Yijia Zhang

Meng Zhang, Jinzhong Ning, Xiaolong Wu et al.

Grounded Multimodal Named Entity Recognition (GMNER) aims to jointly identify named entity mentions in text, predict their semantic types, and ground each entity to a corresponding visual region in an associated image. Existing approaches predominantly adopt pipeline-based architectures that decouple textual entity recognition and visual grounding, leading to error accumulation and suboptimal joint optimization. In this paper, we propose E2E-GMNER, a fully end-to-end generative framework that unifies entity recognition, semantic typing, visual grounding, and implicit knowledge reasoning within a single multimodal large language model. We formulate GMNER as an instruction-tuned conditional generation task and incorporate chain-of-thought reasoning to enable the model to adaptively determine when visual evidence or background knowledge is informative, reducing reliance on noisy cues. To further address the instability of generative bounding box prediction, we introduce Gaussian Risk-Aware Box Perturbation (GRBP), which replaces hard box supervision with probabilistically perturbed soft targets to improve robustness against annotation noise and discretization errors. Extensive experiments on the Twitter-GMNER and Twitter-FMNERG benchmarks demonstrate that E2E-GMNER achieves highly competitive performance compared with state of the art methods, validating the effectiveness of unified end-to-end optimization and noise-aware grounding supervision. Code is available at:https://github.com/Finch-coder/E2E-GMNER

Yijia Zhang, Sicheng Zhang, Shijie Cao et al.

Large language models (LLMs) show great performance in various tasks, but face deployment challenges from limited memory capacity and bandwidth. Low-bit weight quantization can save memory and accelerate inference. Although floating-point (FP) formats show good performance in LLM quantization, they tend to perform poorly with small group sizes or sub-4 bits. We find the reason is that the absence of asymmetry in previous FP quantization makes it unsuitable for handling asymmetric value distribution of LLM weight tensors. In this work, we propose asymmetric FP quantization (AFPQ), which sets separate scales for positive and negative values. Our method leads to large accuracy improvements and can be easily plugged into other quantization methods, including GPTQ and AWQ, for better performance. Besides, no additional storage is needed compared with asymmetric integer (INT) quantization. The code is available at https://github.com/zhangsichengsjtu/AFPQ.

Hui Ma, Jian Wang, Hongfei Lin et al.

Emotion recognition in conversations (ERC), the task of recognizing the emotion of each utterance in a conversation, is crucial for building empathetic machines. Existing studies focus mainly on capturing context- and speaker-sensitive dependencies on the textual modality but ignore the significance of multimodal information. Different from emotion recognition in textual conversations, capturing intra- and inter-modal interactions between utterances, learning weights between different modalities, and enhancing modal representations play important roles in multimodal ERC. In this paper, we propose a transformer-based model with self-distillation (SDT) for the task. The transformer-based model captures intra- and inter-modal interactions by utilizing intra- and inter-modal transformers, and learns weights between modalities dynamically by designing a hierarchical gated fusion strategy. Furthermore, to learn more expressive modal representations, we treat soft labels of the proposed model as extra training supervision. Specifically, we introduce self-distillation to transfer knowledge of hard and soft labels from the proposed model to each modality. Experiments on IEMOCAP and MELD datasets demonstrate that SDT outperforms previous state-of-the-art baselines.

Jinfeng Zhou, Zhuang Chen, Dazhen Wan et al.

In this paper, we present CharacterGLM, a series of models built upon ChatGLM, with model sizes ranging from 6B to 66B parameters. Our CharacterGLM is designed for generating Character-based Dialogues (CharacterDial), which aims to equip a conversational AI system with character customization for satisfying people's inherent social desires and emotional needs. On top of CharacterGLM, we can customize various AI characters or social agents by configuring their attributes (identities, interests, viewpoints, experiences, achievements, social relationships, etc.) and behaviors (linguistic features, emotional expressions, interaction patterns, etc.). Our model outperforms most mainstream close-source large langauge models, including the GPT series, especially in terms of consistency, human-likeness, and engagement according to manual evaluations. We will release our 6B version of CharacterGLM and a subset of training data to facilitate further research development in the direction of character-based dialogue generation.

Xiaosong Yuan, Ke Chen, Wanli Zuo et al.

The present study explores the intricacies of causal relationship extraction, a vital component in the pursuit of causality knowledge. Causality is frequently intertwined with temporal elements, as the progression from cause to effect is not instantaneous but rather ensconced in a temporal dimension. Thus, the extraction of temporal causality holds paramount significance in the field. In light of this, we propose a method for extracting causality from the text that integrates both temporal and causal relations, with a particular focus on the time aspect. To this end, we first compile a dataset that encompasses temporal relationships. Subsequently, we present a novel model, TC-GAT, which employs a graph attention mechanism to assign weights to the temporal relationships and leverages a causal knowledge graph to determine the adjacency matrix. Additionally, we implement an equilibrium mechanism to regulate the interplay between temporal and causal relations. Our experiments demonstrate that our proposed method significantly surpasses baseline models in the task of causality extraction.

Dayou Du, Yijia Zhang, Shijie Cao et al.

The upscaling of Large Language Models (LLMs) has yielded impressive advances in natural language processing, yet it also poses significant deployment challenges. Weight quantization has emerged as a widely embraced solution to reduce memory and computational demands. This paper introduces BitDistiller, a framework that synergizes Quantization-Aware Training (QAT) with Knowledge Distillation (KD) to boost the performance of LLMs at ultra-low precisions (sub-4-bit). Specifically, BitDistiller first incorporates a tailored asymmetric quantization and clipping technique to maximally preserve the fidelity of quantized weights, and then proposes a novel Confidence-Aware Kullback-Leibler Divergence (CAKLD) objective, which is employed in a self-distillation manner to enable faster convergence and superior model performance. Empirical evaluations demonstrate that BitDistiller significantly surpasses existing methods in both 3-bit and 2-bit configurations on general language understanding and complex reasoning benchmarks. Notably, BitDistiller is shown to be more cost-effective, demanding fewer data and training resources. The code is available at https://github.com/DD-DuDa/BitDistiller.

Xinheng He, Yijia Zhang, Haowei Lin et al.

Structure-based drug design has seen significant advancements with the integration of artificial intelligence (AI), particularly in the generation of hit and lead compounds. However, most AI-driven approaches neglect the importance of endogenous protein interactions with peptides, which may result in suboptimal molecule designs. In this work, we present Peptide2Mol, an E(3)-equivariant graph neural network diffusion model that generates small molecules by referencing both the original peptide binders and their surrounding protein pocket environments. Trained on large datasets and leveraging sophisticated modeling techniques, Peptide2Mol not only achieves state-of-the-art performance in non-autoregressive generative tasks, but also produces molecules with similarity to the original peptide binder. Additionally, the model allows for molecule optimization and peptidomimetic design through a partial diffusion process. Our results highlight Peptide2Mol as an effective deep generative model for generating and optimizing bioactive small molecules from protein binding pockets.

Rui Shi, Xiaodong Yu, Shengming Wang et al.

In this paper, we propose RFUAV as a new benchmark dataset for radio-frequency based (RF-based) unmanned aerial vehicle (UAV) identification and address the following challenges: Firstly, many existing datasets feature a restricted variety of drone types and insufficient volumes of raw data, which fail to meet the demands of practical applications. Secondly, existing datasets often lack raw data covering a broad range of signal-to-noise ratios (SNR), or do not provide tools for transforming raw data to different SNR levels. This limitation undermines the validity of model training and evaluation. Lastly, many existing datasets do not offer open-access evaluation tools, leading to a lack of unified evaluation standards in current research within this field. RFUAV comprises approximately 1.3 TB of raw frequency data collected from 37 distinct UAVs using the Universal Software Radio Peripheral (USRP) device in real-world environments. Through in-depth analysis of the RF data in RFUAV, we define a drone feature sequence called RF drone fingerprint, which aids in distinguishing drone signals. In addition to the dataset, RFUAV provides a baseline preprocessing method and model evaluation tools. Rigorous experiments demonstrate that these preprocessing methods achieve state-of-the-art (SOTA) performance using the provided evaluation tools. The RFUAV dataset and baseline implementation are publicly available at https://github.com/kitoweeknd/RFUAV/.

Li Pang, Heng Zhao, Yijia Zhang et al.

Hyperspectral image (HSI) restoration is crucial for reliable analysis, as real HSIs suffer from degradations like noise, blur, and resolution loss. However, existing models trained on source data often fail on target domains lacking clean references, a common occurrence in practice. To address this issue, we present HIR-ALIGN, a plug-and-play target-adaptive augmentation framework that enhances hyperspectral image restoration by augmenting limited training images with synthetic data that closely matches the target distribution using no extra data. It consists of three stages: (i) proxy generation, where off-the-shelf restoration models restore degraded target observations to produce semantics-preserving proxy HSIs that approximate target-domain clean images; (ii) distribution-adaptive synthesis, where a blur-robust unCLIP diffusion model generates target-aligned RGBs from proxy RGBs, with prompt conditioning and embedding-space noise initialization. Then, a warp-based spectral transfer module synthesizes HSIs by aligning each generated RGB with the proxy RGB, estimating soft patch-wise transport weights, and applying these weights and learnable local interpolation kernels to the proxy HSI; and (iii) aligned supervised finetuning, where restoration networks pretrained on the source distribution are finetuned using both the proxy HSIs and synthesized target-aligned HSIs, and are then deployed on degraded target images. We further provide theoretical analysis showing that augmentation-based finetuning can achieve lower target-domain restoration risk by jointly improving target distribution coverage and controlling spectral bias. Extensive experiments on simulated and real datasets across denoising and super-resolution tasks demonstrate that HIR-ALIGN consistently improves source-only supervised baselines, outperforming both source-only counterparts and representative unsupervised methods.

Wenxuan Mu, Jinzhong Ning, Di Zhao et al.

In-context learning (ICL) with large language models (LLMs) has emerged as a promising paradigm for named entity recognition (NER) in low-resource scenarios. However, existing ICL-based NER methods suffer from three key limitations: (1) reliance on dynamic retrieval of annotated examples, which is problematic when annotated data is scarce; (2) limited generalization to unseen domains due to the LLM's insufficient internal domain knowledge; and (3) failure to incorporate external knowledge or resolve entity ambiguities. To address these challenges, we propose KDR-Agent, a novel multi-agent framework for multi-domain low-resource in-context NER that integrates Knowledge retrieval, Disambiguation, and Reflective analysis. KDR-Agent leverages natural-language type definitions and a static set of entity-level contrastive demonstrations to reduce dependency on large annotated corpora. A central planner coordinates specialized agents to (i) retrieve factual knowledge from Wikipedia for domain-specific mentions, (ii) resolve ambiguous entities via contextualized reasoning, and (iii) reflect on and correct model predictions through structured self-assessment. Experiments across ten datasets from five domains demonstrate that KDR-Agent significantly outperforms existing zero-shot and few-shot ICL baselines across multiple LLM backbones. The code and data can be found at https://github.com/MWXGOD/KDR-Agent.

Jinhao Li, Yuxuan Cong, Yingqiao Wang et al.

Diffusion policies have recently emerged as a powerful paradigm for visuomotor control in robotic manipulation due to their ability to model the distribution of action sequences and capture multimodality. However, iterative denoising leads to substantial inference latency, limiting control frequency in real-time closed-loop systems. Existing acceleration methods either reduce sampling steps, bypass diffusion through direct prediction, or reuse past actions, but often struggle to jointly preserve action quality and achieve consistently low latency. In this work, we propose STEP, a lightweight spatiotemporal consistency prediction mechanism to construct high-quality warm-start actions that are both distributionally close to the target action and temporally consistent, without compromising the generative capability of the original diffusion policy. Then, we propose a velocity-aware perturbation injection mechanism that adaptively modulates actuation excitation based on temporal action variation to prevent execution stall especially for real-world tasks. We further provide a theoretical analysis showing that the proposed prediction induces a locally contractive mapping, ensuring convergence of action errors during diffusion refinement. We conduct extensive evaluations on nine simulated benchmarks and two real-world tasks. Notably, STEP with 2 steps can achieve an average 21.6% and 27.5% higher success rate than BRIDGER and DDIM on the RoboMimic benchmark and real-world tasks, respectively. These results demonstrate that STEP consistently advances the Pareto frontier of inference latency and success rate over existing methods.

Jinzhong Ning, Paerhati Tulajiang, Yingying Le et al.

Speech Relation Extraction (SpeechRE) aims to extract relation triplets directly from speech. However, existing benchmark datasets rely heavily on synthetic data, lacking sufficient quantity and diversity of real human speech. Moreover, existing models also suffer from rigid single-order generation templates and weak semantic alignment, substantially limiting their performance. To address these challenges, we introduce CommonVoice-SpeechRE, a large-scale dataset comprising nearly 20,000 real-human speech samples from diverse speakers, establishing a new benchmark for SpeechRE research. Furthermore, we propose the Relation Prompt-Guided Multi-Order Generative Ensemble (RPG-MoGe), a novel framework that features: (1) a multi-order triplet generation ensemble strategy, leveraging data diversity through diverse element orders during both training and inference, and (2) CNN-based latent relation prediction heads that generate explicit relation prompts to guide cross-modal alignment and accurate triplet generation. Experiments show our approach outperforms state-of-the-art methods, providing both a benchmark dataset and an effective solution for real-world SpeechRE. The source code and dataset are publicly available at https://github.com/NingJinzhong/SpeechRE_RPG_MoGe.

Jiaqing Lyu, Changjie Chen, Bing Liang et al.

The AIDS epidemic has killed 40 million people and caused serious global problems. The identification of new HIV-inhibiting molecules is of great importance for combating the AIDS epidemic. Here, the Classifier Guidance Diffusion model and ligand-based virtual screening strategy are combined to discover potential HIV-inhibiting molecules for the first time. We call it Diff4VS. An extra classifier is trained using the HIV molecule dataset, and the gradient of the classifier is used to guide the Diffusion to generate HIV-inhibiting molecules. Experiments show that Diff4VS can generate more candidate HIV-inhibiting molecules than other methods. Inspired by ligand-based virtual screening, a new metric DrugIndex is proposed. The DrugIndex is the ratio of the proportion of candidate drug molecules in the generated molecule to the proportion of candidate drug molecules in the training set. DrugIndex provides a new evaluation method for evolving molecular generative models from a pharmaceutical perspective. Besides, we report a new phenomenon observed when using molecule generation models for virtual screening. Compared to real molecules, the generated molecules have a lower proportion that is highly similar to known drug molecules. We call it Degradation in molecule generation. Based on the data analysis, the Degradation may result from the difficulty of generating molecules with a specific structure in the generative model. Our research contributes to the application of generative models in drug design from method, metric, and phenomenon analysis.

Xiangxin Zhou, Jiaqi Guan, Yijia Zhang et al.

Dual-target therapeutic strategies have become a compelling approach and attracted significant attention due to various benefits, such as their potential in overcoming drug resistance in cancer therapy. Considering the tremendous success that deep generative models have achieved in structure-based drug design in recent years, we formulate dual-target drug design as a generative task and curate a novel dataset of potential target pairs based on synergistic drug combinations. We propose to design dual-target drugs with diffusion models that are trained on single-target protein-ligand complex pairs. Specifically, we align two pockets in 3D space with protein-ligand binding priors and build two complex graphs with shared ligand nodes for SE(3)-equivariant composed message passing, based on which we derive a composed drift in both 3D and categorical probability space in the generative process. Our algorithm can well transfer the knowledge gained in single-target pretraining to dual-target scenarios in a zero-shot manner. We also repurpose linker design methods as strong baselines for this task. Extensive experiments demonstrate the effectiveness of our method compared with various baselines.

Yijia Zhang, Zhihong Gou, Shijie Cao et al.

Deep Neural Networks (DNNs) have revolutionized various fields, but their deployment on GPUs often leads to significant energy consumption. Unlike existing methods for reducing GPU energy consumption, which are either hardware-inflexible or limited by workload constraints, this paper addresses the problem at the GPU kernel level. We propose a novel search-based compilation method to generate energy-efficient GPU kernels by incorporating energy efficiency into the search process. To accelerate the energy evaluation process, we develop an accurate energy cost model based on high-level kernel features. Furthermore, we introduce a dynamic updating strategy for the energy cost model, reducing the need for on-device energy measurements and accelerating the search process. Our evaluation demonstrates that the proposed approach can generate GPU kernels with up to 21.69% reduced energy consumption while maintaining low latency.

Bingyu Wan, Fuxi Zhang, Zhongpeng Qi et al.

Large language models (LLMs) inherently display hallucinations since the precision of generated texts cannot be guaranteed purely by the parametric knowledge they include. Although retrieval-augmented generation (RAG) systems enhance the accuracy and reliability of generative models by incorporating external documents, these retrieved documents often fail to adequately support the model's responses in practical applications. To address this issue, we propose GGatrieval (Fine-\textbf{G}rained \textbf{G}rounded \textbf{A}lignment Re\textbf{trieval} for verifiable generation), which leverages an LLM to dynamically update queries and filter high-quality, reliable retrieval documents. Specifically, we parse the user query into its syntactic components and perform fine-grained grounded alignment with the retrieved documents. For query components that cannot be individually aligned, we propose a dynamic semantic compensation mechanism that iteratively refines and rewrites the query while continuously updating the retrieval results. This iterative process continues until the retrieved documents sufficiently support the query's response. Our approach introduces a novel criterion for filtering retrieved documents, closely emulating human strategies for acquiring targeted information. This ensures that the retrieved content effectively supports and verifies the generated outputs. On the ALCE benchmark, our method significantly surpasses a wide range of baselines, achieving state-of-the-art performance.

Wenqiang Wang, Yijia Zhang, Zikai Zhang et al.

As large language models (LLMs) demonstrate powerful capabilities, deploying them on edge devices has become increasingly crucial, offering advantages in privacy and real-time interaction. QLoRA has emerged as the standard approach for on-device LLMs, leveraging quantized models to reduce memory and computational costs while utilizing LoRA for task-specific adaptability. In this work, we propose ROMA, a QLoRA accelerator with a hybrid storage architecture that uses ROM for quantized base models and SRAM for LoRA weights and KV cache. Our insight is that the quantized base model is stable and converged, making it well-suited for ROM storage. Meanwhile, LoRA modules offer the flexibility to adapt to new data without requiring updates to the base model. To further reduce the area cost of ROM, we introduce a novel B-ROM design and integrate it with the compute unit to form a fused cell for efficient use of chip resources. ROMA can effectively store both a 4-bit 3B and a 2-bit 8B LLaMA model entirely on-chip, achieving a notable generation speed exceeding 20,000 tokens/s without requiring external memory.

Jiyao Wang, Zehua Peng, Yijia Zhang et al.

Traffic flow prediction plays a critical role in the intelligent transportation system, and it is also a challenging task because of the underlying complex Spatio-temporal patterns and heterogeneities evolving across time. However, most present works mostly concentrate on solely capturing Spatial-temporal dependency or extracting implicit similarity graphs, but the hybrid-granularity evolution is ignored in their modeling process. In this paper, we proposed a novel data-driven end-to-end framework, named Spatio-Temporal Aware Hybrid Graph Network (STAHGNet), to couple the hybrid-grained heterogeneous correlations in series simultaneously through an elaborately Hybrid Graph Attention Module (HGAT) and Coarse-granularity Temporal Graph (CTG) generator. Furthermore, an automotive feature engineering with domain knowledge and a random neighbor sampling strategy is utilized to improve efficiency and reduce computational complexity. The MAE, RMSE, and MAPE are used for evaluation metrics. Tested on four real-life datasets, our proposal outperforms eight classical baselines and four state-of-the-art (SOTA) methods (e.g., MAE 14.82 on PeMSD3; MAE 18.92 on PeMSD4). Besides, extensive experiments and visualizations verify the effectiveness of each component in STAHGNet. In terms of computational cost, STAHGNet saves at least four times the space compared to the previous SOTA models. The proposed model will be beneficial for more efficient TFP as well as intelligent transport system construction.

Lintong Du, Huazhen Liu, Yijia Zhang et al.

Spatial phase unwrapping is a key technique for extracting phase information to obtain 3D morphology and other features. Modern industrial measurement scenarios demand high precision, large image sizes, and high speed. However, conventional methods struggle with noise resistance and processing speed. Current deep learning methods are limited by the receptive field size and sparse semantic information, making them ineffective for large size images. To address this issue, we propose a mutual self-distillation (MSD) mechanism and adaptive boosting ensemble segmenters to construct a universal multi-size phase unwrapping network (UMSPU). MSD performs hierarchical attention refinement and achieves cross-layer collaborative learning through bidirectional distillation, ensuring fine-grained semantic representation across image sizes. The adaptive boosting ensemble segmenters combine weak segmenters with different receptive fields into a strong one, ensuring stable segmentation across spatial frequencies. Experimental results show that UMSPU overcomes image size limitations, achieving high precision across image sizes ranging from 256*256 to 2048*2048 (an 8 times increase). It also outperforms existing methods in speed, robustness, and generalization. Its practicality is further validated in structured light imaging and InSAR. We believe that UMSPU offers a universal solution for phase unwrapping, with broad potential for industrial applications.

Yijia Zhang, Yibo Han, Shijie Cao et al.

Running out of GPU memory has become a main bottleneck for large-scale DNN training. How to reduce the memory footprint during training has received intensive research attention. We find that previous gradient accumulation reduces activation memory but fails to be compatible with gradient memory reduction due to a contradiction between preserving gradients and releasing gradients. To address this issue, we propose a novel optimizer accumulation method for Adam, named Adam Accumulation (AdamA), which enables reducing both activation and gradient memory. Specifically, AdamA directly integrates gradients into optimizer states and accumulates optimizer states over micro-batches, so that gradients can be released immediately after use. We mathematically and experimentally demonstrate AdamA yields the same convergence properties as Adam. Evaluated on transformer-based models, AdamA achieves up to 23% memory reduction compared to gradient accumulation with less than 2% degradation in training throughput. Notably, AdamA can work together with memory reduction methods for optimizer states to fit 1.26x~3.14x larger models over PyTorch and DeepSpeed baseline on GPUs with different memory capacities.

Yijia Zhang, Lingran Zhao, Shijie Cao et al.

Efficient deployment of large language models (LLMs) necessitates low-bit quantization to minimize model size and inference cost. While low-bit integer formats (e.g., INT8/INT4) have been the conventional choice, emerging low-bit floating-point formats (e.g., FP8/FP4) offer a compelling alternative and are gaining support from cutting-edge hardware, such as NVIDIA's H100 GPU. However, the superiority of low-bit INT versus FP formats for quantization on LLMs remains unclear. In this study, we conduct a comparative analysis of INT and FP quantization with the same bit-width, revealing that the optimal quantization format varies across different layers due to the complexity and diversity of tensor distribution. Consequently, we advocate the Mixture of Formats Quantization (MoFQ), which selects the optimal format on a layer-wise basis. This simple yet effective approach achieves state-of-the-art results in both weight-only (W-only) and weight-activation (WA) post-training quantization scenarios when tested on LLaMA across various tasks. In 4-bit W-only quantization, MoFQ surpasses GPTQ without complex hyperparameter tuning and with an order of magnitude faster quantization speed. While in 8-bit WA quantization, MoFQ significantly outperforms INT/FP-only methods, achieving performance close to the full precision model. Notably, MoFQ incurs no hardware overhead compared to INT/FP-only quantization, as the bit-width remains unchanged.

Shaoxiong Ji, Wei Sun, Xiaobo Li et al.

Automated medical coding, an essential task for healthcare operation and delivery, makes unstructured data manageable by predicting medical codes from clinical documents. Recent advances in deep learning and natural language processing have been widely applied to this task. However, deep learning-based medical coding lacks a unified view of the design of neural network architectures. This review proposes a unified framework to provide a general understanding of the building blocks of medical coding models and summarizes recent advanced models under the proposed framework. Our unified framework decomposes medical coding into four main components, i.e., encoder modules for text feature extraction, mechanisms for building deep encoder architectures, decoder modules for transforming hidden representations into medical codes, and the usage of auxiliary information. Finally, we introduce the benchmarks and real-world usage and discuss key research challenges and future directions.

Yijia Zhang, Zhiyong Lu

The biomedical literature provides a rich source of knowledge such as protein-protein interactions (PPIs), drug-drug interactions (DDIs) and chemical-protein interactions (CPIs). Biomedical relation extraction aims to automatically extract biomedical relations from biomedical text for various biomedical research. State-of-the-art methods for biomedical relation extraction are primarily based on supervised machine learning and therefore depend on (sufficient) labeled data. However, creating large sets of training data is prohibitively expensive and labor-intensive, especially so in biomedicine as domain knowledge is required. In contrast, there is a large amount of unlabeled biomedical text available in PubMed. Hence, computational methods capable of employing unlabeled data to reduce the burden of manual annotation are of particular interest in biomedical relation extraction. We present a novel semi-supervised approach based on variational autoencoder (VAE) for biomedical relation extraction. Our model consists of the following three parts, a classifier, an encoder and a decoder. The classifier is implemented using multi-layer convolutional neural networks (CNNs), and the encoder and decoder are implemented using both bidirectional long short-term memory networks (Bi-LSTMs) and CNNs, respectively. The semi-supervised mechanism allows our model to learn features from both the labeled and unlabeled data. We evaluate our method on multiple public PPI, DDI and CPI corpora. Experimental results show that our method effectively exploits the unlabeled data to improve the performance and reduce the dependence on labeled data. To our best knowledge, this is the first semi-supervised VAE-based method for (biomedical) relation extraction. Our results suggest that exploiting such unlabeled data can be greatly beneficial to improved performance in various biomedical relation extraction.