated imputations in an independent study. Our method for harmonising plasma lipidomic datasets will facilitate model validation and data integration efforts.

Hi-PART: Going Beyond Graph Pooling with Hierarchical Partition Tree for Graph-Level Representation Learning

Graph pooling refers to the operation that maps a set of node representations into a compact form for graph-level representation learning. However, existing graph pooling methods are limited by the power of the Weisfeiler–Lehman (WL) test in the performance of graph discrimination. In addition, these methods often suffer from hard adaptability to hyper-parameters and training instability. To address these issues, we propose Hi-PART, a simple yet effective graph neural network (GNN) framework with Hi erarchical Par tition T ree (HPT). In HPT, each layer is a partition of the graph with different levels of granularities that are going toward a finer grain from top to bottom. Such an exquisite structure allows us to quantify the graph structure information contained in HPT with the aid of structural information theory. Algorithmically, by employing GNNs to summarize node features into the graph feature based on HPT’s hierarchical structure, Hi-PART is able to adequately leverage the graph structure information and provably goes beyond the power of the WL test. Due to the separation of HPT optimization from graph representation learning, Hi-PART involves the height of HPT as the only extra hyper-parameter and enjoys higher training stability. Empirical results on graph classification benchmarks validate the superior expressive power and generalization ability of Hi-PART compared with state-of-the-art graph pooling approaches.

Deciphering principles of nucleosome interactions and impact of cancer-associated mutations from comprehensive interaction network analysis.

Nucleosomes represent hubs in chromatin organization and gene regulation and interact with a plethora of chromatin factors through different modes. In addition, alterations in histone proteins such as cancer mutations and post-translational modifications have profound effects on histone/nucleosome interactions. To elucidate the principles of histone interactions and the effects of those alterations, we developed histone interactomes for comprehensive mapping of histone-histone interactions (HHIs), histone-DNA interactions (HDIs), histone-partner interactions (HPIs) and DNA-partner interactions (DPIs) of 37 organisms, which contains a total of 3808 HPIs from 2544 binding proteins and 339 HHIs, 100 HDIs and 142 DPIs across 110 histone variants. With the developed networks, we explored histone interactions at different levels of granularities (protein-, domain- and residue-level) and performed systematic analysis on histone interactions at a large scale. Our analyses have characterized the preferred binding hotspots on both nucleosomal/linker DNA and histone octamer and unraveled diverse binding modes between nucleosome and different classes of binding partners. Last, to understand the impact of histone cancer-associated mutations on histone/nucleosome interactions, we complied one comprehensive cancer mutation dataset including 7940 cancer-associated histone mutations and further mapped those mutations onto 419,125 histone interactions at the residue level. Our quantitative analyses point to histone cancer-associated mutations' strongly disruptive effects on HHIs, HDIs and HPIs. We have further predicted 57 recurrent histone cancer mutations that have large effects on histone/nucleosome interactions and may have driver status in oncogenesis.

Risk-informed design of advanced nuclear reactor: A target unavailability approach

Incorporating specified safety and production targets during the design phase of an engineered facility can effectively support reductions in construction and operation costs of nuclear power plants. In addition, this supports efforts toward making nuclear power technology more competitive and profitable than other electric power production forms by incorporating operational and design features into the design phase that directly support the increased likelihood of meeting such originating targets. Unavailability is the key parameter to establish plant-level capabilities that cascade down to function, system, and component levels to ensure that all sources of unavailability are addressed in the facility's design phases. In this article, two methods are presented to propose unavailability targets for nuclear reactor systems to risk-inform and optimize the design features, from an availability perspective: the first method is a simple method, and the second is a non-dominated sorting genetic algorithm III (NSGA-III) multi-objective optimization. These iterative methods are demonstrated in this paper for a hypothetical facility with a design maturity such that there is knowing the main components to comply with the engineering and security functions of the systems. With an assumed mature design, it is implied that generic data to execute quantitative reliability, and availability analyses are available at the systems levels that are sufficient to support a design-specific probabilistic risk assessment (PRA). The proposed methods modify the probabilities of basic events within the fault tree structures that model system and component unavailability sources that will be required for the facility’s operating license. The methods provided are applied to visualize the characteristics of the problem and the quantitative results. This work forms the basis for future work in which design alternatives affecting unavailabilities can be estimated and compared to their associated unavailability targets at different levels of granularity.

A multi granularity information fusion text classification model based on attention mechanism

Existing research on Chinese text classification primarily focuses on classifying data information at different granularities, such as character, word, sentence, and chapter. However, this approach often fails to capture the semantic information embedded in these different levels of granularity. To enhance the extraction of the text’s core content, this study proposes a text classification model that incorporates an attention mechanism to fuse multi-granularity information. The model begins by constructing embedding vectors for characters, words, and sentences. Character and word vectors are generated using the Word2Vec training model, allowing the data to be converted into these respective vectors. To capture contextual semantic features, a bidirectional long and short-term memory network is employed for character and word vectors. Sentence vectors, on the other hand, are processed using the FastText model to extract the features they contain. To extract further important semantic information from the different feature vectors, they are fed into an attention mechanism layer. This layer enables the model to prioritize and emphasize the most significant information within the text. Experimental results demonstrate that the proposed model outperforms both single-granularity classification and combinations of two or more granularities. The model exhibits improved classification accuracy across three publicly available Chinese datasets.

Clustered Graph Matching for Label Recovery and Graph Classification

Given a collection of vertex-aligned networks and an additional label-shuffled network, we propose procedures for leveraging the signal in the vertex-aligned collection to recover the labels of the shuffled network. We consider matching the shuffled network to averages of the networks in the vertex-aligned collection at different levels of granularity. We demonstrate both in theory and practice that if the graphs come from different network classes, then clustering the networks into classes followed by matching the new graph to cluster-averages can yield higher fidelity matching performance than matching to the global average graph. Moreover, by minimizing the graph matching objective function with respect to each cluster average, this approach simultaneously classifies and recovers the vertex labels for the shuffled graph. These theoretical developments are further reinforced via an illuminating real data experiment matching human connectomes.

EHR-KnowGen: Knowledge-enhanced multimodal learning for disease diagnosis generation

Electronic health records (EHRs) contain diverse patient information, including medical notes, clinical events, and laboratory test results. Integrating this multimodal data can improve disease diagnoses using deep learning models. However, effectively combining different modalities for diagnosis remains challenging. Previous approaches, such as attention mechanisms and contrastive learning, have attempted to address this but do not fully integrate the modalities into a unified feature space. This paper presents EHR-KnowGen, a multimodal learning model enhanced with external domain knowledge, for improved disease diagnosis generation from diverse patient information in EHRs. Unlike previous approaches, our model integrates different modalities into a unified feature space with soft prompts learning and leverages large language models (LLMs) to generate disease diagnoses. By incorporating external domain knowledge from different levels of granularity, we enhance the extraction and fusion of multimodal information, resulting in more accurate diagnosis generation. Experimental results on real-world EHR datasets demonstrate the superiority of our generative model over comparative methods, providing explainable evidence to enhance the understanding of diagnosis results.

Behavioral Economics and Neuroeconomics of Environmental Values

Identifying mechanisms of real-life human decision-making is central to inform effective, human-centric public policy. Here, we report larger trends and synthesize preliminary lessons from behavioral economic and neuro-economic investigations focusing on environmental values. We review the currently available evidence at different levels of granularity, from insights into how individuals value natural resources (individual level), evidence from work on group externalities, common pool resources, and social norms (social group level) to the study of incentives, policies, and their impact (institutional level). At each level, we identify viable directions for future scientific research and actionable items for policy-makers. Coupled with new technological and methodological advances, we suggest that behavioral economic and neuroeconomic insights may inform an effective strategy to optimize environmental resources. We conclude that the time is ripe for action to enrich policies with scientifically grounded insights, making an impact in the interest of current and future generations.

Efficient Computation of the Max-Plus Semantics of Synchronous Dataflow Graphs

Streaming systems are naturally modeled with synchronous dataflow graphs (SDFGs). The max-plus semantics of an SDFG is a compact matrix representation of its timing behavior. The max-plus semantics enables us to analyze and control timing properties of the systems, such as the obtainable minimum guaranteed throughput and maximum latency. Deriving the max-plus semantics, and consequently, performance analysis may be computationally expensive since the state-of-the-art method simulates one iteration of an SDFG. This holds, in particular, for systems whose components operate at different levels of granularity, as this results in many executions of some components in one iteration. This paper aims at efficiently calculating the max-plus semantics of SDFGs. The paper proposes an optimization framework exploring decompositions of a given SDFG and finding a composition sequence whose computational effort for compositionally obtaining the max-plus semantics is minimal. Not only does our proposed technique accelerate the performance analysis of multiscale streaming systems, but it also allows us to compute the max-plus semantics of some systems for which the state-of-the-art method does not succeed because of memory limitations.

The SCOPE framework – implementing the ideals of responsible research assessment

Background: Research and researchers are heavily evaluated, and over the past decade it has become apparent that the consequences of evaluating the research enterprise and particularly individual researchers are considerable. This has resulted in the publishing of several guidelines and principles to support moving towards more responsible research assessment (RRA). To ensure that research evaluation is meaningful, responsible, and effective the International Network of Research Management Societies (INORMS) Research Evaluation Group created the SCOPE framework enabling evaluators to deliver on existing principles of RRA. SCOPE bridges the gap between principles and their implementation by providing a structured five-stage framework by which evaluations can be designed and implemented, as well as evaluated. Methods: SCOPE is a step-by-step process designed to help plan, design, and conduct research evaluations as well as check effectiveness of existing evaluations. In this article, four case studies are presented to show how SCOPE has been used in practice to provide value-based research evaluation. Results: This article situates SCOPE within the international work towards more meaningful and robust research evaluation practices and shows through the four case studies how it can be used by different organisations to develop evaluations at different levels of granularity and in different settings. Conclusions: The article demonstrates that the SCOPE framework is rooted firmly in the existing literature. In addition, it is argued that it does not simply translate existing principles of RRA into practice, but provides additional considerations not always addressed in existing RRA principles and practices thus playing a specific role in the delivery of RRA. Furthermore, the use cases show the value of SCOPE across a range of settings, including different institutional types, sizes, and missions.

Individuality-enhanced and multi-granularity consistency-preserving graph neural network for semi-supervised node classification

Semi-supervised node classification is an important task that aims at classifying nodes based on the graph structure, node features, and class labels for a subset of nodes. While most graph convolutional networks (GCNs) perform well when an ample number of labeled nodes are available, they often degenerate when the amount of labeled data is limited. To address this problem, we propose a scheme, namely, Individuality-enhanced and Multi-granularity Consistency-preserving graph neural Network (IMCN), which can alleviate the problem of losing individual information within the encoder while providing a reliable supervised signal for learning purposes. First, one simple encoder based on node features only is integrated to enhance node individuality and amend node commonality learned by the GCN-based encoder. Then, three constraints are defined at different levels of granularity, encompassing node embedding agreement, semantic class alignment, and node-to-class distribution identity. They can maintain the consistency between the individuality and commonality of nodes and be leveraged as latent supervised signals for learning representative embeddings. Finally, the trade-off between the individuality and commonality of nodes captured by two encoders is taken into consideration for node classification. Extensive experiments on six real-world datasets have been conducted to validate the superiority of IMCN against state-of-the-art baselines in handling node classification tasks with scarce labeled data.Graphical abstract