In recent years, visual analytics (VA) has shown promise in alleviating the challenges of interpreting black-box deep learning (DL) models. While the focus of VA for explainable DL has been mainly on classification problems, DL is gaining popularity in high-dimensional-to-high-dimensional (H-H) problems such as image-to-image translation. In contrast to classification, H-H problems have no explicit instance groups or classes to study. Each output is continuous, high-dimensional, and changes in an unknown non-linear manner with changes in the input. These unknown relations between the input, model and output necessitate the user to analyze them in conjunction, leveraging symmetries between them. Since classification tasks do not exhibit some of these challenges, most existing VA systems and frameworks allow limited control of the components required to analyze models beyond classification. Hence, we identify the need for and present a unified conceptual framework, the Transform-and-Perform framework (T&P), to facilitate the design of VA systems for DL model analysis focusing on H-H problems. T&P provides a checklist to structure and identify workflows and analysis strategies to design new VA systems, and understand existing ones to uncover potential gaps for improvements. The goal is to aid the creation of effective VA systems that support the structuring of model understanding and identifying actionable insights for model improvements. We highlight the growing need for new frameworks like T&P with a real-world image-to-image translation application. We illustrate how T&P effectively supports the understanding and identification of potential gaps in existing VA systems.
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http://dx.doi.org/10.1109/TVCG.2022.3219248 | DOI Listing |
J Phys Chem A
September 2024
State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.
The interaction-asymptotic region decomposition (IARD) technique has been proven to be a good solution to the long-standing coordinate problem in reactive scattering calculations. In this work, the IARD technique was further developed using Jacobi coordinates for the interaction region, instead of the previously used hyperspherical coordinates. Although the Jacobi coordinate may not be as optimal as the hyperspherical coordinates for describing the interaction region in reactive scattering processes, it has simpler kinetic operators and provides a more physically intuitive picture.
View Article and Find Full Text PDFNat Nanotechnol
November 2024
Department of Bioengineering and Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Lipid nanoparticle (LNP)-mRNA complexes are transforming medicine. However, the medical applications of LNPs are limited by their low endosomal disruption rates, high toxicity and long tissue persistence times. LNPs that rapidly hydrolyse in endosomes (RD-LNPs) could solve the problems limiting LNP-based therapeutics and dramatically expand their applications but have been challenging to synthesize.
View Article and Find Full Text PDFPhys Rev E
July 2024
School of Physics, Trinity College Dublin, College Green, Dublin 2, D02K8N4, Ireland.
Understanding the entropy production of systems strongly coupled to thermal baths is a core problem of both quantum thermodynamics and mesoscopic physics. While many techniques exist to accurately study entropy production in such systems, they typically require a microscopic description of the baths, which can become numerically intractable to study for large systems. Alternatively an open-systems approach can be employed with all the nuances associated with various levels of approximation.
View Article and Find Full Text PDFJ Chem Phys
August 2024
Department of Physics, Stockholm University, AlbaNova University Center, SE-10691 Stockholm, Sweden.
The problem of asymptotic non-adiabatic couplings in heavy particle collisions is treated using the reprojection method. The mixing matrix that mixes the asymptotic solutions of the coupled states to obtain appropriate boundary conditions is here derived to second order, yielding a faster convergence of the cross section. In addition, the reprojection method is implemented in a diabatic representation and applied to inelastic scattering of Li + Na and H + H collisions and to mutual neutralization in H+ + H- collisions.
View Article and Find Full Text PDFPhys Chem Chem Phys
August 2024
Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Prague 166 10, Czech Republic.
Molecular dynamics with orientational constraints (MDOC) simulations use NMR parameters as tensorial constraints in the stereochemical analysis of small molecules. C-P Residual dipolar couplings-aided MDOC simulations of small phosphorus molecules determined the relative configurations of rigid molecules after including -couplings as additional constraints. However, flexible molecules remain a problem.
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