Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.Comment: Minor update

Essential guidelines for computational method benchmarking

In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology

Rethinking Digital Nudging: A Taxonomical Approach to Defining and Identifying Characteristics of Digital Nudging Interventions

Digital nudging interventions have emerged as soft-paternalistic mechanisms for reducing heuristic limitations and biases in decision-making environments. Prior research has conceptualized digital nudging interventions as subtle modifications in the decision-making environment that nudge a decision maker towards better choices without limiting other alternatives. The approach has received criticism as researchers have achieved limited consensus on its definition, categorized diverse behavior-modulation methodologies as digital nudging, and raised multiple ethical concerns about it. Such ambiguity reduces fidelity while challenging synthesis, application, and replication. In this paper, we posit the need to broaden the definition of digital nudging interventions, reconcile the inconsistencies, and present a coherent frame. Based on a systematic review of the extant literature, we propose an extended definition that is coherent with the libertarian-paternalistic principle, clarifying the intent of digital nudging interventions, and delineating the nature of the digital artifacts involved. We further present a taxonomy with standard vernacular and label its complex underlying principles and the components that can guide practitioners and researchers

The visual preferences for forest regeneration and field afforestation : four case studies in Finland

The overall aim of this dissertation was to study the public's preferences for forest regeneration fellings and field afforestations, as well as to find out the relations of these preferences to landscape management instructions, to ecological healthiness, and to the contemporary theories for predicting landscape preferences. This dissertation includes four case studies in Finland, each based on the visualization of management options and surveys. Guidelines for improving the visual quality of forest regeneration and field afforestation are given based on the case studies. The results show that forest regeneration can be connected to positive images and memories when the regeneration area is small and some time has passed since the felling. Preferences may not depend only on the management alternative itself but also on the viewing distance, viewing point, and the scene in which the management options are implemented. The current Finnish forest landscape management guidelines as well as the ecological healthiness of the studied options are to a large extent compatible with the public's preferences. However, there are some discrepancies. For example, the landscape management instructions as well as ecological hypotheses suggest that the retention trees need to be left in groups, whereas people usually prefer individually located retention trees to those trees in groups. Information and psycho-evolutionary theories provide some possible explanations for people's preferences for forest regeneration and field afforestation, but the results cannot be consistently explained by these theories. The preferences of the different stakeholder groups were very similar. However, the preference ratings of the groups that make their living from forest - forest owners and forest professionals - slightly differed from those of the others. These results provide support for the assumptions that preferences are largely consistent at least within one nation, but that knowledge and a reference group may also influence preferences.Väitöskirjassa tutkittiin ihmisten maisemapreferenssejä (maisemallisia arvostuksia) metsänuudistamishakkuiden ja pellonmetsitysten suhteen sekä analysoitiin näiden preferenssien yhteyksiä maisemanhoito-ohjeisiin, vaihtoehtojen ekologiseen terveyteen ja preferenssejä ennustaviin teorioihin. Väitöskirja sisältää neljä tapaustutkimusta, jotka perustuvat hoitovaihtoehtojen visualisointiin ja kyselytutkimuksiin. Tapaustutkimusten pohjalta annetaan ohjeita siitä, kuinka uudistushakkuiden ja pellonmetsitysten visuaalista laatua voidaan parantaa. Väitöskirjan tulokset osoittavat, että uudistamishakkuut voivat herättää myös myönteisiä mielikuvia ja muistoja, jos uudistusala on pieni ja hakkuun välittömät jäljet ovat jo peittyneet. Preferensseihin vaikuttaa hoitovaihtoehdon lisäksi mm. katseluetäisyys, katselupiste ja ympäristö, jossa vaihtoehto on toteutettu. Eri viiteryhmien (metsäammattilaiset, pääkaupunkiseudun asukkaat, ympäristönsuojelijat, tutkimusalueiden matkailijat, paikalliset asukkaat sekä metsänomistajat) maisemapreferenssit olivat hyvin samankaltaisia. Kuitenkin ne ryhmät, jotka saavat ainakin osan elannostaan metsästä - metsänomistajat ja metsäammattilaiset - pitivät metsänhakkuita esittävistä kuvista hieman enemmän kuin muut ryhmät. Nämä tulokset tukevat oletusta, että maisemapreferenssit ovat laajalti yhteneväisiä ainakin yhden kansan tai kulttuurin keskuudessa, vaikka myös viiteryhmä saattaa vaikuttaa preferensseihin jonkin verran. Nykyiset metsämaisemanhoito-ohjeet ovat pitkälti samankaltaisia tässä väitöskirjassa havaittujen maisemapreferenssien kanssa. Myöskään tutkittujen vaihtoehtoisten hoitotapojen ekologisen paremmuuden ja niihin kohdistuvien maisemallisten arvostusten välillä ei ollut suurta ristiriitaa. Kuitenkin joitakin eroavaisuuksia oli; esimerkiksi sekä maisemanhoito-ohjeiden että ekologisten hypoteesien mukaan säästöpuut tulisi jättää ryhmiin, kun taas ihmiset pitivät eniten yksittäin jätetyistä puista. Informaatiomalli ja psyko-evolutionaarinen teoria tarjoavat mahdollisia selityksiä uudistushakkuisiin ja pellonmetsitykseen kohdistuville preferensseille, vaikkakaan tutkimuksen tuloksia ei voida täysin selittää näillä teorioilla

Towards Exascale Scientific Metadata Management

Advances in technology and computing hardware are enabling scientists from all areas of science to produce massive amounts of data using large-scale simulations or observational facilities. In this era of data deluge, effective coordination between the data production and the analysis phases hinges on the availability of metadata that describe the scientific datasets. Existing workflow engines have been capturing a limited form of metadata to provide provenance information about the identity and lineage of the data. However, much of the data produced by simulations, experiments, and analyses still need to be annotated manually in an ad hoc manner by domain scientists. Systematic and transparent acquisition of rich metadata becomes a crucial prerequisite to sustain and accelerate the pace of scientific innovation. Yet, ubiquitous and domain-agnostic metadata management infrastructure that can meet the demands of extreme-scale science is notable by its absence. To address this gap in scientific data management research and practice, we present our vision for an integrated approach that (1) automatically captures and manipulates information-rich metadata while the data is being produced or analyzed and (2) stores metadata within each dataset to permeate metadata-oblivious processes and to query metadata through established and standardized data access interfaces. We motivate the need for the proposed integrated approach using applications from plasma physics, climate modeling and neuroscience, and then discuss research challenges and possible solutions

Towards an automated system for evaluation of visualizations

The Information Visualization field focuses on the visualization of abstract data, and with the growing interest in big data analysis, the need for analyzing complex datasets is nowadays highly relevant. With the growing amount and diversity of these datasets new and exciting ways to visualize them are being developed. However, being able to thoroughly test and evaluate the effectiveness of these new visualization techniques is an arduous manual process. Moreover, different researchers hold different opinions on how to thoroughly evaluate a new visualization method. A step towards automating the process of evaluation of visualizations, called the Framework for the Evaluation of VizTools (FEV), was developed and is presented in this thesis. The FEV Framework combines, guidelines, scenarios, and tasks, generated by an extensive literature review, into an easy to use open-source and expandable software package. With FEV, researchers are able to generate evaluation task lists based on their own data, and using evaluation methods that have already been vetted by the visualization community. By using the FEV tool with a variety of visualizations, it was possible to generate full evaluation task lists for each of them. By making the framework open-source and with an adaptable architecture, new functionality can easily be added, enabling it to be used by researchers to evaluate an almost limitless number of visualization methods

The Inhumanist Manifesto

International audienceGary Hall's manifesto for Media Theory

THE ROLE OF EMOTION IN VISUALIZATION

The popular notion that emotion and reason are incompatible is no longer defensi- ble. Recent research in psychology and cognitive science has established emotion as a key element in numerous aspects of perception and cognition, including attention, memory, decision-making, risk perception, and creativity. This dissertation centers around the observation that emotion influences many aspects of perception and cog- nition that are crucial for effective visualization. First, I demonstrate that emotion influences accuracy in fundamental visualiza- tion tasks by combining a classic graphical perception experiment (from Cleveland and McGill) with emotion induction procedures from psychology (chapter 3). Next, I expand on the experiments in the first chapter to explore additional techniques for studying emotion and visualization, resulting in an experiment that shows that performance differences between primed individuals persist even as task difficulty in- creases (chapter 4). In a separate experiment, I show how certain emotional states (i.e. frustration and engagement) can be inferred from visualization interaction logs using machine learning (chapter 5). I then discuss a model for individual cognitive dif- ferences in visualization, which situates emotion into existing individual differences research in visualization (chapter 6). Finally, I propose an preliminary model for emotion in visualization (chapter 7)