Linjiang Chen

Wenjin Wu, Aleš Leonardis, Linjiang Chen et al.

Infrared (IR) spectroscopy, a type of vibrational spectroscopy, is widely used for molecular structure determination and provides critical structural information for chemists. However, existing approaches for recovering molecular structures from IR spectra typically rely on one-dimensional SMILES strings or two-dimensional molecular graphs, which fail to capture the intricate relationship between spectral features and three-dimensional molecular geometry. Recent advances in diffusion models have greatly enhanced the ability to generate molecular structures in 3D space. Yet, no existing model has explored the distribution of 3D molecular geometries corresponding to a single IR spectrum. In this work, we introduce IR-GeoDiff, a latent diffusion model that recovers 3D molecular geometries from IR spectra by integrating spectral information into both node and edge representations of molecular structures. We evaluate IR-GeoDiff from both spectral and structural perspectives, demonstrating its ability to recover the molecular distribution corresponding to a given IR spectrum. Furthermore, an attention-based analysis reveals that the model is able to focus on characteristic functional group regions in IR spectra, qualitatively consistent with common chemical interpretation practices.

Zhuo Yang, Jiaqing Xie, Shuaike Shen et al.

Deep learning holds immense promise for spectroscopy, yet research and evaluation in this emerging field often lack standardized formulations. To address this issue, we introduce SpectrumLab, a pioneering unified platform designed to systematize and accelerate deep learning research in spectroscopy. SpectrumLab integrates three core components: a comprehensive Python library featuring essential data processing and evaluation tools, along with leaderboards; an innovative SpectrumAnnotator module that generates high-quality benchmarks from limited seed data; and SpectrumBench, a multi-layered benchmark suite covering 14 spectroscopic tasks and over 10 spectrum types, featuring spectra curated from over 1.2 million distinct chemical substances. Thorough empirical studies on SpectrumBench with 18 cutting-edge multimodal LLMs reveal critical limitations of current approaches. We hope SpectrumLab will serve as a crucial foundation for future advancements in deep learning-driven spectroscopy.

Zikai Xie, Linjiang Chen

Bayesian Optimization (BO) is a powerful tool for black-box optimization, but its application to high-dimensional permutation spaces is severely limited by the challenge of defining scalable representations. The current state-of-the-art BO approach for permutation spaces relies on an exhaustive $Ω(n^2)$ pairwise comparison, inducing a dense representation that is impractical for large-scale permutations. To break this barrier, we introduce a novel framework for generating efficient permutation representations via kernel functions derived from sorting algorithms. Within this framework, the Mallows kernel can be viewed as a special instance derived from enumeration sort. Further, we introduce the \textbf{Merge Kernel} , which leverages the divide-and-conquer structure of merge sort to produce a compact, $Θ(n\log n)$ to achieve the lowest possible complexity with no information loss and effectively capture permutation structure. Our central thesis is that the Merge Kernel performs competitively with the Mallows kernel in low-dimensional settings, but significantly outperforms it in both optimization performance and computational efficiency as the dimension $n$ grows. Extensive evaluations on various permutation optimization benchmarks confirm our hypothesis, demonstrating that the Merge Kernel provides a scalable and more effective solution for Bayesian optimization in high-dimensional permutation spaces, thereby unlocking the potential for tackling previously intractable problems such as large-scale feature ordering and combinatorial neural architecture search.

Zhuo Chen, Yizhen Zheng, Huan Yee Koh et al.

Molecular Relational Learning (MRL) aims to understand interactions between molecular pairs, playing a critical role in advancing biochemical research. With the recent development of large language models (LLMs), a growing number of studies have explored the integration of MRL with LLMs and achieved promising results. However, the increasing availability of diverse LLMs and molecular structure encoders has significantly expanded the model space, presenting major challenges for benchmarking. Currently, there is no LLM framework that supports both flexible molecular input formats and dynamic architectural switching. To address these challenges, reduce redundant coding, and ensure fair model comparison, we propose ModuLM, a framework designed to support flexible LLM-based model construction and diverse molecular representations. ModuLM provides a rich suite of modular components, including 8 types of 2D molecular graph encoders, 11 types of 3D molecular conformation encoders, 7 types of interaction layers, and 7 mainstream LLM backbones. Owing to its highly flexible model assembly mechanism, ModuLM enables the dynamic construction of over 50,000 distinct model configurations. In addition, we provide comprehensive results to demonstrate the effectiveness of ModuLM in supporting LLM-based MRL tasks.