Sen Yang

Yi Xiong, Liang Xiong, Xiaohong Ji et al.

Molecular property optimization is central to drug discovery, yet many deep learning methods rely on black-box scoring and offer limited control over scaffold preservation, often producing unstable or biologically implausible edits. While large language models (LLMs) are promising molecular generators, optimization remains constrained by the lack of chemistry-grounded preference supervision and principled data curation. We introduce \textbf{Scaffold-Conditioned Preference Triplets (SCPT)}, a pipeline that constructs similarity-constrained triplets $\langle\text{scaffold}, \text{better}, \text{worse}\rangle$ via scaffold alignment and chemistry-driven filters for validity, synthesizability, and meaningful property gains. Using these preferences, we align a pretrained molecular LLM as a conditional editor, enabling property-improving edits that retain the scaffold. Across single- and multi-objective benchmarks, SCPT improves optimization success and property gains while maintaining higher scaffold similarity than competitive baselines. Compared with representative non-LLM molecular optimization methods, SCPT-trained LLMs are better suited to scaffold-constrained and multi-objective optimization. In addition, models trained on single-property and two-property supervision generalize effectively to three-property tasks, indicating promising extrapolative generalization under limited higher-order supervision. SCPT also provides controllable data-construction knobs that yield a predictable similarity-gain frontier, enabling systematic adaptation to diverse optimization regimes.

Ze Feng, Sen Yang, Boqiang Duan et al.

Efficient Multimodal Large Language Models (MLLMs) compress vision tokens to reduce resource consumption, but the loss of visual information can degrade comprehension capabilities. Although some priors introduce Knowledge Distillation to enhance student models, they overlook the fundamental differences in fine-grained vision comprehension caused by unbalanced vision tokens between the efficient student and vanilla teacher. In this paper, we propose EM-KD, a novel paradigm that enhances the Efficient MLLMs with Knowledge Distillation. To overcome the challenge of unbalanced vision tokens, we first calculate the Manhattan distance between the vision logits of teacher and student, and then align them in the spatial dimension with the Hungarian matching algorithm. After alignment, EM-KD introduces two distillation strategies: 1) Vision-Language Affinity Distillation (VLAD) and 2) Vision Semantic Distillation (VSD). Specifically, VLAD calculates the affinity matrix between text tokens and aligned vision tokens, and minimizes the smooth L1 distance of the student and the teacher affinity matrices. Considering the semantic richness of vision logits in the final layer, VSD employs the reverse KL divergence to measure the discrete probability distributions of the aligned vision logits over the vocabulary space. Comprehensive evaluation on diverse benchmarks demonstrates that EM-KD trained model outperforms prior Efficient MLLMs on both accuracy and efficiency with a large margin, validating its effectiveness. Compared with previous distillation methods, which are equipped with our proposed vision token matching strategy for fair comparison, EM-KD also achieves better performance.

Huan Liu, Lingyu Xiao, Jiangjiang Liu et al.

With the rapid advancement of Multimodal Large Language Models (MLLMs), a variety of benchmarks have been introduced to evaluate their capabilities. While most evaluations have focused on complex tasks such as scientific comprehension and visual reasoning, little attention has been given to assessing their fundamental image classification abilities. In this paper, we address this gap by thoroughly revisiting the MLLMs with an in-depth analysis of image classification. Specifically, building on established datasets, we examine a broad spectrum of scenarios, from general classification tasks (e.g., ImageNet, ObjectNet) to more fine-grained categories such as bird and food classification. Our findings reveal that the most recent MLLMs can match or even outperform CLIP-style vision-language models on several datasets, challenging the previous assumption that MLLMs are bad at image classification \cite{VLMClassifier}. To understand the factors driving this improvement, we conduct an in-depth analysis of the network architecture, data selection, and training recipe used in public MLLMs. Our results attribute this success to advancements in language models and the diversity of training data sources. Based on these observations, we further analyze and attribute the potential reasons to conceptual knowledge transfer and enhanced exposure of target concepts, respectively. We hope our findings will offer valuable insights for future research on MLLMs and their evaluation in image classification tasks.

Yuci Liang, Xinheng Lyu, Wenting Chen et al.

Recent advancements in computational pathology have produced patch-level Multi-modal Large Language Models (MLLMs), but these models are limited by their inability to analyze whole slide images (WSIs) comprehensively and their tendency to bypass crucial morphological features that pathologists rely on for diagnosis. To address these challenges, we first introduce WSI-Bench, a large-scale morphology-aware benchmark containing 180k VQA pairs from 9,850 WSIs across 30 cancer types, designed to evaluate MLLMs' understanding of morphological characteristics crucial for accurate diagnosis. Building upon this benchmark, we present WSI-LLaVA, a novel framework for gigapixel WSI understanding that employs a three-stage training approach: WSI-text alignment, feature space alignment, and task-specific instruction tuning. To better assess model performance in pathological contexts, we develop two specialized WSI metrics: WSI-Precision and WSI-Relevance. Experimental results demonstrate that WSI-LLaVA outperforms existing models across all capability dimensions, with a significant improvement in morphological analysis, establishing a clear correlation between morphological understanding and diagnostic accuracy.

Yiyu Lin, Yan Wang, You Zhou et al.

As a core mechanism of epigenetic regulation in eukaryotes, protein post-translational modifications (PTMs) require precise prediction to decipher dynamic life activity networks. To address the limitations of existing deep learning models in cross-modal feature fusion, domain generalization, and architectural optimization, this study proposes UniPTMs: the first unified framework for multi-type PTM prediction. The framework innovatively establishes a "Master-Slave" dual-path collaborative architecture: The master path dynamically integrates high-dimensional representations of protein sequences, structures, and evolutionary information through a Bidirectional Gated Cross-Attention (BGCA) module, while the slave path optimizes feature discrepancies and recalibration between structural and traditional features using a Low-Dimensional Fusion Network (LDFN). Complemented by a Multi-scale Adaptive convolutional Pyramid (MACP) for capturing local feature patterns and a Bidirectional Hierarchical Gated Fusion Network (BHGFN) enabling multi-level feature integration across paths, the framework employs a Hierarchical Dynamic Weighting Fusion (HDWF) mechanism to intelligently aggregate multimodal features. Enhanced by a novel Hierarchical Contrastive loss function for feature consistency optimization, UniPTMs demonstrates significant performance improvements (3.2%-11.4% MCC and 4.2%-14.3% AP increases) over state-of-the-art models across five modification types and transcends the Single-Type Prediction Paradigm. To strike a balance between model complexity and performance, we have also developed a lightweight variant named UniPTMs-mini.

Ze Feng, Jiang-Jiang Liu, Sen Yang et al.

In this work, we study the Efficient Multimodal Large Language Model. Redundant vision tokens consume a significant amount of computational memory and resources. Therefore, many previous works compress them in the Vision Projector to reduce the number of vision tokens. However, simply compressing in the Vision Projector can lead to the loss of visual information, especially for tasks that rely on fine-grained spatial relationships, such as OCR and Chart \& Table Understanding. To address this problem, we propose Vision Remember, which is inserted between the LLM decoder layers to allow vision tokens to re-memorize vision features. Specifically, we retain multi-level vision features and resample them with the vision tokens that have interacted with the text token. During the resampling process, each vision token only attends to a local region in vision features, which is referred to as saliency-enhancing local attention. Saliency-enhancing local attention not only improves computational efficiency but also captures more fine-grained contextual information and spatial relationships within the region. Comprehensive experiments on multiple visual understanding benchmarks validate the effectiveness of our method when combined with various Efficient Vision Projectors, showing performance gains without sacrificing efficiency. Based on Vision Remember, LLaVA-VR with only 2B parameters is also superior to previous representative MLLMs such as Tokenpacker-HD-7B and DeepSeek-VL-7B.

Sen Yang, Feng Luo, Jun Zhang et al.

Mitotic count is the most important morphological feature of breast cancer grading. Many deep learning-based methods have been proposed but suffer from domain shift. In this work, we construct a Fourier-based segmentation model for mitosis detection to address the problem. Swapping the low-frequency spectrum of source and target images is shown effective to alleviate the discrepancy between different scanners. Our Fourier-based segmentation method can achieve F1 with 0.7456 on the preliminary test set.