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Ziru Liu

Ziru Liu contributes to research discovery and scholarly infrastructure.

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Published work

2 published item(s)

preprint2026arXiv

Self-Distilled Trajectory-Aware Boltzmann Modeling: Bridging the Training-Inference Discrepancy in Diffusion Language Models

Diffusion Language Models (DLMs) have recently emerged as a promising alternative to autoregressive language models, offering stronger global awareness and highly parallel generation. However, post-training DLMs with standard Negative Evidence Lower Bound (NELBO)-based supervised fine-tuning remains inefficient: training reconstructs randomly masked tokens in a single step, whereas inference follows a confidence-guided, multi-step easy-to-hard denoising trajectory. Recent trajectory-based self-distillation methods exploit such inference trajectories mainly for sampling-step compression and acceleration, often improving decoding efficiency without substantially enhancing the model's underlying capability, and may even degrade performance under full diffusion decoding. In this work, we ask whether self-distilled trajectories can be used not merely for faster inference, but for genuine knowledge acquisition. Although these trajectories lie on the pretrained DLM's own distributional manifold and thus offer a potentially lower optimization barrier, we find that naively fine-tuning on them with standard NELBO objectives yields only marginal gains. To address this limitation, we propose \textbf{T}rajectory-\textbf{A}ligned optimization via \textbf{Bo}ltzmann \textbf{M}odeling (\textbf{TABOM}), a self-distilled trajectory-based post-training framework that aligns training with the easy-to-hard structure of inference. TABOM models the inference unmasking preference as a Boltzmann distribution over predictive entropies and derives a tractable pairwise ranking objective to align the model's certainty ordering with the observed decoding trajectory. Empirically, TABOM achieves substantial gains in new domains, expands the effective knowledge boundary of DLMs, and significantly mitigates catastrophic forgetting compared with standard SFT.

preprint2020arXiv

ItLnc-BXE: a Bagging-XGBoost-ensemble method with multiple features for identification of plant lncRNAs

Motivation: Since long non-coding RNAs (lncRNAs) have involved in a wide range of functions in cellular and developmental processes, an increasing number of methods have been proposed for distinguishing lncRNAs from coding RNAs. However, most of the existing methods are designed for lncRNAs in animal systems, and only a few methods focus on the plant lncRNA identification. Different from lncRNAs in animal systems, plant lncRNAs have distinct characteristics. It is desirable to develop a computational method for accurate and robust identification of plant lncRNAs. Results: Herein, we present a plant lncRNA identification method ItLnc-BXE, which utilizes multiple features and the ensemble learning strategy. First, a diversity of lncRNA features is collected and filtered by feature selection to represent RNA transcripts. Then, several base learners are trained and further combined into a single meta-learner by ensemble learning, and thus an ItLnc-BXE model is constructed. ItLnc-BXE models are evaluated on datasets of six plant species, the results show that ItLnc-BXE outperforms other state-of-the-art plant lncRNA identification methods, achieving better and robust performances (AUC>95.91%). We also perform some experiments about cross-species lncRNA identification, and the results indicate that dicots-based and monocots-based models can be used to accurately identify lncRNAs in lower plant species, such as mosses and algae. Availability: source codes are available at https://github.com/BioMedicalBigDataMiningLab/ItLnc-BXE. Contact: zhangwen@mail.hzau.edu.cn (or) zhangwen@whu.edu.cn Supplementary information: Supplementary data are available at Bioinformatics online.