arXiv subjects

Yuedong Yang

Publications and source records attributed to Yuedong Yang.

At least 19 recordsLinked to original sources

arXiv2026

Video Compression Meets Video Generation: Latent Inter-Frame Pruning with Attention Recovery

Current video generation models suffer from high computational latency, making real-time applications prohibitively costly. In this paper, we address this limitation by exploiting the temporal redundancy inherent in video latent patches. To this end, we propose the Latent Inter-frame Pruning with Attention Recovery (LIPAR) framework, which detects and skips recomputing duplicated latent patches. Additionally, we introduce a novel Attention Recovery mechanism that approximates the attention values of pruned tokens, thereby removing visual artifacts arising from naively applying the pruning method. Empirically, our method increases video editing throughput by $1.53\times$, achieving an average of 19.3 FPS on an NVIDIA RTX 4090 with the 1.3B Self-Forcing model (4-step denoising, FP16). The proposed method does not compromise generation quality and can be seamlessly integrated with the model without additional training. Our approach effectively bridges the gap between traditional compression algorithms and modern generative pipelines.

cs.CV↗

arXiv2026

Fuel Gauge: Estimating Chain-of-Thought Length Ahead of Time in Large Multimodal Models

Reasoning Large Multi-modality Models (LMMs) have become the de facto choice for many applications. However, these models rely on a Chain-of-Thought (CoT) process that is lengthy and unpredictable at runtime, often resulting in inefficient use of computational resources (due to memory fragmentation) and sub-optimal accuracy (due to under- and over-thinking). We observe empirically that the CoT process follows a very simple form, whose behavior is independent of the specific generated samples. This suggests that the CoT length can be estimated ahead of time based on a hidden parameter representing the amount of "fuel" available to support the reasoning process. Based on this insight, we propose Fuel Gauge, the first method which extracts this hidden signal and predicts CoT length ahead of time. We demonstrate the utility on the Fuel Gauge on two downstream tasks: predictive KV cache allocation, which addresses memory fragmentation in LMM serving systems, and CoT length modulation, which mitigates under-thinking and over-thinking. Extensive experiments on LMMs across text-only, image-text, and video-text question answering benchmarks demonstrate the effectiveness, generalizability, and practical value of our Fuel Gauge. For example, on the GPQA-Diamond benchmark, our Fuel Gauge achieves less than half the CoT length prediction error compared to the baseline; this translates into a 13.37x reduction in the memory allocation frequency.

cs.CV↗

arXiv2026

BindCLIP: A Unified Contrastive-Generative Representation Learning Framework for Virtual Screening

Virtual screening aims to efficiently identify active ligands from massive chemical libraries for a given target pocket. Recent CLIP-style models such as DrugCLIP enable scalable virtual screening by embedding pockets and ligands into a shared space. However, our analyses indicate that such representations can be insensitive to fine-grained binding interactions and may rely on shortcut correlations in training data, limiting their ability to rank ligands by true binding compatibility. To address these issues, we propose BindCLIP, a unified contrastive-generative representation learning framework for virtual screening. BindCLIP jointly trains pocket and ligand encoders using CLIP-style contrastive learning together with a pocket-conditioned diffusion objective for binding pose generation, so that pose-level supervision directly shapes the retrieval embedding space toward interaction-relevant features. To further mitigate shortcut reliance, we introduce hard-negative augmentation and a ligand-ligand anchoring regularizer that prevents representation collapse. Experiments on two public benchmarks demonstrate consistent improvements over strong baselines. BindCLIP achieves substantial gains on challenging out-of-distribution virtual screening and improves ligand-analogue ranking on the FEP+ benchmark. Together, these results indicate that integrating generative, pose-level supervision with contrastive learning yields more interaction-aware embeddings and improves generalization in realistic screening settings, bringing virtual screening closer to real-world applicability.

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arXiv2026

De Novo Molecular Generation from Mass Spectra via Many-Body Enhanced Diffusion

Molecular structure generation from mass spectrometry is fundamental for understanding cellular metabolism and discovering novel compounds. Although tandem mass spectrometry (MS/MS) enables the high-throughput acquisition of fragment fingerprints, these spectra often reflect higher-order interactions involving the concerted cleavage of multiple atoms and bonds-crucial for resolving complex isomers and non-local fragmentation mechanisms. However, most existing methods adopt atom-centric and pairwise interaction modeling, overlooking higher-order edge interactions and lacking the capacity to systematically capture essential many-body characteristics for structure generation. To overcome these limitations, we present MBGen, a Many-Body enhanced diffusion framework for de novo molecular structure Generation from mass spectra. By integrating a many-body attention mechanism and higher-order edge modeling, MBGen comprehensively leverages the rich structural information encoded in MS/MS spectra, enabling accurate de novo generation and isomer differentiation for novel molecules. Experimental results on the NPLIB1 and MassSpecGym benchmarks demonstrate that MBGen achieves superior performance, with improvements of up to 230% over state-of-the-art methods, highlighting the scientific value and practical utility of many-body modeling for mass spectrometry-based molecular generation. Further analysis and ablation studies show that our approach effectively captures higher-order interactions and exhibits enhanced sensitivity to complex isomeric and non-local fragmentation information.

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arXiv2025

A Novel Framework for Multi-Modal Protein Representation Learning

Accurate protein function prediction requires integrating heterogeneous intrinsic signals (e.g., sequence and structure) with noisy extrinsic contexts (e.g., protein-protein interactions and GO term annotations). However, two key challenges hinder effective fusion: (i) cross-modal distributional mismatch among embeddings produced by pre-trained intrinsic encoders, and (ii) noisy relational graphs of extrinsic data that degrade GNN-based information aggregation. We propose Diffused and Aligned Multi-modal Protein Embedding (DAMPE), a unified framework that addresses these through two core mechanisms. First, we propose Optimal Transport (OT)-based representation alignment that establishes correspondence between intrinsic embedding spaces of different modalities, effectively mitigating cross-modal heterogeneity. Second, we develop a Conditional Graph Generation (CGG)-based information fusion method, where a condition encoder fuses the aligned intrinsic embeddings to provide informative cues for graph reconstruction. Meanwhile, our theoretical analysis implies that the CGG objective drives this condition encoder to absorb graph-aware knowledge into its produced protein representations. Empirically, DAMPE outperforms or matches state-of-the-art methods such as DPFunc on standard GO benchmarks, achieving AUPR gains of 0.002-0.013 pp and Fmax gains 0.004-0.007 pp. Ablation studies further show that OT-based alignment contributes 0.043-0.064 pp AUPR, while CGG-based fusion adds 0.005-0.111 pp Fmax. Overall, DAMPE offers a scalable and theoretically grounded approach for robust multi-modal protein representation learning, substantially enhancing protein function prediction.

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arXiv2025

OIG-Bench: A Multi-Agent Annotated Benchmark for Multimodal One-Image Guides Understanding

Recent advances in Multimodal Large Language Models (MLLMs) have demonstrated impressive capabilities. However, evaluating their capacity for human-like understanding in One-Image Guides remains insufficiently explored. One-Image Guides are a visual format combining text, imagery, and symbols to present reorganized and structured information for easier comprehension, which are specifically designed for human viewing and inherently embody the characteristics of human perception and understanding. Here, we present OIG-Bench, a comprehensive benchmark focused on One-Image Guide understanding across diverse domains. To reduce the cost of manual annotation, we developed a semi-automated annotation pipeline in which multiple intelligent agents collaborate to generate preliminary image descriptions, assisting humans in constructing image-text pairs. With OIG-Bench, we have conducted a comprehensive evaluation of 29 state-of-the-art MLLMs, including both proprietary and open-source models. The results show that Qwen2.5-VL-72B performs the best among the evaluated models, with an overall accuracy of 77%. Nevertheless, all models exhibit notable weaknesses in semantic understanding and logical reasoning, indicating that current MLLMs still struggle to accurately interpret complex visual-text relationships. In addition, we also demonstrate that the proposed multi-agent annotation system outperforms all MLLMs in image captioning, highlighting its potential as both a high-quality image description generator and a valuable tool for future dataset construction. Datasets are available at https://github.com/XiejcSYSU/OIG-Bench.

cs.CV↗

arXiv2025

A 3D pocket-aware and affinity-guided diffusion model for lead optimization

Molecular optimization, aimed at improving binding affinity or other molecular properties, is a crucial task in drug discovery that often relies on the expertise of medicinal chemists. Recently, deep learning-based 3D generative models showed promise in enhancing the efficiency of molecular optimization. However, these models often struggle to adequately consider binding affinities with protein targets during lead optimization. Herein, we propose a 3D pocket-aware and affinity-guided diffusion model, named Diffleop, to optimize molecules with enhanced binding affinity. The model explicitly incorporates the knowledge of protein-ligand binding affinity to guide the denoising sampling for molecule generation with high affinity. The comprehensive evaluations indicated that Diffleop outperforms baseline models across multiple metrics, especially in terms of binding affinity.

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arXiv2025

Strategic priorities for transformative progress in advancing biology with proteomics and artificial intelligence

Artificial intelligence (AI) is transforming scientific research, including proteomics. Advances in mass spectrometry (MS)-based proteomics data quality, diversity, and scale, combined with groundbreaking AI techniques, are unlocking new challenges and opportunities in biological discovery. Here, we highlight key areas where AI is driving innovation, from data analysis to new biological insights. These include developing an AI-friendly ecosystem for proteomics data generation, sharing, and analysis; improving peptide and protein identification and quantification; characterizing protein-protein interactions and protein complexes; advancing spatial and perturbation proteomics; integrating multi-omics data; and ultimately enabling AI-empowered virtual cells.

q-bio.OT↗

arXiv2024

Incorporating Retrieval-based Causal Learning with Information Bottlenecks for Interpretable Graph Neural Networks

Graph Neural Networks (GNNs) have gained considerable traction for their capability to effectively process topological data, yet their interpretability remains a critical concern. Current interpretation methods are dominated by post-hoc explanations to provide a transparent and intuitive understanding of GNNs. However, they have limited performance in interpreting complicated subgraphs and can't utilize the explanation to advance GNN predictions. On the other hand, transparent GNN models are proposed to capture critical subgraphs. While such methods could improve GNN predictions, they usually don't perform well on explanations. Thus, it is desired for a new strategy to better couple GNN explanation and prediction. In this study, we have developed a novel interpretable causal GNN framework that incorporates retrieval-based causal learning with Graph Information Bottleneck (GIB) theory. The framework could semi-parametrically retrieve crucial subgraphs detected by GIB and compress the explanatory subgraphs via a causal module. The framework was demonstrated to consistently outperform state-of-the-art methods, and to achieve 32.71\% higher precision on real-world explanation scenarios with diverse explanation types. More importantly, the learned explanations were shown able to also improve GNN prediction performance.

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arXiv2023

EC-Conf: An Ultra-fast Diffusion Model for Molecular Conformation Generation with Equivariant Consistency

Despite recent advancement in 3D molecule conformation generation driven by diffusion models, its high computational cost in iterative diffusion/denoising process limits its application. In this paper, an equivariant consistency model (EC-Conf) was proposed as a fast diffusion method for low-energy conformation generation. In EC-Conf, a modified SE (3)-equivariant transformer model was directly used to encode the Cartesian molecular conformations and a highly efficient consistency diffusion process was carried out to generate molecular conformations. It was demonstrated that, with only one sampling step, it can already achieve comparable quality to other diffusion-based models running with thousands denoising steps. Its performance can be further improved with a few more sampling iterations. The performance of EC-Conf is evaluated on both GEOM-QM9 and GEOM-Drugs sets. Our results demonstrate that the efficiency of EC-Conf for learning the distribution of low energy molecular conformation is at least two magnitudes higher than current SOTA diffusion models and could potentially become a useful tool for conformation generation and sampling. We release our code at https://github.com/zhi520/EcConf.

q-bio.BM↗

arXiv2023

Node-based Knowledge Graph Contrastive Learning for Medical Relationship Prediction

The embedding of Biomedical Knowledge Graphs (BKGs) generates robust representations, valuable for a variety of artificial intelligence applications, including predicting drug combinations and reasoning disease-drug relationships. Meanwhile, contrastive learning (CL) is widely employed to enhance the distinctiveness of these representations. However, constructing suitable contrastive pairs for CL, especially within Knowledge Graphs (KGs), has been challenging. In this paper, we proposed a novel node-based contrastive learning method for knowledge graph embedding, NC-KGE. NC-KGE enhances knowledge extraction in embeddings and speeds up training convergence by constructing appropriate contrastive node pairs on KGs. This scheme can be easily integrated with other knowledge graph embedding (KGE) methods. For downstream task such as biochemical relationship prediction, we have incorporated a relation-aware attention mechanism into NC-KGE, focusing on the semantic relationships and node interactions. Extensive experiments show that NC-KGE performs competitively with state-of-the-art models on public datasets like FB15k-237 and WN18RR. Particularly in biomedical relationship prediction tasks, NC-KGE outperforms all baselines on datasets such as PharmKG8k-28, DRKG17k-21, and BioKG72k-14, especially in predicting drug combination relationships. We release our code at https://github.com/zhi520/NC-KGE.

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arXiv2023

Efficient Low-rank Backpropagation for Vision Transformer Adaptation

The increasing scale of vision transformers (ViT) has made the efficient fine-tuning of these large models for specific needs a significant challenge in various applications. This issue originates from the computationally demanding matrix multiplications required during the backpropagation process through linear layers in ViT. In this paper, we tackle this problem by proposing a new Low-rank BackPropagation via Walsh-Hadamard Transformation (LBP-WHT) method. Intuitively, LBP-WHT projects the gradient into a low-rank space and carries out backpropagation. This approach substantially reduces the computation needed for adapting ViT, as matrix multiplication in the low-rank space is far less resource-intensive. We conduct extensive experiments with different models (ViT, hybrid convolution-ViT model) on multiple datasets to demonstrate the effectiveness of our method. For instance, when adapting an EfficientFormer-L1 model on CIFAR100, our LBP-WHT achieves 10.4% higher accuracy than the state-of-the-art baseline, while requiring 9 MFLOPs less computation. As the first work to accelerate ViT adaptation with low-rank backpropagation, our LBP-WHT method is complementary to many prior efforts and can be combined with them for better performance.

cs.CV↗

arXiv2023

Retrieval-based Knowledge Augmented Vision Language Pre-training

With the recent progress in large-scale vision and language representation learning, Vision Language Pre-training (VLP) models have achieved promising improvements on various multi-modal downstream tasks. Albeit powerful, these models have not fully leveraged world knowledge to their advantage. A key challenge of knowledge-augmented VLP is the lack of clear connections between knowledge and multi-modal data. Moreover, not all knowledge present in images/texts is useful, therefore prior approaches often struggle to effectively integrate knowledge, visual, and textual information. In this study, we propose REtrieval-based knowledge Augmented Vision Language (REAVL), a novel knowledge-augmented pre-training framework to address the above issues. For the first time, we introduce a knowledge-aware self-supervised learning scheme that efficiently establishes the correspondence between knowledge and multi-modal data and identifies informative knowledge to improve the modeling of alignment and interactions between visual and textual modalities. By adaptively integrating informative knowledge with visual and textual information, REAVL achieves new state-of-the-art performance uniformly on knowledge-based vision-language understanding and multi-modal entity linking tasks, as well as competitive results on general vision-language tasks while only using 0.2% pre-training data of the best models. Our model shows strong sample efficiency and effective knowledge utilization.

cs.CV↗

arXiv2023

TIPS: Topologically Important Path Sampling for Anytime Neural Networks

Anytime neural networks (AnytimeNNs) are a promising solution to adaptively adjust the model complexity at runtime under various hardware resource constraints. However, the manually-designed AnytimeNNs are biased by designers' prior experience and thus provide sub-optimal solutions. To address the limitations of existing hand-crafted approaches, we first model the training process of AnytimeNNs as a discrete-time Markov chain (DTMC) and use it to identify the paths that contribute the most to the training of AnytimeNNs. Based on this new DTMC-based analysis, we further propose TIPS, a framework to automatically design AnytimeNNs under various hardware constraints. Our experimental results show that TIPS can improve the convergence rate and test accuracy of AnytimeNNs. Compared to the existing AnytimeNNs approaches, TIPS improves the accuracy by 2%-6.6% on multiple datasets and achieves SOTA accuracy-FLOPs tradeoffs.

cs.LG↗

arXiv2023

ZiCo: Zero-shot NAS via Inverse Coefficient of Variation on Gradients

Neural Architecture Search (NAS) is widely used to automatically obtain the neural network with the best performance among a large number of candidate architectures. To reduce the search time, zero-shot NAS aims at designing training-free proxies that can predict the test performance of a given architecture. However, as shown recently, none of the zero-shot proxies proposed to date can actually work consistently better than a naive proxy, namely, the number of network parameters (#Params). To improve this state of affairs, as the main theoretical contribution, we first reveal how some specific gradient properties across different samples impact the convergence rate and generalization capacity of neural networks. Based on this theoretical analysis, we propose a new zero-shot proxy, ZiCo, the first proxy that works consistently better than #Params. We demonstrate that ZiCo works better than State-Of-The-Art (SOTA) proxies on several popular NAS-Benchmarks (NASBench101, NATSBench-SSS/TSS, TransNASBench-101) for multiple applications (e.g., image classification/reconstruction and pixel-level prediction). Finally, we demonstrate that the optimal architectures found via ZiCo are as competitive as the ones found by one-shot and multi-shot NAS methods, but with much less search time. For example, ZiCo-based NAS can find optimal architectures with 78.1%, 79.4%, and 80.4% test accuracy under inference budgets of 450M, 600M, and 1000M FLOPs, respectively, on ImageNet within 0.4 GPU days. Our code is available at https://github.com/SLDGroup/ZiCo.

cs.LG↗

arXiv2023

Efficient On-device Training via Gradient Filtering

Despite its importance for federated learning, continuous learning and many other applications, on-device training remains an open problem for EdgeAI. The problem stems from the large number of operations (e.g., floating point multiplications and additions) and memory consumption required during training by the back-propagation algorithm. Consequently, in this paper, we propose a new gradient filtering approach which enables on-device CNN model training. More precisely, our approach creates a special structure with fewer unique elements in the gradient map, thus significantly reducing the computational complexity and memory consumption of back propagation during training. Extensive experiments on image classification and semantic segmentation with multiple CNN models (e.g., MobileNet, DeepLabV3, UPerNet) and devices (e.g., Raspberry Pi and Jetson Nano) demonstrate the effectiveness and wide applicability of our approach. For example, compared to SOTA, we achieve up to 19$\times$ speedup and 77.1% memory savings on ImageNet classification with only 0.1% accuracy loss. Finally, our method is easy to implement and deploy; over 20$\times$ speedup and 90% energy savings have been observed compared to highly optimized baselines in MKLDNN and CUDNN on NVIDIA Jetson Nano. Consequently, our approach opens up a new direction of research with a huge potential for on-device training.

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arXiv2022

Communicative Subgraph Representation Learning for Multi-Relational Inductive Drug-Gene Interaction Prediction

Illuminating the interconnections between drugs and genes is an important topic in drug development and precision medicine. Currently, computational predictions of drug-gene interactions mainly focus on the binding interactions without considering other relation types like agonist, antagonist, etc. In addition, existing methods either heavily rely on high-quality domain features or are intrinsically transductive, which limits the capacity of models to generalize to drugs/genes that lack external information or are unseen during the training process. To address these problems, we propose a novel Communicative Subgraph representation learning for Multi-relational Inductive drug-Gene interactions prediction (CoSMIG), where the predictions of drug-gene relations are made through subgraph patterns, and thus are naturally inductive for unseen drugs/genes without retraining or utilizing external domain features. Moreover, the model strengthened the relations on the drug-gene graph through a communicative message passing mechanism. To evaluate our method, we compiled two new benchmark datasets from DrugBank and DGIdb. The comprehensive experiments on the two datasets showed that our method outperformed state-of-the-art baselines in the transductive scenarios and achieved superior performance in the inductive ones. Further experimental analysis including LINCS experimental validation and literature verification also demonstrated the value of our model.

cs.LG↗

arXiv2022

SUGAR: Efficient Subgraph-level Training via Resource-aware Graph Partitioning

Graph Neural Networks (GNNs) have demonstrated a great potential in a variety of graph-based applications, such as recommender systems, drug discovery, and object recognition. Nevertheless, resource-efficient GNN learning is a rarely explored topic despite its many benefits for edge computing and Internet of Things (IoT) applications. To improve this state of affairs, this work proposes efficient subgraph-level training via resource-aware graph partitioning (SUGAR). SUGAR first partitions the initial graph into a set of disjoint subgraphs and then performs local training at the subgraph-level. We provide a theoretical analysis and conduct extensive experiments on five graph benchmarks to verify its efficacy in practice. Our results show that SUGAR can achieve up to 33 times runtime speedup and 3.8 times memory reduction on large-scale graphs. We believe SUGAR opens a new research direction towards developing GNN methods that are resource-efficient, hence suitable for IoT deployment.

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