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Zhonglin Cao

dblp:250/4995 · DBLP profile ↗
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3ranked-venue papers
1as first author
3since 2021 · last 2025
—ORCID · unresolved

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 2 · 1 first-author · 2 since 2021Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
2 papers
Generative modeling · 100%
Interdisciplinary, comprehensive, and emerging computing
2 papers
Bioinformatics and computational biology · 67% Computational science and engineering · 33%

Topics — the 7 heaviest of 8, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Machine learning › Generative modeling
flow matching
0.912025
Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow · ICML 2025
Machine learning › Generative modeling › diffusion model
molecular conformation generation
0.912025
Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow · ICML 2025
Machine learning › Generative modeling
normalizing flow
0.912025
Proteina: Scaling Flow-based Protein Structure Generative Models · ICLR 2025
Machine learning › Generative modeling › protein design
protein structure generation
0.912025
Proteina: Scaling Flow-based Protein Structure Generative Models · ICLR 2025
Computational science and engineering
computational chemistry
0.912025
Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow · ICML 2025
Bioinformatics and computational biology › molecular informatics › molecular modeling
molecular conformation generation
0.912025
Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow · ICML 2025
Bioinformatics and computational biology
protein design
0.912025
Proteina: Scaling Flow-based Protein Structure Generative Models · ICLR 2025

Methods — techniques the papers use, named apart from their topics

flow matching · 3.5transformer · 1.7reflow · 1.7distillation · 1.7classifier-free guidance · 1.7SO(3)-averaged flow · 1.7LoRA · 1.7
YearPublicationVenuePosition
2025 Proteina: Scaling Flow-based Protein Structure Generative Models
abstract
Recently, diffusion- and flow-based generative models of protein structures have emerged as a powerful tool for de novo protein design. Here, we develop *Proteina*, a new large-scale flow-based protein backbone generator that utilizes hierarchical fold class labels for conditioning and relies on a tailored scalable transformer architecture with up to $5\times$ as many parameters as previous models. To meaningfully quantify performance, we introduce a new set of metrics that directly measure the distributional similarity of generated proteins with reference sets, complementing existing metrics. We further explore scaling training data to millions of synthetic protein structures and explore improved training and sampling recipes adapted to protein backbone generation. This includes fine-tuning strategies like LoRA for protein backbones, new guidance methods like classifier-free guidance and autoguidance for protein backbones, and new adjusted training objectives. Proteina achieves state-of-the-art performance on de novo protein backbone design and produces diverse and designable proteins at unprecedented length, up to 800 residues. The hierarchical conditioning offers novel control, enabling high-level secondary-structure guidance as well as low-level fold-specific generation.
Tomas Geffner, Kieran Didi, Zuobai Zhang, Danny Reidenbach, Zhonglin Cao, Jason Yim, Mario Geiger, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Karsten Kreis
ICLR5
2025 Efficient Molecular Conformer Generation with SO(3)-Averaged Flow Matching and Reflow
abstract
Fast and accurate generation of molecular conformers is desired for downstream computational chemistry and drug discovery tasks. Currently, training and sampling state-of-the-art diffusion or flow-based models for conformer generation require significant computational resources. In this work, we build upon flow-matching and propose two mechanisms for accelerating training and inference of generative models for 3D molecular conformer generation. For fast training, we introduce the SO(3)-*Averaged Flow* training objective, which leads to faster convergence to better generation quality compared to conditional optimal transport flow or Kabsch-aligned flow. We demonstrate that models trained using SO(3)-*Averaged Flow* can reach state-of-the-art conformer generation quality. For fast inference, we show that the reflow and distillation methods of flow-based models enable few-steps or even one-step molecular conformer generation with high quality. The training techniques proposed in this work show a path towards highly efficient molecular conformer generation with flow-based models.
Zhonglin Cao, Mario Geiger, Allan dos Santos Costa, Danny Reidenbach, Karsten Kreis, Tomas Geffner, Franco Pellegrini, Emine Küçükbenli
ICML1
2025 A Deep-Learning-Based Targeted Interpolation Method for Seismic Data: A Consecutively Missing Trace VSP Case
abstract
Seismic data interpolation is an important processing method for improving the quality of seismic data. Traditional interpolation methods often face limitations due to their dependence on prior information and their challenges in processing continuous missing data. Vertical seismic profiling (VSP) data, owing to its unique acquisition approach, generally do not suffer from missing receivers but can have missing shots, with the locations of these missing shots being known. To address this specific issue of missing shots, a specialized interpolation technique has been proposed for targeted missing data. This technique involves creating datasets from the original complete data that are tailored to fixed missing shot scenarios, allowing for a more effective application of the trained network to field data. Additionally, we have optimized the network structure based on UNet to meet the specific requirements for handling consecutive gaps. Both synthetic and field data demonstrate the effectiveness of this targeted interpolation method.
Wen Yang 0012, Qianggong Song, Zhonglin Cao
IEEE Geosci. Remote. Sens. Lett.5