arXiv subjects

Hao Xuan

Publications and source records attributed to Hao Xuan.

4 recordsLinked to original sources

arXiv2026

Automatic bioinformatic software named entity recognition from literature

Bioinformatics software and databases are essential components of modern life science research, yet their mentions in the scientific literature are often inconsistent and difficult to systematically identify at scale. The lack of a comprehensive and up-to-date catalog of bioinformatics resources hinders efforts toward automated biomedical knowledge extraction and streamlined data analysis. Here we present SNAIL, a hybrid named entity recognition framework designed to automatically identify bioinformatics software and database (SW/DB) names from biomedical texts. SNAIL integrates complementary lexical and semantic modeling strategies. The lexical component captures orthographic patterns and contextual cues characteristic of SW/DB names, while the semantic component leverages contextual embeddings generated by transformer-based language models such as SciBERT, combined with an explicit token-masking strategy to enhance entity-focused representations. A large training corpus was constructed automatically through a hybrid pipeline that integrates citation-hinted extraction with large language model-assisted distillation. Evaluation on two independent benchmark datasets and real-world research articles demonstrates that SNAIL substantially outperforms existing approaches, including domain-specific methods such as bioNerDS2 and general-purpose large language models such as ChatGPT, Gemini, Grok and Claude. Applying SNAIL to large-scale literature analysis further reveals distinct journal-level preferences across bioinformatics subfields. These results demonstrate that SNAIL provides an accurate and scalable solution for identifying bioinformatics resources in scientific texts and enables systematic meta-analysis of tool usage and research trends.

cs.CL↗

arXiv2025

RUB: Evaluating Residual Knowledge in Unlearned Models

Machine Unlearning (MUL) has emerged as a key mechanism for privacy protection and content regulation, yet current techniques often fail to guarantee the complete removal of sensitive information. While most existing works focus on verifying the execution of unlearning, they overlook the critical question of whether models remain robust against adversarial attempts to recover forgotten knowledge. In this work, we advocate for the principle of Robust Unlearning, which requires models to be both indistinguishable from retrained counterparts and resilient against diverse adversarial threats. To instantiate this principle, we propose a unified benchmark, RUB (Robust Unlearning Benchmark), that systematically evaluates the robustness of unlearning algorithms across classification, image-to-image reconstruction, and text-to-image synthesis. Within this framework, we introduce the Unlearning Mapping Attack (UMA) as a generalizable method to detect residual information, and demonstrate how existing attack strategies can be adapted into this framework as long as they conform to the generic UMA framework. Our experiments across discriminative and generative tasks reveal that state-of-the-art unlearning methods remain vulnerable under these evaluations, even when passing standard verification metrics. By positioning robustness as the central criterion and providing a benchmark for adversarial evaluation, we hope RUB paves the way toward more reliable and secure unlearning practices. The codebase and model checkpoints in RUB will be published.

cs.LG↗

arXiv2025

Exploring the Impact of Temperature Scaling in Softmax for Classification and Adversarial Robustness

The softmax function is a fundamental component in deep learning. This study delves into the often-overlooked parameter within the softmax function, known as "temperature," providing novel insights into the practical and theoretical aspects of temperature scaling for image classification. Our empirical studies, adopting convolutional neural networks and transformers on multiple benchmark datasets, reveal that moderate temperatures generally introduce better overall performance. Through extensive experiments and rigorous theoretical analysis, we explore the role of temperature scaling in model training and unveil that temperature not only influences learning step size but also shapes the model's optimization direction. Moreover, for the first time, we discover a surprising benefit of elevated temperatures: enhanced model robustness against common corruption, natural perturbation, and non-targeted adversarial attacks like Projected Gradient Descent. We extend our discoveries to adversarial training, demonstrating that, compared to the standard softmax function with the default temperature value, higher temperatures have the potential to enhance adversarial training. The insights of this work open new avenues for improving model performance and security in deep learning applications.

cs.LG↗

arXiv2023

Advancing Adversarial Robustness Through Adversarial Logit Update

Deep Neural Networks are susceptible to adversarial perturbations. Adversarial training and adversarial purification are among the most widely recognized defense strategies. Although these methods have different underlying logic, both rely on absolute logit values to generate label predictions. In this study, we theoretically analyze the logit difference around successful adversarial attacks from a theoretical point of view and propose a new principle, namely Adversarial Logit Update (ALU), to infer adversarial sample's labels. Based on ALU, we introduce a new classification paradigm that utilizes pre- and post-purification logit differences for model's adversarial robustness boost. Without requiring adversarial or additional data for model training, our clean data synthesis model can be easily applied to various pre-trained models for both adversarial sample detection and ALU-based data classification. Extensive experiments on both CIFAR-10, CIFAR-100, and tiny-ImageNet datasets show that even with simple components, the proposed solution achieves superior robustness performance compared to state-of-the-art methods against a wide range of adversarial attacks. Our python implementation is submitted in our Supplementary document and will be published upon the paper's acceptance.

cs.LG↗