Researcher profile

Zhiyuan Yan

Zhiyuan Yan contributes to research discovery and scholarly infrastructure.

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Published work

6 published item(s)

preprint2026arXiv

Beyond Chemical QA: Evaluating LLM's Chemical Reasoning with Modular Chemical Operations

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

preprint2026arXiv

MoleCode unlocks structural intelligence in large language models

Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in which topology is implicit, forcing LLMs to reconstruct molecular structure before performing the requested chemical operation. Here we introduce MoleCode, an LLM-native, training-free, graph-explicit molecular language in which all molecular components are represented as typed entities with persistent identifiers and explicit relations. MoleCode makes molecular topology directly readable, editable and auditable within the language context, allowing an LLM to operate on structure rather than recover it from syntax. Across molecular reasoning, editing, generation and analysis tasks, this representational shift improves frontier LLMs most strongly when structural access is limiting: unfamiliar molecules, topology-sensitive operations, larger structures and repetitive polymers. It also changes how inference is allocated, replacing long reasoning traces devoted to implicit structural reconstruction with shorter, more chemically directed reasoning over explicit atoms and bonds. In molecular optimization, this enables localized, property-aligned edits that preserve structural similarity to the starting compounds. The same Subgraph--Node--Edge grammar extends beyond small molecules to polymers, Markush structures, mechanism-style transformations and interleaved scientific documents, including research articles and patent disclosures in which chemical information is distributed across text and images. These results suggest that the interface between scientific objects and LLMs should not treat structure as something to be decoded from text. When the object of reasoning is relational, the structure itself should be part of the language.

preprint2026arXiv

Your One-Stop Solution for AI-Generated Video Detection

Recent advances in generative modeling can create remarkably realistic synthetic videos, making it increasingly difficult for humans to distinguish them from real ones and necessitating reliable detection methods. However, two key limitations hinder the development of this field. \textbf{From the dataset perspective}, existing datasets are often limited in scale and constructed using outdated or narrowly scoped generative models, making it difficult to capture the diversity and rapid evolution of modern generative techniques. Moreover, the dataset construction process frequently prioritizes quantity over quality, neglecting essential aspects such as semantic diversity, scenario coverage, and technological representativeness. \textbf{From the benchmark perspective}, current benchmarks largely remain at the stage of dataset creation, leaving many fundamental issues and in-depth analysis yet to be systematically explored. Addressing this gap, we propose AIGVDBench, a benchmark designed to be comprehensive and representative, covering \textbf{31} state-of-the-art generation models and over \textbf{440,000} videos. By executing more than \textbf{1,500} evaluations on \textbf{33} existing detectors belonging to four distinct categories. This work presents \textbf{8 in-depth analyses} from multiple perspectives and identifies \textbf{4 novel findings} that offer valuable insights for future research. We hope this work provides a solid foundation for advancing the field of AI-generated video detection. Our benchmark is open-sourced at https://github.com/LongMa-2025/AIGVDBench.

preprint2022arXiv

HelixADMET: a robust and endpoint extensible ADMET system incorporating self-supervised knowledge transfer

Accurate ADMET (an abbreviation for "absorption, distribution, metabolism, excretion, and toxicity") predictions can efficiently screen out undesirable drug candidates in the early stage of drug discovery. In recent years, multiple comprehensive ADMET systems that adopt advanced machine learning models have been developed, providing services to estimate multiple endpoints. However, those ADMET systems usually suffer from weak extrapolation ability. First, due to the lack of labelled data for each endpoint, typical machine learning models perform frail for the molecules with unobserved scaffolds. Second, most systems only provide fixed built-in endpoints and cannot be customised to satisfy various research requirements. To this end, we develop a robust and endpoint extensible ADMET system, HelixADMET (H-ADMET). H-ADMET incorporates the concept of self-supervised learning to produce a robust pre-trained model. The model is then fine-tuned with a multi-task and multi-stage framework to transfer knowledge between ADMET endpoints, auxiliary tasks, and self-supervised tasks. Our results demonstrate that H-ADMET achieves an overall improvement of 4%, compared with existing ADMET systems on comparable endpoints. Additionally, the pre-trained model provided by H-ADMET can be fine-tuned to generate new and customised ADMET endpoints, meeting various demands of drug research and development requirements.

preprint2022arXiv

The Vehicle Trajectory Prediction Based on ResNet and EfficientNet Model

At present, a major challenge for the application of automatic driving technology is the accurate prediction of vehicle trajectory. With the vigorous development of computer technology and the emergence of convolution depth neural network, the accuracy of prediction results has been improved. But, the depth, width of the network and image resolution are still important reasons that restrict the accuracy of the model and the prediction results. The main innovation of this paper is the combination of RESNET network and efficient net network, which not only greatly increases the network depth, but also comprehensively changes the choice of network width and image resolution, so as to make the model performance better, but also save computing resources as much as possible. The experimental results also show that our proposed model obtains the optimal prediction results. Specifically, the loss value of our method is separately 4 less and 2.1 less than that of resnet and efficientnet method.

preprint2021arXiv

A Novel Key Generation Scheme Using Quaternary PUF Responses and Wiretap Polar Coding

Physical unclonable functions (PUFs) are widely considered in secret key generation for resource constrained devices. However, PUFs require additional hardware overhead. In this paper, we focus on developing a PUF-efficient, robust, and secure key generation scheme. First, a novel method for extracting quaternary PUF responses is proposed to increase the entropy of a PUF response, in which a 2-bit response is extracted from evaluating a single PUF cell multiple times. The probability masses of the responses can be adjusted by setting parameters appropriately. Then, a chosen secret model based fuzzy extractor (FE) is designed to extract secret keys from the quaternary PUF responses. To improve the security of this FE, it is modeled as a wiretap channel system, and wiretap polar coding is adopted to reduce secrecy leakage. An upper bound of secrecy leakage is also given in this paper, and it suggests that an arbitrarily small (even zero) leakage can be achieved by properly choosing parameters of the quaternary PUF responses generation. Comparison results show that the required number of PUF cells to achieve the same level of secrecy in our scheme is as low as half that of the state-of-the-art schemes.