Jinli Ou

Zhijiang Tang, Jiaxin Qi, Yan Cui et al.

DNA sequence encoding is fundamental to gene function prediction, protein synthesis, and diverse downstream biological tasks. Despite the substantial progress achieved by large-scale DNA sequence pretraining, existing studies have overwhelmingly emphasized pretraining scale and custom downstream evaluation datasets, while neglecting some essential components of the pretraining paradigm. In this paper, we reveal three critical yet heretofore overlooked problems in DNA pretraining: inappropriate downstream datasets, inherent flaws in the neighbor-masking strategy, and the lack of detailed discussion on vocabulary. Therefore, we undertake comprehensive investigations and propose principled guidelines, including selection criteria for evaluation datasets, guiding task design, and in-depth vocabulary analysis. Extensive experiments validate the significance of our identified problems and support the rationale behind our recommendations. Finally, we introduce a standardized testbed that enables reproducible and rigorous benchmarking of DNA pretraining methods to advance the development of genomic foundation models.

Kaihua Tang, Jiaxin Qi, Jinli Ou et al.

The emergence of Large Language Models (LLMs) has driven rapid progress in multi-modal learning, particularly in the development of Large Vision-Language Models (LVLMs). However, existing LVLM training paradigms place excessive reliance on the LLM component, giving rise to two critical robustness challenges: language bias and language sensitivity. To address both issues simultaneously, we propose a novel Self-Critical Inference (SCI) framework that extends Visual Contrastive Decoding by conducting multi-round counterfactual reasoning through both textual and visual perturbations. This process further introduces a new strategy for improving robustness by scaling the number of counterfactual rounds. Moreover, we also observe that failure cases of LVLMs differ significantly across models, indicating that fixed robustness benchmarks may not be able to capture the true reliability of LVLMs. To this end, we propose the Dynamic Robustness Benchmark (DRBench), a model-specific evaluation framework targeting both language bias and sensitivity issues. Extensive experiments show that SCI consistently outperforms baseline methods on DRBench, and that increasing the number of inference rounds further boosts robustness beyond existing single-step counterfactual reasoning methods.

Jiaxin Qi, Yan Cui, Jinli Ou et al.

Graph Neural Networks (GNNs) and Transformers share significant similarities in their encoding strategies for interacting with features from nodes of interest, where Transformers use query-key scores and GNNs use edges. Compared to GNNs, which are unable to encode relative positions, Transformers leverage dynamic attention capabilities to better represent relative relationships, thereby becoming the standard backbones in large-scale sequential pre-training. However, the subtle difference prompts us to consider: if positions are no longer crucial, could we substitute Transformers with Graph Neural Networks in some fields such as Single-Cell Transcriptomics? In this paper, we first explore the similarities and differences between GNNs and Transformers, specifically in terms of relative positions. Additionally, we design a synthetic example to illustrate their equivalence where there are no relative positions between tokens in the sample. Finally, we conduct extensive experiments on a large-scale position-agnostic dataset-single-cell transcriptomics-finding that GNNs achieve competitive performance compared to Transformers while consuming fewer computation resources. These findings provide novel insights for researchers in the field of single-cell transcriptomics, challenging the prevailing notion that the Transformer is always the optimum choice.