Scalable visualisation methods for modern Generalized Additive Models

Fasiolo, Matteo; Nedellec, Raphaël; Goude, Yannig; Wood, Simon N.

doi:10.48550/arxiv.1809.10632

Cited by 8 publications

(9 citation statements)

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“…SAS Institute Inc., 2019) and R 3.6.0 (The R Core Team, 2019). GAMs were performed with the R package mgcv 1.8.28 (Wood, 2017) and GAMs figures were produced with the package mgcViz 0.1.4 (Fasiolo et al, 2019). Other figures were plotted with the R packages plotly (Plotly Technologies Inc., 2015) and ggplot2 3.1.0 (Wickham, 2016).…”

Section: Methodsmentioning

confidence: 99%

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates

Reis

Thottathil

Ruiz‐González

et al. 2019

Environmental Microbiology

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Lake methane (CH 4 ) emissions are largely controlled by aerobic methane-oxidizing bacteria (MOB) which mostly belong to the classes Alpha-and Gammaproteobacteria (Alpha-and Gamma-MOB). Despite the known metabolic and ecological differences between the two MOB groups, their main environmental drivers and their relative contribution to CH 4 oxidation rates across lakes remain unknown. Here, we quantified the two MOB groups through CARD-FISH along the water column of six temperate lakes and during incubations in which we measured ambient CH 4 oxidation rates. We found a clear niche separation of Alpha-and Gamma-MOB across lake water columns, which is mostly driven by oxygen concentration. Gamma-MOB appears to dominate methanotrophy throughout the water column, but Alpha-MOB may also be an important player particularly in well-oxygenated bottom waters. The inclusion of Gamma-MOB cell abundance improved environmental models of CH 4 oxidation rate, explaining part of the variation that could not be explained by environmental factors alone. Altogether, our results show that MOB composition is linked to CH 4 oxidation rates in lakes and that information on the MOB community can help predict CH 4 oxidation rates and thus emissions from lakes. Received

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Section: Methodsmentioning

confidence: 99%

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates

Reis

Thottathil

Ruiz‐González

et al. 2019

Environmental Microbiology

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“…Thus, all types of similarity explain significant parts of the variance in the human ratings on their own, with IMG similarity contributing the most to variance explained, followed by cbow similarity and PRO similarity. In the model containing all three types of similarity, the relations between all three predictors and the rating values are positive, as displayed in Figure 10; Fasiolo et al, 2018 (the falloff for very high values of language-based similarity is based only on very few items and should therefore not be overinterpreted, as is also indicated by the wide confidence interval band in that area)…”

Section: Resultsmentioning

confidence: 88%

“…types of similarity, the relations between all three predictors and the rating values are positive, as displayed in Figure10;Fasiolo et al, 2018 (the falloff for very high values of language-based similarity is based only on very few items and should therefore not be overinterpreted, as is also indicated by the wide confidence interval band in that area).…”

mentioning

confidence: 88%

ViSpa (Vision Spaces): A computer-vision-based representation system for individual images and concept prototypes, with large-scale evaluation.

Günther¹,

Marelli²,

Tureski³

et al. 2023

Psychological Review

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Quantitative, data-driven models for mental representations have long enjoyed popularity and success in psychology (e.g., distributional semantic models in the language domain), but have largely been missing for the visual domain. To overcome this, we present ViSpa (Vision Spaces), high-dimensional vector spaces that include vision-based representation for naturalistic images as well as concept prototypes. These vectors are derived directly from visual stimuli through a deep convolutional neural network trained to classify images and allow us to compute vision-based similarity scores between any pair of images and/or concept prototypes. We successfully evaluate these similarities against human behavioral data in a series of large-scale studies, including off-line judgments-visual similarity judgments for the referents of word pairs (Study 1) and for image pairs (Study 2), and typicality judgments for images given a label (Study 3)-as well as online processing times and error rates in a discrimination (Study 4) and priming task (Study 5) with naturalistic image material. ViSpa similarities predict behavioral data across all tasks, which renders ViSpa a theoretically appealing model for vision-based representations and a valuable research tool for data analysis and the construction of experimental material: ViSpa allows for precise control over experimental material consisting of images and/or words denoting imageable concepts and introduces a specifically vision-based similarity for word pairs. To make ViSpa available to a wide audience, this article (a) includes (video) tutorials on how to use ViSpa in R and (b) presents a user-friendly web interface at http://vispa.fritzguenther.de.

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“…These terms were fit with a first-derivative penalty to shrink them towards the population-level. Models were fit with an AR(1) process using the itsadug package (v2.3;van Rij et al, 2017), and assessed using the mgcV iz package (v0.1.6; Fasiolo et al, 2018).…”

Section: Discussionmentioning

confidence: 99%

Be still my heart: Cardiac regulation as a mode of uncertainty reduction

2021

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Decreased heart rate (HR) and variability (HRV) are well-established correlates of attention; however, the functional significance of these dynamics remains unclear. Here, we investigate whether attention-related cardiac modulation is sensitive to different varieties of uncertainty. Thirty-nine adults performed a binocular rivalry-replay task in which changes in visual perception were driven either internally (in response to constant, conflicting stimuli; rivalry) or externally (in response to physically alternating stimuli; replay). Tonic HR and high-frequency HRV linearly decreased as participants progressed from resting-state baseline (minimal visual uncertainty) through replay (temporal uncertainty) to rivalry (temporal uncertainty and ambiguity). Time-resolved frequency estimates revealed that cardiac deceleration was sustained throughout the trial period and modulated by ambiguity, novelty, and switch rate. These findings suggest cardiac regulation during active attention may play an instrumental role in uncertainty reduction.

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Scalable visualisation methods for modern Generalized Additive Models

Cited by 8 publications

References 0 publications

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates

Niche separation within aerobic methanotrophic bacteria across lakes and its link to methane oxidation rates

ViSpa (Vision Spaces): A computer-vision-based representation system for individual images and concept prototypes, with large-scale evaluation.

Be still my heart: Cardiac regulation as a mode of uncertainty reduction

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