Deep neural networks are now rivaling human accuracy in several pattern recognition problems. Compared to traditional classifiers, where features are handcrafted, neural networks learn increasingly complex features directly from the data. Instead of handcrafting the features, it is now the network architecture that is manually engineered. The network architecture parameters such as the number of layers or the number of filters per layer and their interconnections are essential for good performance. Even though basic design guidelines exist, designing a neural network is an iterative trial-and-error process that takes days or even weeks to perform due to the large datasets used for training. In this paper, we present DeepEyes, a Progressive Visual Analytics system that supports the design of neural networks during training. We present novel visualizations, supporting the identification of layers that learned a stable set of patterns and, therefore, are of interest for a detailed analysis. The system facilitates the identification of problems, such as superfluous filters or layers, and information that is not being captured by the network. We demonstrate the effectiveness of our system through multiple use cases, showing how a trained network can be compressed, reshaped and adapted to different problems.@en

Recent advances in single-cell acquisition technology have led to a shift towards single-cell analysis in many fields of biology. In immunology, detailed knowledge of the cellular composition is of interest, as it can be the cause of deregulated immune responses, which cause diseases. Similarly, vaccination is based on triggering proper immune responses; however, many vaccines are ineffective or only work properly in a subset of those who are vaccinated. Identifying differences in the cellular composition of the immune system in such cases can lead to more precise treatment. Cytosplore is an integrated, interactive visual analysis framework for the exploration of large single-cell datasets. We have developed Cytosplore in close collaboration with immunology researchers and several partners use the software in their daily workflow. Cytosplore enables efficient data analysis and has led to several discoveries alongside high-impact publications.@en

Recent advances in single-cell acquisition technology have led to a shift towards single-cell analysis in many fields of biology. In immunology, detailed knowledge of the cellular composition is of interest, as it can be the cause of deregulated immune responses, which cause diseases. Similarly, vaccination is based on triggering proper immune responses; however, many vaccines are ineffective or only work properly in a subset of those who are vaccinated. Identifying differences in the cellular composition of the immune system in such cases can lead to more precise treatment. Cytosplore is an integrated, interactive visual analysis framework for the exploration of large single-cell datasets. We have developed Cytosplore in close collaboration with immunology researchers and several partners use the software in their daily workflow. Cytosplore enables efficient data analysis and has led to several discoveries alongside high-impact publications.@en

Single-cell analysis through mass cytometry has become an increasingly important tool for immunologists to study the immune system in health and disease. Mass cytometry creates a high-dimensional description vector for single cells by time-of-flight measurement. Recently, t-Distributed Stochastic Neighborhood Embedding (t-SNE) has emerged as one of the state-of-the-art techniques for the visualization and exploration of single-cell data. Ever increasing amounts of data lead to the adoption of Hierarchical Stochastic Neighborhood Embedding (HSNE), enabling the hierarchical representation of the data. Here, the hierarchy is explored selectively by the analyst, who can request more and more detail in areas of interest. Such hierarchies are usually explored by visualizing disconnected plots of selections in different levels of the hierarchy. This poses problems for navigation, by imposing a high cognitive load on the analyst. In this work, we present an interactive summary-visualization to tackle this problem. CyteGuide guides the analyst through the exploration of hierarchically represented single-cell data, and provides a complete overview of the current state of the analysis. We conducted a two-phase user study with domain experts that use HSNE for data exploration. We first studied their problems with their current workflow using HSNE and the requirements to ease this workflow in a field study. These requirements have been the basis for our visual design. In the second phase, we verified our proposed solution in a user evaluation.@en

Spatial and temporal brain transcriptomics has recently emerged as an invaluable data source for molecular neuroscience. The complexity of such data poses considerable challenges for analysis and visualization. We present BrainScope: A web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human brain transcriptome. Through a novel methodology to explore high-dimensional data (dual t-SNE), BrainScope enables the linked, all-in-one visualization of genes and samples across the whole brain and genome, and across developmental stages. We show that densities in t-SNE scatter plots of the spatial samples coincide with anatomical regions, and that densities in t-SNE scatter plots of the genes represent gene co-expression modules that are significantly enriched for biological functions. We also show that the topography of the gene t-SNE maps reflect brain region-specific gene functions, enabling hypothesis and data driven research. We demonstrate the discovery potential of BrainScope through three examples: (i) analysis of cell type specific gene sets, (ii) analysis of a set of stable gene co-expression modules across the adult human donors and (iii) analysis of the evolution of co-expression of oligodendrocyte specific genes over developmental stages. Brain- Scope is publicly accessible at www.brainscope.nl.@en

To understand how the immune system works, one needs to have a clear picture of its cellular compositon and the cells’ corresponding properties and functionality. Mass cytometry is a novel technique to determine the properties of single-cells with unprecedented detail. This amount of detail allows for much finer differentiation but also comes at the cost of more complex analysis. In this work, we present Cytosplore, implementing an interactive workflow to analyze mass cytometry data in an integrated system, providing multiple linked views, showing different levels of detail and enabling the rapid definition of known and unknown cell types. Cytosplore handles millions of cells, each represented as a high-dimensional data point, facilitates hypothesis generation and confirmation, and provides a significant speed up of the current workflow. We show the effectiveness of Cytosplore in a case study evaluation.@en

Progressive Visual Analytics aims at improving the interactivity in existing analytics techniques by means of visualization as well as interaction with intermediate results. One key method for data analysis is dimensionality reduction, for example, to produce 2D embeddings that can be visualized and analyzed efficiently. t-Distributed Stochastic Neighbor Embedding (tSNE) is a well-suited technique for the visualization of high-dimensional data. tSNE can create meaningful intermediate results but suffers from a slow initialization that constrains its application in Progressive Visual Analytics. We introduce a controllable tSNE approximation (A-tSNE), which trades off speed and accuracy, to enable interactive data exploration. We offer real-time visualization techniques, including a density-based solution and a Magic Lens to inspect the degree of approximation. With this feedback, the user can decide on local refinements and steer the approximation level during the analysis. We demonstrate our technique with several datasets, in a real-world research scenario and for the real-time analysis of high-dimensional streams to illustrate its effectiveness for interactive data analysis.@en

Technological advances in mass spectrometry imaging (MSI) have contributed to growing interest in 3D MSI. However, the large size of 3D MSI data sets has made their efficient analysis and visualization and the identification of informative molecular patterns computationally challenging. Hierarchical stochastic neighbor embedding (HSNE), a nonlinear dimensionality reduction technique that aims at finding hierarchical and multiscale representations of large data sets, is a recent development that enables the analysis of millions of data points, with manageable time and memory complexities. We demonstrate that HSNE can be used to analyze large 3D MSI data sets at full mass spectral and spatial resolution. To benchmark the technique as well as demonstrate its broad applicability, we have analyzed a number of publicly available 3D MSI data sets, recorded from various biological systems and spanning different mass-spectrometry ionization techniques. We demonstrate that HSNE is able to rapidly identify regions of interest within these large high-dimensionality data sets as well as aid the identification of molecular ions that characterize these regions of interest; furthermore, through clearly separating measurement artifacts, the HSNE analysis exhibits a degree of robustness to measurement batch effects, spatially correlated noise, and mass spectral misalignment.@en

Mass cytometry allows high-resolution dissection of the cellular composition of the immune system. However, the high-dimensionality, large size, and non-linear structure of the data poses considerable challenges for the data analysis. In particular, dimensionality reduction-based techniques like t-SNE offer single-cell resolution but are limited in the number of cells that can be analyzed. Here we introduce Hierarchical Stochastic Neighbor Embedding (HSNE) for the analysis of mass cytometry data sets. HSNE constructs a hierarchy of non-linear similarities that can be interactively explored with a stepwise increase in detail up to the single-cell level. We apply HSNE to a study on gastrointestinal disorders and three other available mass cytometry data sets. We find that HSNE efficiently replicates previous observations and identifies rare cell populations that were previously missed due to downsampling. Thus, HSNE removes the scalability limit of conventional t-SNE analysis, a feature that makes it highly suitable for the analysis of massive high-dimensional data sets.@en

Hierarchical embeddings, such as HSNE, address critical visual and computational scalability issues of traditional techniques for dimensionality reduction. The improved scalability comes at the cost of the need for increased user interaction for exploration. In this paper, we provide a solution for the interactive visual Focus+Context exploration of such embeddings. We explain how to integrate embedding parts from different levels of detail, corresponding to focus and context groups, in a joint visualization. We devise an according interaction model that relates typical semantic operations on a Focus+Context visualization with the according changes in the level-of-detail-hierarchy of the embedding, including also a mode for comparative Focus+Context exploration and extend HSNE to incorporate the presented interaction model. In order to demonstrate the effectiveness of our approach, we present a use case based on the visual exploration of multi-dimensional images.@en

In recent years the t-distributed Stochastic Neighbor Embedding (t-SNE) algorithm has become one of the most used and insightful techniques for exploratory data analysis of high-dimensional data. It reveals clusters of high-dimensional data points at different scales while only requiring minimal tuning of its parameters. However, the computational complexity of the algorithm limits its application to relatively small datasets. To address this problem, several evolutions of t-SNE have been developed in recent years, mainly focusing on the scalability of the similarity computations between data points. However, these contributions are insufficient to achieve interactive rates when visualizing the evolution of the t-SNE embedding for large datasets. In this work, we present a novel approach to the minimization of the t-SNE objective function that heavily relies on graphics hardware and has linear computational complexity. Our technique decreases the computational cost of running t-SNE on datasets by orders of magnitude and retains or improves on the accuracy of past approximated techniques. We propose to approximate the repulsive forces between data points by splatting kernel textures for each data point. This approximation allows us to reformulate the t-SNE minimization problem as a series of tensor operations that can be efficiently executed on the graphics card. An efficient implementation of our technique is integrated and available for use in the widely used Google TensorFlow.js, and an open-source C++ library.@en

Quality assessment of different Magnetic Resonance Fingerprinting (MRF) sequences and their corresponding dictionaries remains an unsolved problem. In this work we present a method in which we approach analysis of MRF dictionaries by performing dimensionality reduction and representing them as low-dimensional point sets (embeddings). Dimensionality reduction was performed using a modification of the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm. First, we demonstrated stability of calculated embeddings that allows neglecting the stochastic nature of t-SNE. Next, we proposed and analyzed two algorithms for comparing the embeddings. Finally, we performed two simulations in which we reduced the MRF sequence/dictionary in length or size and analyzed the influence of this reduction on the resulting embedding. We believe that this research can pave the way to development of a software tool for analysis, including better understanding, optimization and comparison, of different MRF sequences.@en

Accurate segmentation of brain white matter hyperintensities (WMHs) is important for prognosis and disease monitoring. To this end, classifiers are often trained – usually, using T1 and FLAIR weighted MR images. Incorporating additional features, derived from diffusion weighted MRI, could improve classification. However, the multitude of diffusion-derived features requires selecting the most adequate. For this, automated feature selection is commonly employed, which can often be sub-optimal. In this work, we propose a different approach, introducing a semi-automated pipeline to select interactively features for WMH classification. The advantage of this solution is the integration of the knowledge and skills of experts in the process. In our pipeline, a Visual Analytics (VA) system is employed, to enable user-driven feature selection. The resulting features are T1, FLAIR, Mean Diffusivity (MD), and Radial Diffusivity (RD) – and secondarily, C S  CS and Fractional Anisotropy (FA). The next step in the pipeline is to train a classifier with these features, and compare its results to a similar classifier, used in previous work with automated feature selection. Finally, VA is employed again, to analyze and understand the classifier performance and results.@en

Accurate segmentation of brain white matter hyperintensities (WMHs) is important for prognosis and disease monitoring. To this end, classifiers are often trained – usually, using T1 and FLAIR weighted MR images. Incorporating additional features, derived from diffusion weighted MRI, could improve classification. However, the multitude of diffusion-derived features requires selecting the most adequate. For this, automated feature selection is commonly employed, which can often be sub-optimal. In this work, we propose a different approach, introducing a semi-automated pipeline to select interactively features for WMH classification. The advantage of this solution is the integration of the knowledge and skills of experts in the process. In our pipeline, a Visual Analytics (VA) system is employed, to enable user-driven feature selection. The resulting features are T1, FLAIR, Mean Diffusivity (MD), and Radial Diffusivity (RD) – and secondarily, C S  CS and Fractional Anisotropy (FA). The next step in the pipeline is to train a classifier with these features, and compare its results to a similar classifier, used in previous work with automated feature selection. Finally, VA is employed again, to analyze and understand the classifier performance and results.@en

Controlled human infections provide opportunities to study the interaction between the immune system and malaria parasites, which is essential for vaccine development. Here, we compared immune signatures of malaria-naive Europeans and of Africans with lifelong malaria exposure using mass cytometry, RNA sequencing and data integration, before and 5 and 11 days after venous inoculation with Plasmodium falciparum sporozoites. We observed differences in immune cell populations, antigen-specific responses and gene expression profiles between Europeans and Africans and among Africans with differing degrees of immunity. Before inoculation, an activated/differentiated state of both innate and adaptive cells, including elevated CD161+CD4+ T cells and interferon-γ production, predicted Africans capable of controlling parasitemia. After inoculation, the rapidity of the transcriptional response and clusters of CD4+ T cells, plasmacytoid dendritic cells and innate T cells were among the features distinguishing Africans capable of controlling parasitemia from susceptible individuals. These findings can guide the development of a vaccine effective in malaria-endemic regions.@en

Auto-reactive CD8 T-cells play an important role in the destruction of pancreatic β-cells resulting in type 1 diabetes (T1D). However, the phenotype of these auto-reactive cytolytic CD8 T-cells has not yet been extensively described. We used high-dimensional mass cytometry to phenotype autoantigen- (pre-proinsulin), neoantigen- (insulin-DRIP) and virus-(cytomegalovirus) reactive CD8 T-cells in peripheral blood mononuclear cells (PBMCs) of T1D patients. A panel of 33 monoclonal antibodies was designed to further characterise these cells at the single-cell level. HLA-A2 class I tetramers were used for the detection of antigen-specific CD8 T-cells. Using a novel Hierarchical Stochastic Neighbor Embedding (HSNE) tool (implemented in Cytosplore), we identified 42 clusters within the CD8 T-cell compartment of three T1D patients and revealed profound heterogeneity between individuals, as each patient displayed a distinct cluster distribution. Single-cell analysis of pre-proinsulin, insulin-DRIP and cytomegalovirus-specific CD8 T-cells showed that the detected specificities were heterogeneous between and within patients. These findings emphasize the challenge to define the obscure nature of auto-reactive CD8 T-cells.@en

Visual analysis of high dimensional data is a challenging process. Direct visualizations work well for a few dimensions but do not scale to the hundreds or thousands of dimensions that have become increasingly common in current data analytics problems. Visual analytics is the science of analytical reasoning facilitated by interactive visual interfaces, and it has been proven as an effective tool for high dimensional data analysis. In visual analytics systems, several visualizations are jointly analyzed in order to discover patterns in the data. One of the fundamental tools that has been integrated in visual analytics, is nonlinear dimensionality-reduction; a tool for the indirect visualization aimed at the discovery and analysis of non-linear patterns in the high-dimensional data. However, the computational complexity of non-linear dimensionality-reduction techniques does not allow direct employment in interactive systems. This limitation makes the analytic process a time-consuming task that can take hours, days or even weeks to be performed. In this thesis, we present novel algorithmic solutions that enable integration of non-linear dimensionality-reduction techniques in visual analytics systems. Our proposed algorithms are, not only much faster than existing solutions, but provide richer insights into the data at hand. This result, is achieved by introducing new data processing and optimization techniques and by embracing the recently introduced concept of Progressive Visual Analytics; a computational paradigm that enables the interactivity of complex analytics techniques by means of visualization as well as interaction with intermediate results. Moreover, we present several applications that are designed to provide unprecedented analytical capabilities in several domains. These applications are powered by the algorithms introduced in this dissertation and led to several discoveries in areas ranging from the biomedical research field, to social-network data analysis and machine-learning models interpretability. @en

Innate lymphoid cells (ILCs) are abundant in mucosal tissues and involved in tissue homeostasis and barrier function. Although several ILC subsets have been identified, it is unknown if additional heterogeneity exists, and their differentiation pathways remain largely unclear. We applied mass cytometry to analyze ILCs in the human fetal intestine and distinguished 34 distinct clusters through a t-SNE-based analysis. A lineage (Lin)-CD7+CD127-CD45RO+CD56+ population clustered between the CD127+ ILC and natural killer (NK) cell subsets, and expressed diverse levels of Eomes, T-bet, GATA3, and RORγt. By visualizing the dynamics of the t-SNE computation, we identified smooth phenotypic transitions from cells within the Lin-CD7+CD127-CD45RO+CD56+ cluster to both the NK cells and CD127+ ILCs, revealing potential differentiation trajectories. In functional differentiation assays, the Lin-CD7+CD127-CD45RO+CD56+CD8a- cells could develop into CD45RA+ NK cells and CD127+RORγt+ ILC3-like cells. Thus, we identified a previously unknown intermediate innate subset that can differentiate into ILC3 and NK cells.@en

A bipartite graph is a powerful abstraction for modeling relationships between two collections. Visualizations of bipartite graphs allow users to understand the mutual relationships between the elements in the two collections, e.g., by identifying clusters of similarly connected elements. However, commonly-used visual representations do not scale for the analysis of large bipartite graphs containing tens of millions of vertices, often resorting to an a-priori clustering of the sets. To address this issue, we present the Who's-Active-On-What-Visualization (WAOW-Vis) that allows for multiscale exploration of a bipartite social-network without imposing an a-priori clustering. To this end, we propose to treat a bipartite graph as a high-dimensional space and we create the WAOW-Vis adapting the multiscale dimensionality-reduction technique HSNE. The application of HSNE for bipartite graph requires several modifications that form the contributions of this work. Given the nature of the problem, a set-based similarity is proposed. For efficient and scalable computations, we use compressed bitmaps to represent sets and we present a novel space partitioning tree to efficiently compute similarities; the Sets Intersection Tree. Finally, we validate WAOW-Vis on several datasets connecting Twitter-users and -streams in different domains: news, computer science and politics. We show how WAOW-Vis is particularly effective in identifying hierarchies of communities among social-media users.@en

In recent years, dimensionality-reduction techniques have been developed and are widely used for hypothesis generation in Exploratory Data Analysis. However, these techniques are confronted with overcoming the trade-off between computation time and the quality of the provided dimensionality reduction. In this work, we address this limitation, by introducing Hierarchical Stochastic Neighbor Embedding (Hierarchical-SNE). Using a hierarchical representation of the data, we incorporate the well-known mantra of Overview-First, Details-On-Demand in non-linear dimensionality reduction. First, the analysis shows an embedding, that reveals only the dominant structures in the data (Overview). Then, by selecting structures that are visible in the overview, the user can filter the data and drill down in the hierarchy. While the user descends into the hierarchy, detailed visualizations of the high-dimensional structures will lead to new insights. In this paper, we explain how Hierarchical-SNE scales to the analysis of big datasets. In addition, we show its application potential in the visualization of Deep-Learning architectures and the analysis of hyperspectral images. @en