Yijie Ding

Yizheng Wang, Yixiao Zhai, Yijie Ding et al.

Proteins play a pivotal role in biological systems. The use of machine learning algorithms for protein classification can assist and even guide biological experiments, offering crucial insights for biotechnological applications. We introduce the Support Bio-Sequence Machine for Proteins (SBSM-Pro), a model purpose-built for the classification of biological sequences. This model starts with raw sequences and groups amino acids based on their physicochemical properties. It incorporates sequence alignment to measure the similarities between proteins and uses a novel multiple kernel learning (MKL) approach to integrate various types of information, utilizing support vector machines for classification prediction. The results indicate that our model demonstrates commendable performance across ten datasets in terms of the identification of protein function and posttranslational modification. This research not only exemplifies state-of-the-art work in protein classification but also paves avenues for new directions in this domain, representing a beneficial endeavor in the development of platforms tailored for the classification of biological sequences. SBSM-Pro is available for access at http://lab.malab.cn/soft/SBSM-Pro/.

Manish Dhakal, Venkat R. Dasari, Raj Sunderraman et al.

Parameter-efficient fine-tuning (PEFT) significantly reduces computational and memory costs by updating only a small subset of the model's parameters, enabling faster adaptation to new tasks with minimal loss in performance. Previous studies have introduced PEFTs tailored for point cloud data, as general approaches are suboptimal. To further reduce the number of trainable parameters, we propose a point-cloud-specific PEFT, termed Graph Features Tuning (GFT), which learns a dynamic graph from initial tokenized inputs of the transformer using a lightweight graph convolution network and passes these graph features to deeper layers via skip connections and efficient cross-attention modules. Extensive experiments on object classification and segmentation tasks show that GFT operates in the same domain, rivalling existing methods, while reducing the trainable parameters. Code is at https://github.com/manishdhakal/GFT.

Yi Ding, Ruqi Zhang

Reasoning Vision-Language Models (VLMs) have shown promising performance on complex multimodal tasks. However, they still face significant challenges: they are highly sensitive to reasoning errors, require large volumes of annotated data or accurate verifiers, and struggle to generalize beyond specific domains. To address these limitations, we explore self-correction as a strategy to enhance reasoning VLMs. We first conduct an in-depth analysis of reasoning VLMs' self-correction abilities and identify key gaps. Based on our findings, we introduce Sherlock, a self-correction and self-improvement training framework. Sherlock introduces a trajectory-level self-correction objective, a preference data construction method based on visual perturbation, and a dynamic $β$ for preference tuning. Once the model acquires self-correction capabilities using only 20k randomly sampled annotated data, it continues to self-improve without external supervision. Built on the Llama3.2-Vision-11B model, Sherlock achieves remarkable results across eight benchmarks, reaching an average accuracy of 64.1 with direct generation and 65.4 after self-correction. It outperforms LLaVA-CoT (63.2), Mulberry (63.9), and LlamaV-o1 (63.4) while using less than 20% of the annotated data.

Xushuo Tang, Yi Ding, Zhengyi Yang et al.

Large language models (LLMs) are increasingly deployed in sensitive contexts where fairness and inclusivity are critical. Pronoun usage, especially concerning gender-neutral and neopronouns, remains a key challenge for responsible AI. Prior work, such as the MISGENDERED benchmark, revealed significant limitations in earlier LLMs' handling of inclusive pronouns, but was constrained to outdated models and limited evaluations. In this study, we introduce MISGENDERED+, an extended and updated benchmark for evaluating LLMs' pronoun fidelity. We benchmark five representative LLMs, GPT-4o, Claude 4, DeepSeek-V3, Qwen Turbo, and Qwen2.5, across zero-shot, few-shot, and gender identity inference. Our results show notable improvements compared with previous studies, especially in binary and gender-neutral pronoun accuracy. However, accuracy on neopronouns and reverse inference tasks remains inconsistent, underscoring persistent gaps in identity-sensitive reasoning. We discuss implications, model-specific observations, and avenues for future inclusive AI research.

Chaoqing Tang, Huanze Zhuang, Guiyun Tian et al.

Pre-trained large models attract widespread attention in recent years, but they face challenges in applications that require high interpretability or have limited resources, such as physical sensing, medical imaging, and bioinformatics. Compressed Sensing (CS) is a well-proved theory that drives many recent breakthroughs in these applications. However, as a typical under-determined linear system, CS suffers from excessively long sparse reconstruction times when using traditional iterative methods, particularly with large-scale data. Current AI methods like deep unfolding fail to substitute them because pre-trained models exhibit poor generality beyond their training conditions and dataset distributions, or lack interpretability. Instead of following the big model fervor, this paper proposes ultra-small artificial neural models called coefficients learning (CL), enabling training-free and rapid sparse reconstruction while perfectly inheriting the generality and interpretability of traditional iterative methods, bringing new feature of incorporating prior knowledges. In CL, a signal of length $n$ only needs a minimal of $n$ trainable parameters. A case study model called CLOMP is implemented for evaluation. Experiments are conducted on both synthetic and real one-dimensional and two-dimensional signals, demonstrating significant improvements in efficiency and accuracy. Compared to representative iterative methods, CLOMP improves efficiency by 100 to 1000 folds for large-scale data. Test results on eight diverse image datasets indicate that CLOMP improves structural similarity index by 292%, 98%, 45% for sampling rates of 0.1, 0.3, 0.5, respectively. We believe this method can truly usher CS reconstruction into the AI era, benefiting countless under-determined linear systems that rely on sparse solution.

Yuqing Qian, Ziyu Zheng, Prayag Tiwari et al.

Drug-side effect prediction has become an essential area of research in the field of pharmacology. As the use of medications continues to rise, so does the importance of understanding and mitigating the potential risks associated with them. At present, researchers have turned to data-driven methods to predict drug-side effects. Drug-side effect prediction is a link prediction problem, and the related data can be described from various perspectives. To process these kinds of data, a multi-view method, called Multiple Kronecker RLS fusion-based link propagation (MKronRLSF-LP), is proposed. MKronRLSF-LP extends the Kron-RLS by finding the consensus partitions and multiple graph Laplacian constraints in the multi-view setting. Both of these multi-view settings contribute to a higher quality result. Extensive experiments have been conducted on drug-side effect datasets, and our empirical results provide evidence that our approach is effective and robust.