HUMAP: Hierarchical Uniform Manifold Approximation and Projection.

Dimensionality reduction (DR) techniques help analysts to understand patterns in high-dimensional spaces. These techniques, often represented by scatter plots, are employed in diverse science domains and facilitate similarity analysis among clusters and data samples. For datasets containing many granularities or when analysis follows the information visualization mantra, hierarchical DR techniques are the most suitable approach since they present major structures beforehand and details on demand.

Analysis of Macronutrients in Soil Using Impedimetric Multisensor Arrays.

The need to increase food production to address the world population growth can only be fulfilled with precision agriculture strategies to increase crop yield with minimal expansion of the cultivated area. One example is site-specific fertilization based on accurate monitoring of soil nutrient levels, which can be made more cost-effective using sensors. This study developed an impedimetric multisensor array using ion-selective membranes to analyze soil samples enriched with macronutrients (N, P, and K), which is compared with another array based on layer-by-layer films.

Multidimensional calibration spaces in Staphylococcus Aureus detection using chitosan-based genosensors and electronic tongue.

Mastitis diagnosis can be made by detecting Staphylococcus aureus (S. aureus), which requires high sensitivity and selectivity. Here, we report on microfluidic genosensors and electronic tongues to detect S.

ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization.

Molecular dynamics (MD) simulations provide a powerful means of exploring the dynamic behavior of biomolecular systems at the atomic level. However, analyzing the vast data sets generated by MD simulations poses significant challenges. This article discusses the energy landscape visualization method (ELViM), a multidimensional reduction technique inspired by the energy landscape theory.

A Grid-Based Method for Removing Overlaps of Dimensionality Reduction Scatterplot Layouts.

Dimensionality Reduction (DR) scatterplot layouts have become a ubiquitous visualization tool for analyzing multidimensional datasets. Despite their popularity, such scatterplots suffer from occlusion, especially when informative glyphs are used to represent data instances, potentially obfuscating critical information for the analysis under execution. Different strategies have been devised to address this issue, either producing overlap-free layouts that lack the powerful capabilities of contemporary DR techniques in uncovering interesting data patterns or eliminating overlaps as a post-processing strategy.

Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop.

Molecular dynamics (MD) simulations have become increasingly powerful and can now describe the folding/unfolding of small biomolecules in atomic detail. However, a major challenge in MD simulations is to represent the complex energy landscape of biomolecules using a small number of reaction coordinates. In this study, we investigate the folding pathways of an RNA tetraloop, gcGCAAgc, using five classical MD simulations with a combined simulation time of approximately 120 μs.

Associations of active and passive smartphone use with measures of youth mental health during the COVID-19 pandemic.

Smartphone use provides a significant amount of screen-time for youth, and there have been growing concerns regarding its impact on their mental health. While time spent in a passive manner on the device is frequently considered deleterious, more active engagement with the phone might be protective for mental health. Recent developments in mobile sensing technology provide a unique opportunity to examine behaviour in a naturalistic manner.

Nanoarchitectonic E-Tongue of Electrospun Zein/Curcumin Carbon Dots for Detecting in Milk.

We report a nanoarchitectonic electronic tongue made with flexible electrodes coated with curcumin carbon dots and zein electrospun nanofibers, which could detect () in milk using electrical impedance spectroscopy. Electronic tongues are based on the global selectivity concept in which the electrical responses of distinct sensing units are combined to provide a unique pattern, which in this case allowed the detection of through non-specific interactions. The electronic tongue used here comprised 3 sensors with electrodes coated with zein nanofibers, carbon dots, and carbon dots with zein nanofibers.

Multivariate Data Explanation by Jumping Emerging Patterns Visualization.

Multivariate or multidimensional visualization plays an essential role in exploratory data analysis by allowing users to derive insights and formulate hypotheses. Despite their popularity, it is usually users' responsibility to (visually) discover the data patterns, which can be cumbersome and time-consuming. Visual Analytics (VA) and machine learning techniques can be instrumental in mitigating this problem by automatically discovering and representing such patterns.

Using machine learning and an electronic tongue for discriminating saliva samples from oral cavity cancer patients and healthy individuals.

The diagnosis of cancer and other diseases using data from non-specific sensors - such as the electronic tongues (e-tongues) - is challenging owing to the lack of selectivity, in addition to the variability of biological samples. In this study, we demonstrate that impedance data obtained with an e-tongue in saliva samples can be used to diagnose cancer in the mouth. Data taken with a single-response microfluidic e-tongue applied to the saliva of 27 individuals were treated with multidimensional projection techniques and non-supervised and supervised machine learning algorithms.

Explainable Matrix - Visualization for Global and Local Interpretability of Random Forest Classification Ensembles.

Over the past decades, classification models have proven to be essential machine learning tools given their potential and applicability in various domains. In these years, the north of the majority of the researchers had been to improve quantitative metrics, notwithstanding the lack of information about models' decisions such metrics convey. This paradigm has recently shifted, and strategies beyond tables and numbers to assist in interpreting models' decisions are increasing in importance.

A Future with Ubiquitous Sensing and Intelligent Systems.

In this paper, we discuss the relevance of sensing and biosensing for the ongoing revolution in science and technology as a product of the merging of machine learning and Big Data into affordable technologies and accessible everyday products. Possible scenarios for the next decades are described with examples of intelligent systems for various areas, most of which will rely on ubiquitous sensing. The technological and societal challenges for developing the full potential of such intelligent systems are also addressed.

Information Visualization and Feature Selection Methods Applied to Detect Gliadin in Gluten-Containing Foodstuff with a Microfluidic Electronic Tongue.

The fast growth of celiac disease diagnosis has sparked the production of gluten-free food and the search for reliable methods to detect gluten in foodstuff. In this paper, we report on a microfluidic electronic tongue (e-tongue) capable of detecting trace amounts of gliadin, a protein of gluten, down to 0.005 mg kg in ethanol solutions, and distinguishing between gluten-free and gluten-containing foodstuff.

Layer-by-Layer Thin Film of Iron Phthalocyanine as a Simple and Fast Sensor for Polyphenol Determination in Tea Samples.

Polyphenols have attracted attention due to their antioxidant capacity and beneficial effects to health. Therefore, fast, inexpensive, and efficient methods to discriminate and to quantify polyphenols are of interest for food industry. In this paper, Layer-by-Layer films of poly(allylamine hydrochloride) and iron tetrasulfonated phthalocyanine were employed as sensor for determination of polyphenols in green tea (camellia sinensis), and green and roasted mate teas (ilex paraguariensis).

On the convergence of nanotechnology and Big Data analysis for computer-aided diagnosis.

An overview is provided of the challenges involved in building computer-aided diagnosis systems capable of precise medical diagnostics based on integration and interpretation of data from different sources and formats. The availability of massive amounts of data and computational methods associated with the Big Data paradigm has brought hope that such systems may soon be available in routine clinical practices, which is not the case today. We focus on visual and machine learning analysis of medical data acquired with varied nanotech-based techniques and on methods for Big Data infrastructure.

Nmap: A Novel Neighborhood Preservation Space-filling Algorithm.

Space-filling techniques seek to use as much as possible the visual space to represent a dataset, splitting it into regions that represent the data elements. Amongst those techniques, Treemaps have received wide attention due to its simplicity, reduced visual complexity, and compact use of the available space. Several different Treemap algorithms have been proposed, however the core idea is the same, to divide the visual space into rectangles with areas proportional to some data attribute or weight.

Visualization of protein folding funnels in lattice models.

Protein folding occurs in a very high dimensional phase space with an exponentially large number of states, and according to the energy landscape theory it exhibits a topology resembling a funnel. In this statistical approach, the folding mechanism is unveiled by describing the local minima in an effective one-dimensional representation. Other approaches based on potential energy landscapes address the hierarchical structure of local energy minima through disconnectivity graphs.

On the distinct molecular architectures of dipping- and spray-LbL films containing lipid vesicles.

The introduction of spraying procedures to fabricate layer-by-layer (LbL) films has brought new possibilities for the control of molecular architectures and for making the LbL technique compliant with industrial processes. In this study we show that significantly distinct architectures are produced for dipping and spray-LbL films of the same components, which included DODAB/DPPG vesicles. The films differed notably in their thickness and stratified nature.

SERS mapping in Langmuir-Blodgett films and single-molecule detection.

Plasmon-enhanced spectroscopic techniques have expanded single-molecule detection (SMD) and are revolutionizing areas such as bio-imaging and single-cell manipulation. Surface-enhanced (resonance) Raman scattering (SERS or SERRS) combines high sensitivity with molecular-fingerprint information at the single-molecule level. Spectra originating from single-molecule SERS experiments are rare events, which occur only if a single molecule is located in a hot-spot zone.

Molecularly designed layer-by-layer (LbL) films to detect catechol using information visualization methods.

The control of molecular architectures has been exploited in layer-by-layer (LbL) films deposited on Au interdigitated electrodes, thus forming an electronic tongue (e-tongue) system that reached an unprecedented high sensitivity (down to 10(-12) M) in detecting catechol. Such high sensitivity was made possible upon using units containing the enzyme tyrosinase, which interacted specifically with catechol, and by processing impedance spectroscopy data with information visualization methods. These latter methods, including the parallel coordinates technique, were also useful for identifying the major contributors to the high distinguishing ability toward catechol.

Information visualization to enhance sensitivity and selectivity in biosensing.

An overview is provided of the various methods for analyzing biosensing data, with emphasis on information visualization approaches such as multidimensional projection techniques. Emphasis is placed on the importance of data analysis methods, with a description of traditional techniques, including the advantages and limitations of linear and non-linear methods to generate layouts that emphasize similarity/dissimilarity relationships among data instances. Particularly important are recent methods that allow processing high-dimensional data, thus taking full advantage of the capabilities of modern equipment.

Toward the optimization of an e-tongue system using information visualization: a case study with perylene tetracarboxylic derivative films in the sensing units.

The wide variety of molecular architectures used in sensors and biosensors and the large amount of data generated with some principles of detection have motivated the use of computational methods, such as information visualization techniques, not only to handle the data but also to optimize sensing performance. In this study, we combine projection techniques with micro-Raman scattering and atomic force microscopy (AFM) to address critical issues related to practical applications of electronic tongues (e-tongues) based on impedance spectroscopy. Experimentally, we used sensing units made with thin films of a perylene derivative (AzoPTCD acronym), coating Pt interdigitated electrodes, to detect CuCl(2) (Cu(2+)), methylene blue (MB), and saccharose in aqueous solutions, which were selected due to their distinct molecular sizes and ionic character in solution.

Local Affine Multidimensional Projection.

Multidimensional projection techniques have experienced many improvements lately, mainly regarding computational times and accuracy. However, existing methods do not yet provide flexible enough mechanisms for visualization-oriented fully interactive applications. This work presents a new multidimensional projection technique designed to be more flexible and versatile than other methods.

Skeleton-based edge bundling for graph visualization.

In this paper, we present a novel approach for constructing bundled layouts of general graphs. As layout cues for bundles, we use medial axes, or skeletons, of edges which are similar in terms of position information. We combine edge clustering, distance fields, and 2D skeletonization to construct progressively bundled layouts for general graphs by iteratively attracting edges towards the centerlines of level sets of their distance fields.