Jiwei Zhu

Siao Liu, Zhaoyu Chen, Wei Li et al.

Recently, adversarial attacks have been applied in visual object tracking to deceive deep trackers by injecting imperceptible perturbations into video frames. However, previous work only generates the video-specific perturbations, which restricts its application scenarios. In addition, existing attacks are difficult to implement in reality due to the real-time of tracking and the re-initialization mechanism. To address these issues, we propose an offline universal adversarial attack called Efficient Universal Shuffle Attack. It takes only one perturbation to cause the tracker malfunction on all videos. To improve the computational efficiency and attack performance, we propose a greedy gradient strategy and a triple loss to efficiently capture and attack model-specific feature representations through the gradients. Experimental results show that EUSA can significantly reduce the performance of state-of-the-art trackers on OTB2015 and VOT2018.

Zhao Yang, Yi Duan, Jiwei Zhu et al.

Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target genes from hundreds of kilobases away. Our work first reveals that for current models, long sequence modeling can decrease performance. Even carefully designed algorithms only mitigate the performance degradation caused by long sequences. Instead, we find that proximal multimodal epigenomic signals near target genes prove more essential. Hence we focus on how to better integrate these signals, which has been overlooked. We find that different signal types serve distinct biological roles, with some directly marking active regulatory elements while others reflect background chromatin patterns that may introduce confounding effects. Simple concatenation may lead models to develop spurious associations with these background patterns. To address this challenge, we propose Prism, a framework that learns multiple combinations of high-dimensional epigenomic features to represent distinct background chromatin states and uses backdoor adjustment to mitigate confounding effects. Our experimental results demonstrate that proper modeling of multimodal epigenomic signals achieves state-of-the-art performance using only short sequences for gene expression prediction.

Zhao Yang, Jiwei Zhu, Bing Su

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our $\textbf{S}$pecies-$\textbf{P}$rofile $\textbf{A}$daptive $\textbf{C}$ollaborative $\textbf{E}$xperts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners. The code is available at https://github.com/ZhuJiwei111/SPACE.