arXiv subjects

Ondrej Strnad

Publications and source records attributed to Ondrej Strnad.

2 recordsLinked to original sources

arXiv2023

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↗

arXiv2020

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↗