Orthogonal graph layout algorithms aim to produce clear, compact, and readable network diagrams by arranging nodes and edges along horizontal and vertical lines, while minimizing bends and crossings. Most existing orthogonal layout methods focus primarily on quality criteria such as area usage, total edge length, and bend minimization. Explicitly controlling the global aspect ratio (AR) of the resulting layout is as of now unexplored. Existing orthogonal layout methods offer no control over the resulting AR and their rigid geometric constraints make adaptation of finished layouts difficult. With the increasing variety of aspect ratios encountered in daily life, from wide monitors to tall mobile devices or fixed-size interface panels, there is a clear need for aspect ratio control in orthogonal layout methods. To tackle this issue, we introduce Aspect Ratio-Constrained Orthogonal Layout (ARCOL). Building upon the Human-like Orthogonal Layout Algorithm (HOLA)~\cite{Kieffer2016}, we integrate aspect ratio at two different stages: (1) into the stress minimization phase, as a soft constraint, allowing the layout algorithm to gently guide node positions toward a specified target AR, while preserving visual clarity and topological faithfulness; and (2) into the tree reattachment phase, where we modify the cost function to favor placements that improve the AR. We evaluate our approach through quantitative evaluation and a user study, as well as expert interviews. Our evaluations show that ARCOL produces balanced and space efficient orthogonal layouts across diverse aspect ratios.

We introduce DiffFit, a differentiable algorithm for fitting protein atomistic structures into an experimental reconstructed Cryo-Electron Microscopy (cryo-EM) volume map. In structural biology, this process is necessary to semi-automatically composite large mesoscale models of complex protein assemblies and complete cellular structures that are based on measured cryo-EM data. The current approaches require manual fitting in three dimensions to start, resulting in approximately aligned structures followed by an automated fine-tuning of the alignment. The DiffFit approach enables domain scientists to fit new structures automatically and visualize the results for inspection and interactive revision. The fitting begins with differentiable three-dimensional (3D) rigid transformations of the protein atom coordinates followed by sampling the density values at the atom coordinates from the target cryo-EM volume. To ensure a meaningful correlation between the sampled densities and the protein structure, we proposed a novel loss function based on a multi-resolution volume-array approach and the exploitation of the negative space. This loss function serves as a critical metric for assessing the fitting quality, ensuring the fitting accuracy and an improved visualization of the results. We assessed the placement quality of DiffFit with several large, realistic datasets and found it to be superior to that of previous methods. We further evaluated our method in two use cases: automating the integration of known composite structures into larger protein complexes and facilitating the fitting of predicted protein domains into volume densities to aid researchers in identifying unknown proteins. We implemented our algorithm as an open-source plugin (github.com/nanovis/DiffFit) in ChimeraX, a leading visualization software in the field. All supplemental materials are available at osf. io/5tx4q.

The authors would like to make the following errata after correcting the initialization related bugs in the associated program.