Tabular data embedded in PDF files, web pages, and other types of documents is prevalent in various domains. These tables, which we call human-centric tables (HCTs for short), are dense in information but often exhibit complex structural and semantic layouts. To query these HCTs, some existing solutions focus on transforming them into relational formats. However, they fail to handle the diverse and complex layouts of HCTs, making them not amenable to easy querying with SQL-based approaches. Another emerging option is to use Large Language Models (LLMs) and Vision Language Models (VLMs). However, there is a lack of standard evaluation benchmarks to measure and compare the performance of models to query HCTs using natural language. To address this gap, we propose the HumanCentric Tables Question-Answering extensive benchmark (HCTQA) consisting of thousands of HCTs with several thousands of natural language questions with their respective answers. More specifically, HCT-QA includes 1,880 real-world HCTs with 9,835 QA pairs in addition to 4,679 synthetic HCTs with 67.7K QA pairs. Also, we show through extensive experiments the performance of 25 and 9 different LLMS and VLMs, respectively, in an answering HCT-QA's questions. In addition, we show how finetuning an LLM on HCT-QA improves F1 scores by up to 25 percentage points compared to the off-the-shelf model. Compared to existing benchmarks, HCT-QA stands out for its broad complexity and diversity of covered HCTs and generated questions, its comprehensive metadata enabling deeper insight and analysis, and its novel synthetic data and QA generator.

This study introduces a novel encoding scheme for DNA/RNA sequences, integrating Komlós and Hadamard transforms. Unlike traditional One-Hot encoding, this approach offers a more informative representation of omics data while significantly reducing computational complexity. However, it is important to note that the Komlós transform component provides fewer features and does not utilize sparse codes. By leveraging the inherent properties of these transforms, our method effectively captures complex patterns within the data, leading to improved model accuracy and reduced training times. When combined with an image transformation, this encoding scheme demonstrates particularly efficient results, achieving superior performance across various predictive tasks with significantly lower computational resource demands compared to One-Hot encoding. Our findings suggest that this novel encoding scheme, particularly when integrated with Hilbert Curve mapping or sequence to image analysis, holds significant promise for advancing DNA/RNA data analysis by offering a more efficient and effective approach to feature representation.

Visual cluster analysis is a central task to explore multidimensional data. Dimensionality Reduction (DR) techniques support this task by spatializing multidimensional (MD) data similarities as point patterns in scatterplots. However, unavoidable false and missing neighbor distortions limit their accuracy. For instance, false neighbors make truly separated data clusters appear to overlap in the layout, while missing neighbors split true clusters into falsely separated groups. In general, both types of distortions exist in DR layouts except for orthogonal linear projections (OLP) that only generate false neighbors. In this work, we propose Isometric Seriation-based Dimensionality Reductions (ISilDR) that provably generate at most missing neighbors. We study how ISilDR and OLP together could be leveraged to discover true MD clusters. An ISilDR first creates a seriation of the MD data points, i.e., an ordering along a one-dimensional projection axis, and then each pair of consecutive points along this axis is spaced by their MD distance. An $m$D ISilDR can be obtained by combining $m$ 1D ISilDRs. We study the theoretical and empirical characteristics of different variants of ISilDRs and OLPs and propose a systematic and formal analysis based on ε-neighborhood graphs. From there, we derive rules to discover cluster patterns in MD data from interactive linking of ISilDR and OLP coordinated layouts. We then conduct case studies and illustrate scenarios for trustworthy visual cluster analysis using a combination of ISilDR and other classical DR techniques.

Brushing is a common interaction technique in 2D scatterplots, allowing users to select clustered points within a continuous, enclosed region for further analysis or filtering. However, applying conventional brushing to 2D representations of multidimensional (MD) data, i.e., Multidimensional Projections (MDPs), can lead to unreliable cluster analysis due to MDP-induced distortions that inaccurately represent the cluster structure of the original MD data. To alleviate this problem, we introduce a novel brushing technique for MDPs called Distortion-aware brushing. As users perform brushing, Distortion-aware brushing correct distortions around the currently brushed points by dynamically relocating points in the projection, pulling data points close to the brushed points in MD space while pushing distant ones apart. This dynamic adjustment helps users brush MD clusters more accurately, leading to more reliable cluster analysis. Our user studies with 24 participants show that Distortion-aware brushing significantly outperforms previous brushing techniques for MDPs in accurately separating clusters in the MD space and remains robust against distortions. We further demonstrate the effectiveness of our technique through two use cases: (1) conducting cluster analysis of geospatial data and (2) interactively labeling MD clusters.

The paper explores the synergy between wearable data and augmented Artificial Intelligence (AI) through findings from two interconnected studies. The first study (study 1) focuses on medical professionals’ perceptions of wearable data and AI, and the second study (Study 2) extends it focuses on how differences in the level of granularity in the data presented affect the professionals’ understanding, interpretation, and trust in AI recommendations. This system allows medical professionals to view AI-generated recommendations for sleep and activity improvement and explanations of the underlying rationale. While each study has distinct research questions, Study 2 builds upon Study 1's foundation. Both studies employed scenario-based interviews. Thematic analysis of Study 1 identified trust as a crucial factor in the acceptance of wearable data and AI, influencing Study 2's exploration of factors affecting trust, such as explainability, data granularity, representativeness, and user interaction. Study 2 highlighted varying perspectives on information sufficiency and data sharing from the AI system linked to professionals’ roles and tasks. The work offers insights into data granularity’s impact on engagement with AI recommendations.

Clustering techniques are often validated using benchmark datasets where class labels are used as ground-truth clusters. However, depending on the datasets, class labels may not align with the actual data clusters, and such misalignment hampers accurate validation. Therefore, it is essential to evaluate and compare datasets regarding their cluster-label matching (CLM), i.e., how well their class labels match actual clusters. Internal validation measures (IVMs), like Silhouette, can compare CLM over different labeling of the same dataset, but are not designed to do so across different datasets. We thus introduce Adjusted IVMs as fast and reliable methods to evaluate and compare CLM across datasets. We establish four axioms that require validation measures to be independent of data properties not related to cluster structure (e.g., dimensionality, dataset size). Then, we develop standardized protocols to convert any IVM to satisfy these axioms, and use these protocols to adjust six widely used IVMs. Quantitative experiments (1) verify the necessity and effectiveness of our protocols and (2) show that adjusted IVMs outperform the competitors, including standard IVMs, in accurately evaluating CLM both within and across datasets. We also show that the datasets can be filtered or improved using our method to form more reliable benchmarks for clustering validation.

A common way to evaluate the reliability of dimensionality reduction (DR) embeddings is to quantify how well labeled classes form compact, mutually separated clusters in the embeddings. This approach is based on the assumption that the classes stay as clear clusters in the original high-dimensional space. However, in reality, this assumption can be violated; a single class can be fragmented into multiple separated clusters, and multiple classes can be merged into a single cluster. We thus cannot always assure the credibility of the evaluation using class labels. In this paper, we introduce two novel quality measures-Label-Trustworthiness and Label-Continuity (Label-T&C)-advancing the process of DR evaluation based on class labels. Instead of assuming that classes are well-clustered in the original space, Label-T&C work by (1) estimating the extent to which classes form clusters in the original and embedded spaces and (2) evaluating the difference between the two. A quantitative evaluation showed that Label-T&C outperform widely used DR evaluation measures (e.g., Trustworthiness and Continuity, Kullback-Leibler divergence) in terms of the accuracy in assessing how well DR embeddings preserve the cluster structure, and are also scalable. Moreover, we present case studies demonstrating that Label-T&C can be successfully used for revealing the intrinsic characteristics of DR techniques and their hyperparameters.

Exploratory visual analysis of multidimensional labeled data is challenging.Multidimensional Projections for labeled data attempt to separate classes while preserving neighborhoods.In this work, we consider the case where instances are assigned multiple labels with probabilities or weights: for example, the output of a probabilistic classifier, fuzzy membership functions in fuzzy logic, or the share of votes for each candidate in an election.We propose a new technique to better preserve neighborhoods of such data.Our experiments show improved qualitative results compared to unsupervised, and existing dimensionality reduction techniques.* The work of SM and SL has been realized with the participation of INES.2S.The work of DD has been

We propose Compadre, a tool for visual analysis for comparing distances of high-dimensional (HD) data and their low-dimensional projections. At the heart is a matrix visualization to represent the discrepancy between distance matrices, linked side-by-side with 2D scatterplot projections of the data. Using different examples and datasets, we illustrate how this approach fosters (1) evaluating dimensionality reduction techniques w.r.t. how well they project the HD data, (2) comparing them to each other side-by-side, and (3) evaluate important data features through subspace comparison. We also present a case study, in which we analyze IEEE VIS authors from 1990 to 2018, and gain new insights on the relationships between coauthors, citations, and keywords. The coauthors are projected as accurately with UMAP as with t-SNE but the projections show different insights. The structure of the citation subspace is very different from the coauthor subspace. The keyword subspace is noisy yet consistent among the three IEEE VIS sub-conferences.

Nonlinear dimensionality reduction of high-dimensional data is challenging as the low-dimensional embedding will necessarily contain distortions, and it can be hard to determine which distortions are the most important to avoid. When annotation of data into known relevant classes is available, it can be used to guide the embedding to avoid distortions that worsen class separation. The supervised mapping method introduced in the present paper, called ClassNeRV, proposes an original stress function that takes class annotation into account and evaluates embedding quality both in terms of false neighbors and missed neighbors. ClassNeRV shares the theoretical framework of a family of methods descended from Stochastic Neighbor Embedding (SNE). Our approach has a key advantage over previous ones: in the literature supervised methods often emphasize class separation at the price of distorting the data neighbors' structure; conversely, unsupervised methods provide better preservation of structure at the price of often mixing classes. Experiments show that ClassNeRV can preserve both neighbor structure and class separation, outperforming nine state of the art alternatives.

MOTIVATION: It is important to characterize individual relatedness in terms of familial relationships and underlying population structure in genome-wide association studies for correct downstream analysis. The characterization of individual relatedness becomes vital if the cohort is to be used as reference panel in other studies for association tests and for identifying ethnic diversities. In this paper, we propose a kinship visualization tool to detect cryptic relatedness between subjects. We utilize multi-dimensional scaling, bar charts, heat maps and node-link visualizations to enable analysis of relatedness information. AVAILABILITY AND IMPLEMENTATION: Available online as well as can be downloaded at http://shiny-vis.qcri.org/public/kinvis/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Abstract We propose ClustMe, a new visual quality measure to rank monochrome scatterplots based on cluster patterns. ClustMe is based on data collected from a human‐subjects study, in which34participants judged synthetically generated cluster patterns in1000scatterplots. We generated these patterns by carefully varying the free parameters of a simple Gaussian Mixture Model with two components, and asked the participants to count the number of clusters they could see (1 or more than 1). Based on the results, we form ClustMe by selecting the model that best predicts these human judgments among7different state‐of‐the‐art merging techniques (Demp). To quantitatively evaluate ClustMe, we conducted a second study, in which31human subjects ranked 435 pairs of scatterplots of real and synthetic data in terms of cluster patterns complexity. We use this data to compare ClustMe's performance to 4 other state‐of‐the‐art clustering measures, including the well‐known Clumpiness scagnostics. We found that of all measures, ClustMe is in strongest agreement with the human rankings.

Visual analysis of multidimensional data requires expressive and effective ways to reduce data dimensionality to encode them visually. Multidimensional projections (MDP) figure among the most important visualization techniques in this context, transforming multidimensional data into scatter plots whose visual patterns reflect some notion of similarity in the original data. However, MDP come with distortions that make these visual patterns not trustworthy, hindering users to infer actual data characteristics. Moreover, the patterns present in the scatter plots might not be enough to allow a clear understanding of multidimensional data, motivating the development of layout enrichment methodologies to operate together with MDP. This survey attempts to cover the main aspects of MDP as a visualization and visual analytic tool. It provides detailed analysis and taxonomies as to the organization of MDP techniques according to their main properties and traits, discussing the impact of such properties for visual perception and other human factors. The survey also approaches the different types of distortions that can result from MDP mappings and it overviews existing mechanisms to quantitatively evaluate such distortions. A qualitative analysis of the impact of distortions on the different analytic tasks performed by users when exploring multidimensional data through MDP is also presented. Guidelines for choosing the best MDP for an intended task are also provided as a result of this analysis. Finally, layout enrichment schemes to debunk MDP distortions and/or reveal relevant information not directly inferable from the scatter plot are reviewed and discussed in the light of new taxonomies. We conclude the survey providing future research axes to fill discovered gaps in this domain.

Obesity is one of the major health risk factors behind the rise of non-communicable conditions. Understanding the factors influencing obesity is very complex since there are many variables that can affect the health behaviors leading to it. Nowadays, multiple data sources can be used to study health behaviors, such as wearable sensors for physical activity and sleep, social media, mobile and health data. In this paper we describe the design of a dashboard for the visualization of actigraphy and biometric data from a childhood obesity camp in Qatar. This dashboard allows quantitative discoveries that can be used to guide patient behavior and orient qualitative research.

Our goal is to accurately model human class separation judgements in color-coded scatterplots. Towards this goal, we propose a set of 2002 visual separation measures, by systematically combining 17 neighborhood graphs and 14 class purity functions, with different parameterizations. Using a Machine Learning framework, we evaluate these measures based on how well they predict human separation judgements. We found that more than 58% of the 2002 new measures outperform the best state-of-the-art Distance Consistency (DSC) measure. Among the 2002, the best measure is the average proportion of same-class neighbors among the 0.35-Observable Neighbors of each point of the target class (short GONG 0.35 DIR CPT), with a prediction accuracy of 92.9%, which is 11.7% better than DSC. We also discuss alternative, well-performing measures and give guidelines when to use which.

Genome Wide Association Studies (GWAS) examine genetic variants in different individuals to detect variants associated to specific diseases. The 1000 Genomes project is such a collaborative research effort to sequence the genomes of at least 1000 participants of 26 different ethnicities, to establish a detailed summary of human genetic variation. The kinship information is a measure of individuals ancestor relationships within the considered populations. We study the design of kinship data visualizations allowing the experts to discover anomalies in GWAS data. The visual analysis of the 1000 Genomes Project kinship data reveals inconsistencies which call for a deeper analysis of the data quality within this project.

Distributed Reflective Denial of Service attacks (DRDoS) represent an ever growing security threat. These attacks are characterized by spoofed UDP traffic that is sent to genuine machines, called amplifiers, whose response to the spoofed IP, i.e. the victim machine, is amplified and could be 500 times larger in size than the originating request. In this paper, we provide a method and a tool for Internet Service Providers (ISPs) to assess and visualize the amount of traffic that enters and leaves their network in case it contains innocent amplifiers. We show that amplified traffic usually goes undetected and can consume a significant bandwidth, even when a small number of amplifiers is present. The tool also enables ISPs to simulate various rule-based mitigation strategies and estimate their impact, based on real-world data obtained from amplification honeypots.

BACKGROUND: The post-genomic era with its wealth of sequences gave rise to a broad range of protein residue-residue contact detecting methods. Although various coevolution methods such as PSICOV, DCA and plmDCA provide correct contact predictions, they do not completely overlap. Hence, new approaches and improvements of existing methods are needed to motivate further development and progress in the field. We present a new contact detecting method, COUSCOus, by combining the best shrinkage approach, the empirical Bayes covariance estimator and GLasso. RESULTS: Using the original PSICOV benchmark dataset, COUSCOus achieves mean accuracies of 0.74, 0.62 and 0.55 for the top L/10 predicted long, medium and short range contacts, respectively. In addition, COUSCOus attains mean areas under the precision-recall curves of 0.25, 0.29 and 0.30 for long, medium and short contacts and outperforms PSICOV. We also observed that COUSCOus outperforms PSICOV w.r.t. Matthew's correlation coefficient criterion on full list of residue contacts. Furthermore, COUSCOus achieves on average 10% more gain in prediction accuracy compared to PSICOV on an independent test set composed of CASP11 protein targets. Finally, we showed that when using a simple random forest meta-classifier, by combining contact detecting techniques and sequence derived features, PSICOV predictions should be replaced by the more accurate COUSCOus predictions. CONCLUSION: We conclude that the consideration of superior covariance shrinkage approaches will boost several research fields that apply the GLasso procedure, amongst the presented one of residue-residue contact prediction as well as fields such as gene network reconstruction.

Abstract Visual quality measures seek to algorithmically imitate human judgments of patterns such as class separability, correlation, or outliers. In this paper, we propose a novel data‐driven framework for evaluating such measures. The basic idea is to take a large set of visually encoded data, such as scatterplots, with reliable human “ground truth” judgements, and to use this human‐labeled data to learn how well a measure would predict human judgements on previously unseen data. Measures can then be evaluated based on predictive performance—an approach that is crucial for generalizing across datasets but has gained little attention so far. To illustrate our framework, we use it to evaluate 15 state‐of‐the‐art class separation measures, using human ground truth data from 828 class separation judgments on color‐coded 2D scatterplots.

Multidimensional scaling techniques are unsupervised Dimension Reduction (DR) techniques which use multidimensional data pairwise similarities to represent data into a plane enabling their visual exploratory analysis. Considering labeled data, the DR techniques face two objectives with potentially different priorities: one is to account for the data points' similarities, the other for the data classes' structures. Unsupervised DR techniques attempt to preserve original data similarities, but they do not consider their class label hence they can map originally separated classes as overlapping ones. Conversely, the state-of-the-art so-called supervised DR techniques naturally handle labeled data, but they do so in a predictive modeling framework where they attempt to separate the classes in order to improve a classification accuracy measure in the low-dimensional space, hence they can map as separated even originally overlapping classes. We propose ClassiMap, a DR technique which optimizes a new objective function enabling Exploratory Data Analysis (EDA) of labeled data. Mapping distortions known as tears and false neighborhoods cannot be avoided in general due to the reduction of the data dimension. ClassiMap intends primarily to preserve data similarities but tends to distribute preferentially unavoidable tears among the different-label data and unavoidable false neighbors among the same-label data. Standard quality measures to evaluate the quality of unsupervised mappings cannot tell about the preservation of within-class or between-class structures, while classification accuracy used to evaluate supervised mappings is only relevant to the framework of predictive modeling. We propose two measures better suited to the evaluation of DR of labeled data in an EDA framework. We use these two label-aware indices and four other standard unsupervised indices to compare ClassiMap to other state-of-the-art supervised and unsupervised DR techniques on synthetic and real datasets. ClassiMap appears to provide a better tradeoff between pairwise similarities and class structure preservation according to these new measures.

Abstract Multidimensional scaling is a must‐have tool for visual data miners, projecting multidimensional data onto a two‐dimensional plane. However, what we see is not necessarily what we think about. In many cases, end‐users do not take care of scaling the projection space with respect to the multidimensional space. Anyway, when using non‐linear mappings, scaling is not even possible. Yet, without scaling geometrical structures which might appear do not make more sense than considering a random map. Without scaling, we shall not make inference from the display back to the multidimensional space. No clusters, no trends, no outliers, there is nothing to infer without first quantifying the mapping quality. Several methods to qualify mappings have been devised. Here, we propose CheckViz, a new method belonging to the framework of Verity Visualization. We define a two‐dimensional perceptually uniform colour coding which allows visualizing tears and false neighbourhoods, the two elementary and complementary types of geometrical mapping distortions, straight onto the map at the location where they occur. As examples shall demonstrate, this visualization method is essential to help users make sense out of the mappings and to prevent them from over interpretations. It could be applied to check other mappings as well.

Given a set of points and a set of prototypes representing them, how to create a graph of the prototypes whose topology accounts for that of the points? This problem had not yet been explored in the framework of statistical learning theory. In this work, we propose a generative model based on the Delaunay graph of the prototypes and the ExpectationMaximization algorithm to learn the parameters. This work is a first step towards the construction of a topological model of a set of points grounded on statistics.

An algorithm for function approximation with an artificial neural network is presented. It is based on neural-gas networks which combine self-organization of the neurons in the input space and supervised learning of the output values according to the function to approximate. The original learning rule of the input weights is modified to take into account the output error. The neurons with a greater error tend to "recruit" their neighbors to help them in their approximation task. The resulting network called a "recruiting neural-gas", organizes the neurons in the input space respecting the input data distribution and also the output error density. This algorithm gives very promising results and perspectives.