Xiantao Cai

Qiwei Li, Zuchao Li, Xiantao Cai et al.

In recent years, the use of multi-modal pre-trained Transformers has led to significant advancements in visually-rich document understanding. However, existing models have mainly focused on features such as text and vision while neglecting the importance of layout relationship between text nodes. In this paper, we propose GraphLayoutLM, a novel document understanding model that leverages the modeling of layout structure graph to inject document layout knowledge into the model. GraphLayoutLM utilizes a graph reordering algorithm to adjust the text sequence based on the graph structure. Additionally, our model uses a layout-aware multi-head self-attention layer to learn document layout knowledge. The proposed model enables the understanding of the spatial arrangement of text elements, improving document comprehension. We evaluate our model on various benchmarks, including FUNSD, XFUND and CORD, and achieve state-of-the-art results among these datasets. Our experimental results demonstrate that our proposed method provides a significant improvement over existing approaches and showcases the importance of incorporating layout information into document understanding models. We also conduct an ablation study to investigate the contribution of each component of our model. The results show that both the graph reordering algorithm and the layout-aware multi-head self-attention layer play a crucial role in achieving the best performance.

Kun Li, Xiantao Cai, Jia Wu et al.

Molecular optimization is a crucial aspect of drug discovery, aimed at refining molecular structures to enhance drug efficacy and minimize side effects, ultimately accelerating the overall drug development process. Many molecular optimization methods have been proposed, significantly advancing drug discovery. These methods primarily on understanding the specific drug target structures or their hypothesized roles in combating diseases. However, challenges such as a limited number of available targets and a difficulty capturing clear structures hinder innovative drug development. In contrast, phenotypic drug discovery (PDD) does not depend on clear target structures and can identify hits with novel and unbiased polypharmacology signatures. As a result, PDD-based molecular optimization can reduce potential safety risks while optimizing phenotypic activity, thereby increasing the likelihood of clinical success. Therefore, we propose a fragment-masked molecular optimization method based on PDD (FMOP). FMOP employs a regression-free diffusion model to conditionally optimize the molecular masked regions, effectively generating new molecules with similar scaffolds. On the large-scale drug response dataset GDSCv2, we optimize the potential molecules across all 985 cell lines. The overall experiments demonstrate that the in-silico optimization success rate reaches 95.4\%, with an average efficacy increase of 7.5\%. Additionally, we conduct extensive ablation and visualization experiments, confirming that FMOP is an effective and robust molecular optimization method. The code is available at: https://anonymous.4open.science/r/FMOP-98C2.

Kun Li, Yong Luo, Xiantao Cai et al.

Conventional deep learning methods typically employ supervised learning for drug response prediction (DRP). This entails dependence on labeled response data from drugs for model training. However, practical applications in the preclinical drug screening phase demand that DRP models predict responses for novel compounds, often with unknown drug responses. This presents a challenge, rendering supervised deep learning methods unsuitable for such scenarios. In this paper, we propose a zero-shot learning solution for the DRP task in preclinical drug screening. Specifically, we propose a Multi-branch Multi-Source Domain Adaptation Test Enhancement Plug-in, called MSDA. MSDA can be seamlessly integrated with conventional DRP methods, learning invariant features from the prior response data of similar drugs to enhance real-time predictions of unlabeled compounds. We conducted experiments using the GDSCv2 and CellMiner datasets. The results demonstrate that MSDA efficiently predicts drug responses for novel compounds, leading to a general performance improvement of 5-10\% in the preclinical drug screening phase. The significance of this solution resides in its potential to accelerate the drug discovery process, improve drug candidate assessment, and facilitate the success of drug discovery.

Haibin He, Maoyuan Ye, Jing Zhang et al.

Large Multimodal Models (LMMs) have become increasingly versatile, accompanied by impressive Optical Character Recognition (OCR) related capabilities. Existing OCR-related benchmarks emphasize evaluating LMMs' abilities of relatively simple visual question answering, visual-text parsing, etc. However, the extent to which LMMs can deal with complex logical reasoning problems based on OCR cues is relatively unexplored. To this end, we introduce the Reasoning-OCR benchmark, which challenges LMMs to solve complex reasoning problems based on the cues that can be extracted from rich visual-text. Reasoning-OCR covers six visual scenarios and encompasses 150 meticulously designed questions categorized into six reasoning challenges. Additionally, Reasoning-OCR minimizes the impact of field-specialized knowledge. Our evaluation offers some insights for proprietary and open-source LMMs in different reasoning challenges, underscoring the urgent to improve the reasoning performance. We hope Reasoning-OCR can inspire and facilitate future research on enhancing complex reasoning ability based on OCR cues. Reasoning-OCR is publicly available at https://github.com/Hxyz-123/ReasoningOCR.

Kun Li, Longtao Hu, Xiantao Cai et al.

Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through transformations such as adding, deleting, and modifying atoms and chemical bonds, reflecting specific evolutionary paths. Existing molecular representation methods mainly focus on mining data, such as atomic-level structures and chemical bonds directly from the molecules, often overlooking their evolutionary history. Consequently, we aim to explore the possibility of enhancing molecular representations by simulating the evolutionary process. We extract and analyze the changes in the evolutionary pathway and explore combining it with existing molecular representations. Therefore, this paper proposes the molecular evolutionary network (MEvoN) for molecular representations. First, we construct the MEvoN using molecules with a small number of atoms and generate evolutionary paths utilizing similarity calculations. Then, by modeling the atomic-level changes, MEvoN reveals their impact on molecular properties. Experimental results show that the MEvoN-based molecular property prediction method significantly improves the performance of traditional end-to-end algorithms on several molecular datasets. The code is available at https://anonymous.4open.science/r/MEvoN-7416/.

Jiameng Chen, Xiantao Cai, Jia Wu et al.

Antibody design remains a critical challenge in therapeutic and diagnostic development, particularly for complex antigens with diverse binding interfaces. Current computational methods face two main limitations: (1) capturing geometric features while preserving symmetries, and (2) generalizing novel antigen interfaces. Despite recent advancements, these methods often fail to accurately capture molecular interactions and maintain structural integrity. To address these challenges, we propose \textbf{AbMEGD}, an end-to-end framework integrating \textbf{M}ulti-scale \textbf{E}quivariant \textbf{G}raph \textbf{D}iffusion for antibody sequence and structure co-design. Leveraging advanced geometric deep learning, AbMEGD combines atomic-level geometric features with residue-level embeddings, capturing local atomic details and global sequence-structure interactions. Its E(3)-equivariant diffusion method ensures geometric precision, computational efficiency, and robust generalizability for complex antigens. Furthermore, experiments using the SAbDab database demonstrate a 10.13\% increase in amino acid recovery, 3.32\% rise in improvement percentage, and a 0.062~Å reduction in root mean square deviation within the critical CDR-H3 region compared to DiffAb, a leading antibody design model. These results highlight AbMEGD's ability to balance structural integrity with improved functionality, establishing a new benchmark for sequence-structure co-design and affinity optimization. The code is available at: https://github.com/Patrick221215/AbMEGD.

Jiameng Chen, Yida Xiong, Kun Li et al.

Computational antibody design holds immense promise for therapeutic discovery, yet existing generative models are fundamentally limited by two core challenges: (i) a lack of dynamical consistency, which yields physically implausible structures, and (ii) poor generalization due to data scarcity and structural bias. We introduce FP-AbDiff, the first antibody generator to enforce Fokker-Planck Equation (FPE) physics along the entire generative trajectory. Our method minimizes a novel FPE residual loss over the mixed manifold of CDR geometries (R^3 x SO(3)), compelling locally-learned denoising scores to assemble into a globally coherent probability flow. This physics-informed regularizer is synergistically integrated with deep biological priors within a state-of-the-art SE(3)-equivariant diffusion framework. Rigorous evaluation on the RAbD benchmark confirms that FP-AbDiff establishes a new state-of-the-art. In de novo CDR-H3 design, it achieves a mean Root Mean Square Deviation of 0.99 Å when superposing on the variable region, a 25% improvement over the previous state-of-the-art model, AbX, and the highest reported Contact Amino Acid Recovery of 39.91%. This superiority is underscored in the more challenging six-CDR co-design task, where our model delivers consistently superior geometric precision, cutting the average full-chain Root Mean Square Deviation by ~15%, and crucially, achieves the highest full-chain Amino Acid Recovery on the functionally dominant CDR-H3 loop (45.67%). By aligning generative dynamics with physical laws, FP-AbDiff enhances robustness and generalizability, establishing a principled approach for physically faithful and functionally viable antibody design.

Kun Li, Longtao Hu, Yida Xiong et al.

Molecular representation learning aims to learn vector embeddings that capture molecular structure and geometry, thereby enabling property prediction and downstream scientific applications. In many AI for science tasks, labeled data are expensive to obtain and therefore limited in availability. Under the few-shot setting, models trained with scarce supervision often learn brittle structure-property relationships, resulting in substantially higher prediction errors and reduced generalization to unseen molecules. To address this limitation, we propose PCEvo, a path-consistent representation method that learns from virtual paths through dynamic structural evolution. PCEvo enumerates multiple chemically feasible edit paths between retrieved similar molecular pairs under topological dependency constraints. It transforms the labels of the two molecules into stepwise supervision along each virtual evolutionary path. It introduces a path-consistency objective that enforces prediction invariance across alternative paths connecting the same two molecules. Comprehensive experiments on the QM9 and MoleculeNet datasets demonstrate that PCEvo substantially improves the few-shot generalization performance of baseline methods. The code is available at https://anonymous.4open.science/r/PCEvo-4BF2.

Siyuan Fan, Bo Du, Xiantao Cai et al.

In this work, we propose TextIM, a novel framework for synthesizing TEXT-driven human Interactive Motions, with a focus on the precise alignment of part-level semantics. Existing methods often overlook the critical roles of interactive body parts and fail to adequately capture and align part-level semantics, resulting in inaccuracies and even erroneous movement outcomes. To address these issues, TextIM utilizes a decoupled conditional diffusion framework to enhance the detailed alignment between interactive movements and corresponding semantic intents from textual descriptions. Our approach leverages large language models, functioning as a human brain, to identify interacting human body parts and to comprehend interaction semantics to generate complicated and subtle interactive motion. Guided by the refined movements of the interacting parts, TextIM further extends these movements into a coherent whole-body motion. We design a spatial coherence module to complement the entire body movements while maintaining consistency and harmony across body parts using a part graph convolutional network. For training and evaluation, we carefully selected and re-labeled interactive motions from HUMANML3D to develop a specialized dataset. Experimental results demonstrate that TextIM produces semantically accurate human interactive motions, significantly enhancing the realism and applicability of synthesized interactive motions in diverse scenarios, even including interactions with deformable and dynamically changing objects.

Liqi He, Zuchao Li, Xiantao Cai et al.

Chain-of-thought (CoT) reasoning has exhibited impressive performance in language models for solving complex tasks and answering questions. However, many real-world questions require multi-modal information, such as text and images. Previous research on multi-modal CoT has primarily focused on extracting fixed image features from off-the-shelf vision models and then fusing them with text using attention mechanisms. This approach has limitations because these vision models were not designed for complex reasoning tasks and do not align well with language thoughts. To overcome this limitation, we introduce a novel approach for multi-modal CoT reasoning that utilizes latent space learning via diffusion processes to generate effective image features that align with language thoughts. Our method fuses image features and text representations at a deep level and improves the complex reasoning ability of multi-modal CoT. We demonstrate the efficacy of our proposed method on multi-modal ScienceQA and machine translation benchmarks, achieving state-of-the-art performance on ScienceQA. Overall, our approach offers a more robust and effective solution for multi-modal reasoning in language models, enhancing their ability to tackle complex real-world problems.

Xuxu Liu, Siyuan Liang, Mengya Han et al.

Generative large language models are crucial in natural language processing, but they are vulnerable to backdoor attacks, where subtle triggers compromise their behavior. Although backdoor attacks against LLMs are constantly emerging, existing benchmarks remain limited in terms of sufficient coverage of attack, metric system integrity, backdoor attack alignment. And existing pre-trained backdoor attacks are idealized in practice due to resource access constraints. Therefore we establish $\textit{ELBA-Bench}$, a comprehensive and unified framework that allows attackers to inject backdoor through parameter efficient fine-tuning ($\textit{e.g.,}$ LoRA) or without fine-tuning techniques ($\textit{e.g.,}$ In-context-learning). $\textit{ELBA-Bench}$ provides over 1300 experiments encompassing the implementations of 12 attack methods, 18 datasets, and 12 LLMs. Extensive experiments provide new invaluable findings into the strengths and limitations of various attack strategies. For instance, PEFT attack consistently outperform without fine-tuning approaches in classification tasks while showing strong cross-dataset generalization with optimized triggers boosting robustness; Task-relevant backdoor optimization techniques or attack prompts along with clean and adversarial demonstrations can enhance backdoor attack success while preserving model performance on clean samples. Additionally, we introduce a universal toolbox designed for standardized backdoor attack research, with the goal of propelling further progress in this vital area.

Qihuang Zhong, Liang Ding, Xiantao Cai et al.

Supervised fine-tuning (SFT) is a common approach to improve the domain-specific question-answering (QA) performance of large language models (LLMs). However, recent literature reveals that due to the conflicts between LLMs' internal knowledge and the context knowledge of training data, vanilla SFT using the full QA training set is usually suboptimal. In this paper, we first design a query diversification strategy for robust conflict detection and then conduct a series of experiments to analyze the impact of knowledge conflict. We find that 1) training samples with varied conflicts contribute differently, where SFT on the data with large conflicts leads to catastrophic performance drops; 2) compared to directly filtering out the conflict data, appropriately applying the conflict data would be more beneficial. Motivated by this, we propose a simple-yet-effective Knowledge-aware Fine-tuning (namely KaFT) approach to effectively boost LLMs' performance. The core of KaFT is to adapt the training weight by assigning different rewards for different training samples according to conflict level. Extensive experiments show that KaFT brings consistent and significant improvements across four LLMs. More analyses prove that KaFT effectively improves the model generalization and alleviates the hallucination.

Siyuan Fan, Wenke Huang, Xiantao Cai et al.

3D human interaction generation has emerged as a key research area, focusing on producing dynamic and contextually relevant interactions between humans and various interactive entities. Recent rapid advancements in 3D model representation methods, motion capture technologies, and generative models have laid a solid foundation for the growing interest in this domain. Existing research in this field can be broadly categorized into three areas: human-scene interaction, human-object interaction, and human-human interaction. Despite the rapid advancements in this area, challenges remain due to the need for naturalness in human motion generation and the accurate interaction between humans and interactive entities. In this survey, we present a comprehensive literature review of human interaction generation, which, to the best of our knowledge, is the first of its kind. We begin by introducing the foundational technologies, including model representations, motion capture methods, and generative models. Subsequently, we introduce the approaches proposed for the three sub-tasks, along with their corresponding datasets and evaluation metrics. Finally, we discuss potential future research directions in this area and conclude the survey. Through this survey, we aim to offer a comprehensive overview of the current advancements in the field, highlight key challenges, and inspire future research works.

Yida Xiong, Jiameng Chen, Kun Li et al.

Molecular graph generation is essentially a classification generation problem, aimed at predicting categories of atoms and bonds. Currently, prevailing paradigms such as continuous diffusion models are trained to predict continuous numerical values, treating the training process as a regression task. However, the final generation necessitates a rounding step to convert these predictions back into discrete classification categories, which is intrinsically a classification operation. Given that the rounding operation is not incorporated during training, there exists a significant discrepancy between the model's training objective and its inference procedure. As a consequence, an excessive emphasis on point-wise precision can lead to overfitting and inefficient learning. This occurs because considerable efforts are devoted to capturing intra-bin variations that are ultimately irrelevant to the discrete nature of the task at hand. Such a flaw results in diminished molecular diversity and constrains the model's generalization capabilities. To address this fundamental limitation, we propose GraphBFN, a novel hierarchical coarse-to-fine framework based on Bayesian Flow Networks that operates on the parameters of distributions. By innovatively introducing Cumulative Distribution Function, GraphBFN is capable of calculating the probability of selecting the correct category, thereby unifying the training objective with the sampling rounding operation. We demonstrate that our method achieves superior performance and faster generation, setting new state-of-the-art results on the QM9 and ZINC250k molecular graph generation benchmarks.

Kun Li, Yida Xiong, Hongzhi Zhang et al.

Due to their excellent drug-like and pharmacokinetic properties, small molecule drugs are widely used to treat various diseases, making them a critical component of drug discovery. In recent years, with the rapid development of deep learning (DL) techniques, DL-based small molecule drug discovery methods have achieved excellent performance in prediction accuracy, speed, and complex molecular relationship modeling compared to traditional machine learning approaches. These advancements enhance drug screening efficiency and optimization and provide more precise and effective solutions for various drug discovery tasks. Contributing to this field's development, this paper aims to systematically summarize and generalize the recent key tasks and representative techniques in graph-structured small molecule drug discovery in recent years. Specifically, we provide an overview of the major tasks in small molecule drug discovery and their interrelationships. Next, we analyze the six core tasks, summarizing the related methods, commonly used datasets, and technological development trends. Finally, we discuss key challenges, such as interpretability and out-of-distribution generalization, and offer our insights into future research directions for small molecule drug discovery.

Zelin Yao, Chuang Liu, Xueqi Ma et al.

Graph contrastive learning (GCL) is a popular method for leaning graph representations by maximizing the consistency of features across augmented views. Traditional GCL methods utilize single-perspective i.e. data or model-perspective) augmentation to generate positive samples, restraining the diversity of positive samples. In addition, these positive samples may be unreliable due to uncontrollable augmentation strategies that potentially alter the semantic information. To address these challenges, this paper proposed a innovative framework termed dual-perspective cross graph contrastive learning (DC-GCL), which incorporates three modifications designed to enhance positive sample diversity and reliability: 1) We propose dual-perspective augmentation strategy that provide the model with more diverse training data, enabling the model effective learning of feature consistency across different views. 2) From the data perspective, we slightly perturb the original graphs using controllable data augmentation, effectively preserving their semantic information. 3) From the model perspective, we enhance the encoder by utilizing more powerful graph transformers instead of graph neural networks. Based on the model's architecture, we propose three pruning-based strategies to slightly perturb the encoder, providing more reliable positive samples. These modifications collectively form the DC-GCL's foundation and provide more diverse and reliable training inputs, offering significant improvements over traditional GCL methods. Extensive experiments on various benchmarks demonstrate that DC-GCL consistently outperforms different baselines on various datasets and tasks.