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Deng Luo

Publications and source records attributed to Deng Luo.

5 recordsLinked to original sources

EfficientMonoHair: Fast Strand-Level Reconstruction from Monocular Video via Multi-View Direction Fusion

Strand-level hair geometry reconstruction is a fundamental problem in virtual human modeling and the digitization of hairstyles. However, existing methods still suffer from a significant trade-off between accuracy and efficiency. Implicit neural representations can capture the global hair shape but often fail to preserve fine-grained strand details, while explicit optimization-based approaches achieve high-fidelity reconstructions at the cost of heavy computation and poor scalability. To address this issue, we propose EfficientMonoHair, a fast and accurate framework that combines the implicit neural network with multi-view geometric fusion for strand-level reconstruction from monocular video. Our method introduces a fusion-patch-based multi-view optimization that reduces the number of optimization iterations for point cloud direction, as well as a novel parallel hair-growing strategy that relaxes voxel occupancy constraints, allowing large-scale strand tracing to remain stable and robust even under inaccurate or noisy orientation fields. Extensive experiments on representative real-world hairstyles demonstrate that our method can robustly reconstruct high-fidelity strand geometries with accuracy. On synthetic benchmarks, our method achieves reconstruction quality comparable to state-of-the-art methods, while improving runtime efficiency by nearly an order of magnitude.

cs.CV

DiffFit: Visually-Guided Differentiable Fitting of Molecule Structures to a Cryo-EM Map

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.

q-bio.QM

VOICE: Visual Oracle for Interaction, Conversation, and Explanation

We present VOICE, a novel approach to science communication that connects large language models' (LLM) conversational capabilities with interactive exploratory visualization. VOICE introduces several innovative technical contributions that drive our conversational visualization framework. Our foundation is a pack-of-bots that can perform specific tasks, such as assigning tasks, extracting instructions, and generating coherent content. We employ fine-tuning and prompt engineering techniques to tailor bots' performance to their specific roles and accurately respond to user queries. Our interactive text-to-visualization method generates a flythrough sequence matching the content explanation. Besides, natural language interaction provides capabilities to navigate and manipulate the 3D models in real-time. The VOICE framework can receive arbitrary voice commands from the user and respond verbally, tightly coupled with corresponding visual representation with low latency and high accuracy. We demonstrate the effectiveness of our approach by applying it to the molecular visualization domain: analyzing three 3D molecular models with multi-scale and multi-instance attributes. We finally evaluate VOICE with the identified educational experts to show the potential of our approach. All supplemental materials are available at https://osf.io/g7fbr.

cs.HC

SynopSet: Multiscale Visual Abstraction Set for Explanatory Analysis of DNA Nanotechnology Simulations

We propose a new abstraction set (SynopSet) that has a continuum of visual representations for the explanatory analysis of molecular dynamics simulations (MDS) in the DNA nanotechnology domain. By re-purposing the commonly used progress bar and designing novel visuals, as well as transforming the data from the domain format to a format that better fits the newly designed visuals, we compose this new set of representations. This set is also designed to be capable of showing all spatial and temporal details, and all structural complexity, or abstracting these to various degrees, enabling both the slow playback of the simulation for detailed examinations or very fast playback for an overview that helps to efficiently identify events of interest, as well as several intermediate levels between these two extremes. For any pair of successive representations, we demonstrate smooth, continuous transitions, enabling users to keep track of relevant information from one representation to the next. By providing multiple representations suited to different temporal resolutions and connected by smooth transitions, we enable time-efficient simulation analysis, giving users the opportunity to examine and present important phases in great detail, or leverage abstract representations to go over uneventful phases much faster. Domain experts can thus gain actionable insight about their simulations and communicate it in a much shorter time. Further, the novel representations are more intuitive and also enable researchers unfamiliar with MDS analysis graphs to better understand the simulation results. We assessed the effectiveness of SynopSet on 12 DNA nanostructure simulations together with a domain expert. We have also shown that our set of representations can be systematically located in a visualization space, dubbed SynopSpace.

q-bio.QM

Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models

We present a new technique for rapid modeling and construction of scientifically accurate mesoscale biological models. Resulting 3D models are based on few 2D microscopy scans and the latest knowledge about the biological entity represented as a set of geometric relationships. Our new technique is based on statistical and rule-based modeling approaches that are rapid to author, fast to construct, and easy to revise. From a few 2D microscopy scans, we learn statistical properties of various structural aspects, such as the outer membrane shape, spatial properties and distribution characteristics of the macromolecular elements on the membrane. This information is utilized in 3D model construction. Once all imaging evidence is incorporated in the model, additional information can be incorporated by interactively defining rules that spatially characterize the rest of the biological entity, such as mutual interactions among macromolecules, their distances and orientations to other structures. These rules are defined through an intuitive 3D interactive visualization and modeling feedback loop. We demonstrate the utility of our approach on a use case of the modeling procedure of the SARS-CoV-2 virus particle ultrastructure. Its first complete atomistic model, which we present here, can steer biological research to new promising directions in fighting spread of the virus.

q-bio.QM