Papers by Zikang Chen
Large Language Models in Bioinformatics: A Survey (2025.findings-acl)
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| Challenge: | Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. |
| Approach: | They examine the evolution of Large Language Models (LLMs) in bioinformatics and precision medicine by focusing on genomic sequence modeling, RNA structure prediction, protein function inference, and single-cell transcriptomics. |
| Outcome: | The proposed models are capable of predicting RNA structure and function and predicting single-cell transcriptomics. |
VRoPE: Rotary Position Embedding for Video Large Language Models (2025.emnlp-main)
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Zikang Liu, Longteng Guo, Yepeng Tang, Tongtian Yue, Junxian Cai, Kai Ma, Qingbin Liu, Xi Chen, Jing Liu
| Challenge: | Existing versions of Large Language Models (LLMs) lack a positional encoding strategy for video. |
| Approach: | They propose a new positional encoding method tailored for Video-LLMs that mitigates positional biases and ensures a more uniform distribution of spatial focus. |
| Outcome: | The proposed method outperforms existing versions of RoPE in video understanding and reasoning tasks. |
LM2Protein: A Structure-to-Token Protein Large Language Model (2025.findings-emnlp)
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| Challenge: | RNA-binding proteins are critical for various molecular functions, relying on their precise tertiary structures. |
| Approach: | They propose a method to integrate protein 3D structural data within a sequence processing framework. |
| Outcome: | The proposed method achieves high sequence recovery in inverse folding and protein-conditioned RNA design. |
HICD: Hallucination-Inducing via Attention Dispersion for Contrastive Decoding to Mitigate Hallucinations in Large Language Models (2025.findings-acl)
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| Challenge: | Large Language Models (LLMs) often generate hallucinations, producing outputs that are contextually inaccurate or factually incorrect. |
| Approach: | They propose a method that selects attention heads crucial to the model's prediction as inducing heads and induces hallucinations by dispersing attention of these inducers. |
| Outcome: | The proposed method significantly improves performance on tasks requiring contextual faithfulness, reading comprehension, and question answering. |
Evaluating the Expressive Appropriateness of Speech in Rich Contexts (2026.acl-long)
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Tianrui Wang, Ziyang Ma, Yizhou Peng, Haoyu Wang, Zhikang Niu, Zikang Huang, Yihao Wu, Yi-Wen Chao, Yu Jiang, Yuheng Lu, Guanrou Yang, Xuanchen Li, Hexin Liu, Chunyu Qiang, Cheng Gong, Yifan Yang, Tianchi Liu, Junyu Wang, Nana Hou, Meng Ge, Fuming You, Yang Wei, Zhongqian Sun, Hu Haifeng, Xiaobao Wang, Eng Siong Chng, Xie Chen, Longbiao Wang, Jianwu Dang
| Challenge: | Existing methods for evaluating expressive speech focus on word accuracy, naturalness, signal quality, or emotional intensity at the utterance level. |
| Approach: | They propose a framework for Evaluating Expressive Appropriateness in speech that assesses whether a speech sample aligns with the underlying communicative intent implied by its discourse-level narrative context. |
| Outcome: | The proposed framework outperforms existing speech evaluation and analysis systems on a human-annotated test set. |