MMMU: A Massive Multi-discipline Multimodal Understanding and Reasoning Benchmark for Expert AGIXiang Yue, Yuansheng Ni, Kai Zhang et al. · microsoft-research, princeton
We introduce MMMU: a new benchmark designed to evaluate multimodal models on massive multi-discipline tasks demanding college-level subject knowledge and deliberate reasoning. MMMU includes 11.5K meticulously collected multimodal questions from college exams, quizzes, and textbooks, covering six core disciplines: Art & Design, Business, Science, Health & Medicine, Humanities & Social Science, and Tech & Engineering. These questions span 30 subjects and 183 subfields, comprising 30 highly heterogeneous image types, such as charts, diagrams, maps, tables, music sheets, and chemical structures. Unlike existing benchmarks, MMMU focuses on advanced perception and reasoning with domain-specific knowledge, challenging models to perform tasks akin to those faced by experts. The evaluation of 14 open-source LMMs as well as the proprietary GPT-4V(ision) and Gemini highlights the substantial challenges posed by MMMU. Even the advanced GPT-4V and Gemini Ultra only achieve accuracies of 56% and 59% respectively, indicating significant room for improvement. We believe MMMU will stimulate the community to build next-generation multimodal foundation models towards expert artificial general intelligence.
34.3CLSep 11, 2023Code
MAmmoTH: Building Math Generalist Models through Hybrid Instruction TuningXiang Yue, Xingwei Qu, Ge Zhang et al. · microsoft-research
We introduce MAmmoTH, a series of open-source large language models (LLMs) specifically tailored for general math problem-solving. The MAmmoTH models are trained on MathInstruct, our meticulously curated instruction tuning dataset. MathInstruct is compiled from 13 math datasets with intermediate rationales, six of which have rationales newly curated by us. It presents a unique hybrid of chain-of-thought (CoT) and program-of-thought (PoT) rationales, and also ensures extensive coverage of diverse fields in math. The hybrid of CoT and PoT not only unleashes the potential of tool use but also allows different thought processes for different math problems. As a result, the MAmmoTH series substantially outperform existing open-source models on nine mathematical reasoning datasets across all scales with an average accuracy gain between 16% and 32%. Remarkably, our MAmmoTH-7B model reaches 33% on MATH (a competition-level dataset), which exceeds the best open-source 7B model (WizardMath) by 23%, and the MAmmoTH-34B model achieves 44% accuracy on MATH, even surpassing GPT-4's CoT result. Our work underscores the importance of diverse problem coverage and the use of hybrid rationales in developing superior math generalist models.
Roll Up Your Sleeves: Working with a Collaborative and Engaging Task-Oriented Dialogue SystemLingbo Mo, Shijie Chen, Ziru Chen et al. · microsoft-research
We introduce TacoBot, a user-centered task-oriented digital assistant designed to guide users through complex real-world tasks with multiple steps. Covering a wide range of cooking and how-to tasks, we aim to deliver a collaborative and engaging dialogue experience. Equipped with language understanding, dialogue management, and response generation components supported by a robust search engine, TacoBot ensures efficient task assistance. To enhance the dialogue experience, we explore a series of data augmentation strategies using LLMs to train advanced neural models continuously. TacoBot builds upon our successful participation in the inaugural Alexa Prize TaskBot Challenge, where our team secured third place among ten competing teams. We offer TacoBot as an open-source framework that serves as a practical example for deploying task-oriented dialogue systems.
40.4CLSep 4, 2024
MMMU-Pro: A More Robust Multi-discipline Multimodal Understanding BenchmarkXiang Yue, Tianyu Zheng, Yuansheng Ni et al. · microsoft-research
This paper introduces MMMU-Pro, a robust version of the Massive Multi-discipline Multimodal Understanding and Reasoning (MMMU) benchmark. MMMU-Pro rigorously assesses multimodal models' true understanding and reasoning capabilities through a three-step process based on MMMU: (1) filtering out questions answerable by text-only models, (2) augmenting candidate options, and (3) introducing a vision-only input setting where questions are embedded within images. This setting challenges AI to truly "see" and "read" simultaneously, testing a fundamental human cognitive skill of seamlessly integrating visual and textual information. Results show that model performance is substantially lower on MMMU-Pro than on MMMU, ranging from 16.8% to 26.9% across models. We explore the impact of OCR prompts and Chain of Thought (CoT) reasoning, finding that OCR prompts have minimal effect while CoT generally improves performance. MMMU-Pro provides a more rigorous evaluation tool, closely mimicking real-world scenarios and offering valuable directions for future research in multimodal AI.
Synthetic Text Generation with Differential Privacy: A Simple and Practical RecipeXiang Yue, Huseyin A. Inan, Xuechen Li et al. · stanford
Privacy concerns have attracted increasing attention in data-driven products due to the tendency of machine learning models to memorize sensitive training data. Generating synthetic versions of such data with a formal privacy guarantee, such as differential privacy (DP), provides a promising path to mitigating these privacy concerns, but previous approaches in this direction have typically failed to produce synthetic data of high quality. In this work, we show that a simple and practical recipe in the text domain is effective: simply fine-tuning a pretrained generative language model with DP enables the model to generate useful synthetic text with strong privacy protection. Through extensive empirical analyses on both benchmark and private customer data, we demonstrate that our method produces synthetic text that is competitive in terms of utility with its non-private counterpart, meanwhile providing strong protection against potential privacy leakages.
C-MORE: Pretraining to Answer Open-Domain Questions by Consulting Millions of ReferencesXiang Yue, Xiaoman Pan, Wenlin Yao et al. · tencent-ai
We consider the problem of pretraining a two-stage open-domain question answering (QA) system (retriever + reader) with strong transfer capabilities. The key challenge is how to construct a large amount of high-quality question-answer-context triplets without task-specific annotations. Specifically, the triplets should align well with downstream tasks by: (i) covering a wide range of domains (for open-domain applications), (ii) linking a question to its semantically relevant context with supporting evidence (for training the retriever), and (iii) identifying the correct answer in the context (for training the reader). Previous pretraining approaches generally fall short of one or more of these requirements. In this work, we automatically construct a large-scale corpus that meets all three criteria by consulting millions of references cited within Wikipedia. The well-aligned pretraining signals benefit both the retriever and the reader significantly. Our pretrained retriever leads to 2%-10% absolute gains in top-20 accuracy. And with our pretrained reader, the entire system improves by up to 4% in exact match.
23.2CLNov 15, 2023Code
TableLlama: Towards Open Large Generalist Models for TablesTianshu Zhang, Xiang Yue, Yifei Li et al.
Semi-structured tables are ubiquitous. There has been a variety of tasks that aim to automatically interpret, augment, and query tables. Current methods often require pretraining on tables or special model architecture design, are restricted to specific table types, or have simplifying assumptions about tables and tasks. This paper makes the first step towards developing open-source large language models (LLMs) as generalists for a diversity of table-based tasks. Towards that end, we construct TableInstruct, a new dataset with a variety of realistic tables and tasks, for instruction tuning and evaluating LLMs. We further develop the first open-source generalist model for tables, TableLlama, by fine-tuning Llama 2 (7B) with LongLoRA to address the long context challenge. We experiment under both in-domain setting and out-of-domain setting. On 7 out of 8 in-domain tasks, TableLlama achieves comparable or better performance than the SOTA for each task, despite the latter often has task-specific design. On 6 out-of-domain datasets, it achieves 5-44 absolute point gains compared with the base model, showing that training on TableInstruct enhances the model's generalizability. We open-source our dataset and trained model to boost future work on developing open generalist models for tables.
0.8CLJul 11, 2022
Bootstrapping a User-Centered Task-Oriented Dialogue SystemShijie Chen, Ziru Chen, Xiang Deng et al. · microsoft-research
We present TacoBot, a task-oriented dialogue system built for the inaugural Alexa Prize TaskBot Challenge, which assists users in completing multi-step cooking and home improvement tasks. TacoBot is designed with a user-centered principle and aspires to deliver a collaborative and accessible dialogue experience. Towards that end, it is equipped with accurate language understanding, flexible dialogue management, and engaging response generation. Furthermore, TacoBot is backed by a strong search engine and an automated end-to-end test suite. In bootstrapping the development of TacoBot, we explore a series of data augmentation strategies to train advanced neural language processing models and continuously improve the dialogue experience with collected real conversations. At the end of the semifinals, TacoBot achieved an average rating of 3.55/5.0.
Synthetic Question Value Estimation for Domain Adaptation of Question AnsweringXiang Yue, Ziyu Yao, Huan Sun
Synthesizing QA pairs with a question generator (QG) on the target domain has become a popular approach for domain adaptation of question answering (QA) models. Since synthetic questions are often noisy in practice, existing work adapts scores from a pretrained QA (or QG) model as criteria to select high-quality questions. However, these scores do not directly serve the ultimate goal of improving QA performance on the target domain. In this paper, we introduce a novel idea of training a question value estimator (QVE) that directly estimates the usefulness of synthetic questions for improving the target-domain QA performance. By conducting comprehensive experiments, we show that the synthetic questions selected by QVE can help achieve better target-domain QA performance, in comparison with existing techniques. We additionally show that by using such questions and only around 15% of the human annotations on the target domain, we can achieve comparable performance to the fully-supervised baselines.
Demystifying Long Chain-of-Thought Reasoning in LLMsEdward Yeo, Yuxuan Tong, Morry Niu et al.
Scaling inference compute enhances reasoning in large language models (LLMs), with long chains-of-thought (CoTs) enabling strategies like backtracking and error correction. Reinforcement learning (RL) has emerged as a crucial method for developing these capabilities, yet the conditions under which long CoTs emerge remain unclear, and RL training requires careful design choices. In this study, we systematically investigate the mechanics of long CoT reasoning, identifying the key factors that enable models to generate long CoT trajectories. Through extensive supervised fine-tuning (SFT) and RL experiments, we present four main findings: (1) While SFT is not strictly necessary, it simplifies training and improves efficiency; (2) Reasoning capabilities tend to emerge with increased training compute, but their development is not guaranteed, making reward shaping crucial for stabilizing CoT length growth; (3) Scaling verifiable reward signals is critical for RL. We find that leveraging noisy, web-extracted solutions with filtering mechanisms shows strong potential, particularly for out-of-distribution (OOD) tasks such as STEM reasoning; and (4) Core abilities like error correction are inherently present in base models, but incentivizing these skills effectively for complex tasks via RL demands significant compute, and measuring their emergence requires a nuanced approach. These insights provide practical guidance for optimizing training strategies to enhance long CoT reasoning in LLMs. Our code is available at: https://github.com/eddycmu/demystify-long-cot.
41.3SEFeb 22, 2024Code
OpenCodeInterpreter: Integrating Code Generation with Execution and RefinementTianyu Zheng, Ge Zhang, Tianhao Shen et al.
The introduction of large language models has significantly advanced code generation. However, open-source models often lack the execution capabilities and iterative refinement of advanced systems like the GPT-4 Code Interpreter. To address this, we introduce OpenCodeInterpreter, a family of open-source code systems designed for generating, executing, and iteratively refining code. Supported by Code-Feedback, a dataset featuring 68K multi-turn interactions, OpenCodeInterpreter integrates execution and human feedback for dynamic code refinement. Our comprehensive evaluation of OpenCodeInterpreter across key benchmarks such as HumanEval, MBPP, and their enhanced versions from EvalPlus reveals its exceptional performance. Notably, OpenCodeInterpreter-33B achieves an accuracy of 83.2 (76.4) on the average (and plus versions) of HumanEval and MBPP, closely rivaling GPT-4's 84.2 (76.2) and further elevates to 91.6 (84.6) with synthesized human feedback from GPT-4. OpenCodeInterpreter brings the gap between open-source code generation models and proprietary systems like GPT-4 Code Interpreter.
Data Engineering for Scaling Language Models to 128K ContextYao Fu, Rameswar Panda, Xinyao Niu et al.
We study the continual pretraining recipe for scaling language models' context lengths to 128K, with a focus on data engineering. We hypothesize that long context modeling, in particular \textit{the ability to utilize information at arbitrary input locations}, is a capability that is mostly already acquired through large-scale pretraining, and that this capability can be readily extended to contexts substantially longer than seen during training~(e.g., 4K to 128K) through lightweight continual pretraining on appropriate data mixture. We investigate the \textit{quantity} and \textit{quality} of the data for continual pretraining: (1) for quantity, we show that 500 million to 5 billion tokens are enough to enable the model to retrieve information anywhere within the 128K context; (2) for quality, our results equally emphasize \textit{domain balance} and \textit{length upsampling}. Concretely, we find that naively upsampling longer data on certain domains like books, a common practice of existing work, gives suboptimal performance, and that a balanced domain mixture is important. We demonstrate that continual pretraining of the full model on 1B-5B tokens of such data is an effective and affordable strategy for scaling the context length of language models to 128K. Our recipe outperforms strong open-source long-context models and closes the gap to frontier models like GPT-4 128K.
9.8LGFeb 27, 2023
Efficient Informed Proposals for Discrete Distributions via Newton's Series ApproximationYue Xiang, Dongyao Zhu, Bowen Lei et al.
Gradients have been exploited in proposal distributions to accelerate the convergence of Markov chain Monte Carlo algorithms on discrete distributions. However, these methods require a natural differentiable extension of the target discrete distribution, which often does not exist or does not provide effective gradient guidance. In this paper, we develop a gradient-like proposal for any discrete distribution without this strong requirement. Built upon a locally-balanced proposal, our method efficiently approximates the discrete likelihood ratio via Newton's series expansion to enable a large and efficient exploration in discrete spaces. We show that our method can also be viewed as a multilinear extension, thus inheriting its desired properties. We prove that our method has a guaranteed convergence rate with or without the Metropolis-Hastings step. Furthermore, our method outperforms a number of popular alternatives in several different experiments, including the facility location problem, extractive text summarization, and image retrieval.
24.0CLApr 9, 2024Code
VisualWebBench: How Far Have Multimodal LLMs Evolved in Web Page Understanding and Grounding?Junpeng Liu, Yifan Song, Bill Yuchen Lin et al. · pku
Multimodal Large Language models (MLLMs) have shown promise in web-related tasks, but evaluating their performance in the web domain remains a challenge due to the lack of comprehensive benchmarks. Existing benchmarks are either designed for general multimodal tasks, failing to capture the unique characteristics of web pages, or focus on end-to-end web agent tasks, unable to measure fine-grained abilities such as OCR, understanding, and grounding. In this paper, we introduce \bench{}, a multimodal benchmark designed to assess the capabilities of MLLMs across a variety of web tasks. \bench{} consists of seven tasks, and comprises 1.5K human-curated instances from 139 real websites, covering 87 sub-domains. We evaluate 14 open-source MLLMs, Gemini Pro, Claude-3 series, and GPT-4V(ision) on \bench{}, revealing significant challenges and performance gaps. Further analysis highlights the limitations of current MLLMs, including inadequate grounding in text-rich environments and subpar performance with low-resolution image inputs. We believe \bench{} will serve as a valuable resource for the research community and contribute to the creation of more powerful and versatile MLLMs for web-related applications.
19.9CLOct 21, 2024Code
Pangea: A Fully Open Multilingual Multimodal LLM for 39 LanguagesXiang Yue, Yueqi Song, Akari Asai et al. · cmu
Despite recent advances in multimodal large language models (MLLMs), their development has predominantly focused on English- and western-centric datasets and tasks, leaving most of the world's languages and diverse cultural contexts underrepresented. This paper introduces Pangea, a multilingual multimodal LLM trained on PangeaIns, a diverse 6M instruction dataset spanning 39 languages. PangeaIns features: 1) high-quality English instructions, 2) carefully machine-translated instructions, and 3) culturally relevant multimodal tasks to ensure cross-cultural coverage. To rigorously assess models' capabilities, we introduce PangeaBench, a holistic evaluation suite encompassing 14 datasets covering 47 languages. Results show that Pangea significantly outperforms existing open-source models in multilingual settings and diverse cultural contexts. Ablation studies further reveal the importance of English data proportions, language popularity, and the number of multimodal training samples on overall performance. We fully open-source our data, code, and trained checkpoints, to facilitate the development of inclusive and robust multilingual MLLMs, promoting equity and accessibility across a broader linguistic and cultural spectrum.
23.4SDApr 9, 2024Code
MuPT: A Generative Symbolic Music Pretrained TransformerXingwei Qu, Yuelin Bai, Yinghao Ma et al.
In this paper, we explore the application of Large Language Models (LLMs) to the pre-training of music. While the prevalent use of MIDI in music modeling is well-established, our findings suggest that LLMs are inherently more compatible with ABC Notation, which aligns more closely with their design and strengths, thereby enhancing the model's performance in musical composition. To address the challenges associated with misaligned measures from different tracks during generation, we propose the development of a Synchronized Multi-Track ABC Notation (SMT-ABC Notation), which aims to preserve coherence across multiple musical tracks. Our contributions include a series of models capable of handling up to 8192 tokens, covering 90% of the symbolic music data in our training set. Furthermore, we explore the implications of the Symbolic Music Scaling Law (SMS Law) on model performance. The results indicate a promising direction for future research in music generation, offering extensive resources for community-led research through our open-source contributions.
18.7SEApr 4, 2024Code
CodeEditorBench: Evaluating Code Editing Capability of Large Language ModelsJiawei Guo, Ziming Li, Xueling Liu et al.
Large Language Models (LLMs) for code are rapidly evolving, with code editing emerging as a critical capability. We introduce CodeEditorBench, an evaluation framework designed to rigorously assess the performance of LLMs in code editing tasks, including debugging, translating, polishing, and requirement switching. Unlike existing benchmarks focusing solely on code generation, CodeEditorBench emphasizes real-world scenarios and practical aspects of software development. We curate diverse coding challenges and scenarios from five sources, covering various programming languages, complexity levels, and editing tasks. Evaluation of 19 LLMs reveals that closed-source models (particularly Gemini-Ultra and GPT-4), outperform open-source models in CodeEditorBench, highlighting differences in model performance based on problem types and prompt sensitivities. CodeEditorBench aims to catalyze advancements in LLMs by providing a robust platform for assessing code editing capabilities. We will release all prompts and datasets to enable the community to expand the dataset and benchmark emerging LLMs. By introducing CodeEditorBench, we contribute to the advancement of LLMs in code editing and provide a valuable resource for researchers and practitioners.
ESPnet-SpeechLM: An Open Speech Language Model ToolkitJinchuan Tian, Jiatong Shi, William Chen et al. · nvidia
We present ESPnet-SpeechLM, an open toolkit designed to democratize the development of speech language models (SpeechLMs) and voice-driven agentic applications. The toolkit standardizes speech processing tasks by framing them as universal sequential modeling problems, encompassing a cohesive workflow of data preprocessing, pre-training, inference, and task evaluation. With ESPnet-SpeechLM, users can easily define task templates and configure key settings, enabling seamless and streamlined SpeechLM development. The toolkit ensures flexibility, efficiency, and scalability by offering highly configurable modules for every stage of the workflow. To illustrate its capabilities, we provide multiple use cases demonstrating how competitive SpeechLMs can be constructed with ESPnet-SpeechLM, including a 1.7B-parameter model pre-trained on both text and speech tasks, across diverse benchmarks. The toolkit and its recipes are fully transparent and reproducible at: https://github.com/espnet/espnet/tree/speechlm.
13.0CLJun 21, 2025Code
OpusLM: A Family of Open Unified Speech Language ModelsJinchuan Tian, William Chen, Yifan Peng et al. · nvidia
This paper presents Open Unified Speech Language Models (OpusLMs), a family of open foundational speech language models (SpeechLMs) up to 7B. Initialized from decoder-only text language models, the OpusLMs are continuously pre-trained on 213K hours of speech-text pairs and 292B text-only tokens. We demonstrate our OpusLMs achieve comparable (or even superior) performance with existing SpeechLMs in speech recognition, speech synthesis, and text-only capabilities. Technically, this paper articulates our SpeechLM designs on tokenization, multi-stream language models, and multi-stage training strategies. We experimentally demonstrate the importance of model size scaling and the effect of annealing data selection. The OpusLMs are all built from publicly available materials and are fully transparent models. We release our code, data, checkpoints, and training logs to facilitate open SpeechLM research
17.6SEJun 4, 2025Code
VisCoder: Fine-Tuning LLMs for Executable Python Visualization Code GenerationYuansheng Ni, Ping Nie, Kai Zou et al.
Large language models (LLMs) often struggle with visualization tasks like plotting diagrams, charts, where success depends on both code correctness and visual semantics. Existing instruction-tuning datasets lack execution-grounded supervision and offer limited support for iterative code correction, resulting in fragile and unreliable plot generation. We present VisCode-200K, a large-scale instruction tuning dataset for Python-based visualization and self-correction. It contains over 200K examples from two sources: (1) validated plotting code from open-source repositories, paired with natural language instructions and rendered plots; and (2) 45K multi-turn correction dialogues from Code-Feedback, enabling models to revise faulty code using runtime feedback. We fine-tune Qwen2.5-Coder-Instruct on VisCode-200K to create VisCoder, and evaluate it on PandasPlotBench. VisCoder significantly outperforms strong open-source baselines and approaches the performance of proprietary models like GPT-4o-mini. We further adopt a self-debug evaluation protocol to assess iterative repair, demonstrating the benefits of feedback-driven learning for executable, visually accurate code generation.
Long-context LLMs Struggle with Long In-context LearningTianle Li, Ge Zhang, Quy Duc Do et al.
Large Language Models (LLMs) have made significant strides in handling long sequences. Some models like Gemini could even to be capable of dealing with millions of tokens. However, their performance evaluation has largely been confined to metrics like perplexity and synthetic tasks, which may not fully capture their true abilities in more challenging, real-world scenarios. We introduce a benchmark (LongICLBench) for long in-context learning in extreme-label classification using six datasets with 28 to 174 classes and input lengths from 2K to 50K tokens. Our benchmark requires LLMs to comprehend the entire input to recognize the massive label spaces to make correct predictions. We evaluate on 15 long-context LLMs and find that they perform well on less challenging classification tasks with smaller label space and shorter demonstrations. However, they struggle with more challenging task like Discovery with 174 labels, suggesting a gap in their ability to process long, context-rich sequences. Further analysis reveals a bias towards labels presented later in the sequence and a need for improved reasoning over multiple pieces of information. Our study reveals that long context understanding and reasoning is still a challenging task for the existing LLMs. We believe LongICLBench could serve as a more realistic evaluation for the future long-context LLMs.
Trial and Error: Exploration-Based Trajectory Optimization for LLM AgentsYifan Song, Da Yin, Xiang Yue et al. · allen-ai, pku
Large Language Models (LLMs) have become integral components in various autonomous agent systems. In this study, we present an exploration-based trajectory optimization approach, referred to as ETO. This learning method is designed to enhance the performance of open LLM agents. Contrary to previous studies that exclusively train on successful expert trajectories, our method allows agents to learn from their exploration failures. This leads to improved performance through an iterative optimization framework. During the exploration phase, the agent interacts with the environment while completing given tasks, gathering failure trajectories to create contrastive trajectory pairs. In the subsequent training phase, the agent utilizes these trajectory preference pairs to update its policy using contrastive learning methods like DPO. This iterative cycle of exploration and training fosters continued improvement in the agents. Our experiments on three complex tasks demonstrate that ETO consistently surpasses baseline performance by a large margin. Furthermore, an examination of task-solving efficiency and potential in scenarios lacking expert trajectory underscores the effectiveness of our approach.
29.8CLMay 6, 2024Code
MAmmoTH2: Scaling Instructions from the WebXiang Yue, Tuney Zheng, Ge Zhang et al.
Instruction tuning improves the reasoning abilities of large language models (LLMs), with data quality and scalability being the crucial factors. Most instruction tuning data come from human crowd-sourcing or GPT-4 distillation. We propose a paradigm to efficiently harvest 10 million naturally existing instruction data from the pre-training web corpus to enhance LLM reasoning. Our approach involves (1) recalling relevant documents, (2) extracting instruction-response pairs, and (3) refining the extracted pairs using open-source LLMs. Fine-tuning base LLMs on this dataset, we build MAmmoTH2 models, which significantly boost performance on reasoning benchmarks. Notably, MAmmoTH2-7B's (Mistral) performance increases from 11% to 36.7% on MATH and from 36% to 68.4% on GSM8K without training on any in-domain data. Further training MAmmoTH2 on public instruction tuning datasets yields MAmmoTH2-Plus, achieving state-of-the-art performance on several reasoning and chatbot benchmarks. Our work demonstrates how to harvest large-scale, high-quality instruction data without costly human annotation or GPT-4 distillation, providing a new paradigm for building better instruction tuning data.
COUGH: A Challenge Dataset and Models for COVID-19 FAQ RetrievalXinliang Frederick Zhang, Heming Sun, Xiang Yue et al.
We present a large, challenging dataset, COUGH, for COVID-19 FAQ retrieval. Similar to a standard FAQ dataset, COUGH consists of three parts: FAQ Bank, Query Bank and Relevance Set. The FAQ Bank contains ~16K FAQ items scraped from 55 credible websites (e.g., CDC and WHO). For evaluation, we introduce Query Bank and Relevance Set, where the former contains 1,236 human-paraphrased queries while the latter contains ~32 human-annotated FAQ items for each query. We analyze COUGH by testing different FAQ retrieval models built on top of BM25 and BERT, among which the best model achieves 48.8 under P@5, indicating a great challenge presented by COUGH and encouraging future research for further improvement. Our COUGH dataset is available at https://github.com/sunlab-osu/covid-faq.
Machine Unlearning of Pre-trained Large Language ModelsJin Yao, Eli Chien, Minxin Du et al.
This study investigates the concept of the `right to be forgotten' within the context of large language models (LLMs). We explore machine unlearning as a pivotal solution, with a focus on pre-trained models--a notably under-researched area. Our research delineates a comprehensive framework for machine unlearning in pre-trained LLMs, encompassing a critical analysis of seven diverse unlearning methods. Through rigorous evaluation using curated datasets from arXiv, books, and GitHub, we establish a robust benchmark for unlearning performance, demonstrating that these methods are over $10^5$ times more computationally efficient than retraining. Our results show that integrating gradient ascent with gradient descent on in-distribution data improves hyperparameter robustness. We also provide detailed guidelines for efficient hyperparameter tuning in the unlearning process. Our findings advance the discourse on ethical AI practices, offering substantive insights into the mechanics of machine unlearning for pre-trained LLMs and underscoring the potential for responsible AI development.
Grokked Transformers are Implicit Reasoners: A Mechanistic Journey to the Edge of GeneralizationBoshi Wang, Xiang Yue, Yu Su et al. · microsoft-research
We study whether transformers can learn to implicitly reason over parametric knowledge, a skill that even the most capable language models struggle with. Focusing on two representative reasoning types, composition and comparison, we consistently find that transformers can learn implicit reasoning, but only through grokking, i.e., extended training far beyond overfitting. The levels of generalization also vary across reasoning types: when faced with out-of-distribution examples, transformers fail to systematically generalize for composition but succeed for comparison. We delve into the model's internals throughout training, conducting analytical experiments that reveal: 1) the mechanism behind grokking, such as the formation of the generalizing circuit and its relation to the relative efficiency of generalizing and memorizing circuits, and 2) the connection between systematicity and the configuration of the generalizing circuit. Our findings guide data and training setup to better induce implicit reasoning and suggest potential improvements to the transformer architecture, such as encouraging cross-layer knowledge sharing. Furthermore, we demonstrate that for a challenging reasoning task with a large search space, GPT-4-Turbo and Gemini-1.5-Pro based on non-parametric memory fail badly regardless of prompting styles or retrieval augmentation, while a fully grokked transformer can achieve near-perfect accuracy, showcasing the power of parametric memory for complex reasoning.
14.6CLFeb 26, 2024
StructLM: Towards Building Generalist Models for Structured Knowledge GroundingAlex Zhuang, Ge Zhang, Tianyu Zheng et al.
Structured data sources, such as tables, graphs, and databases, are ubiquitous knowledge sources. Despite the demonstrated capabilities of large language models (LLMs) on plain text, their proficiency in interpreting and utilizing structured data remains limited. Our investigation reveals a notable deficiency in LLMs' ability to process structured data, e.g., ChatGPT lags behind state-of-the-art (SoTA) model by an average of 35%. To augment the Structured Knowledge Grounding (SKG) capabilities in LLMs, we have developed a comprehensive instruction tuning dataset comprising 1.1 million examples. Utilizing this dataset, we train a series of models, referred to as StructLM, based on the Mistral and the CodeLlama model family, ranging from 7B to 34B parameters. Our StructLM series surpasses task-specific models on 16 out of 18 evaluated datasets and establishes new SoTA performance on 8 SKG tasks. Furthermore, StructLM demonstrates strong generalization across 6 novel held-out SKG tasks, outperforming TableLlama by an average of 35\% and Flan-UL2 20B by an average of 10\%. Contrary to expectations, we observe that scaling model size offers marginal benefits, with StructLM-34B showing only slight improvements over StructLM-7B. This suggests that structured knowledge grounding is still a challenging task and requires more innovative design to push to a new level.
MEGA-Bench: Scaling Multimodal Evaluation to over 500 Real-World TasksJiacheng Chen, Tianhao Liang, Sherman Siu et al. · amazon-science
We present MEGA-Bench, an evaluation suite that scales multimodal evaluation to over 500 real-world tasks, to address the highly heterogeneous daily use cases of end users. Our objective is to optimize for a set of high-quality data samples that cover a highly diverse and rich set of multimodal tasks, while enabling cost-effective and accurate model evaluation. In particular, we collected 505 realistic tasks encompassing over 8,000 samples from 16 expert annotators to extensively cover the multimodal task space. Instead of unifying these problems into standard multi-choice questions (like MMMU, MMBench, and MMT-Bench), we embrace a wide range of output formats like numbers, phrases, code, \LaTeX, coordinates, JSON, free-form, etc. To accommodate these formats, we developed over 40 metrics to evaluate these tasks. Unlike existing benchmarks, MEGA-Bench offers a fine-grained capability report across multiple dimensions (e.g., application, input type, output format, skill), allowing users to interact with and visualize model capabilities in depth. We evaluate a wide variety of frontier vision-language models on MEGA-Bench to understand their capabilities across these dimensions.
Evaluating Language Models as Synthetic Data GeneratorsSeungone Kim, Juyoung Suk, Xiang Yue et al. · cmu
Given the increasing use of synthetic data in language model (LM) post-training, an LM's ability to generate high-quality data has become nearly as crucial as its ability to solve problems directly. While prior works have focused on developing effective data generation methods, they lack systematic comparison of different LMs as data generators in a unified setting. To address this gap, we propose AgoraBench, a benchmark that provides standardized settings and metrics to evaluate LMs' data generation abilities. Through synthesizing 1.26 million training instances using 6 LMs and training 99 student models, we uncover key insights about LMs' data generation capabilities. First, we observe that LMs exhibit distinct strengths. For instance, GPT-4o excels at generating new problems, while Claude-3.5-Sonnet performs better at enhancing existing ones. Furthermore, our analysis reveals that an LM's data generation ability doesn't necessarily correlate with its problem-solving ability. Instead, multiple intrinsic features of data quality-including response quality, perplexity, and instruction difficulty-collectively serve as better indicators. Finally, we demonstrate that strategic choices in output format and cost-conscious model selection significantly impact data generation effectiveness.
11.9CLMay 7, 2024
Long Context Alignment with Short Instructions and Synthesized PositionsWenhao Wu, Yizhong Wang, Yao Fu et al.
Effectively handling instructions with extremely long context remains a challenge for Large Language Models (LLMs), typically necessitating high-quality long data and substantial computational resources. This paper introduces Step-Skipping Alignment (SkipAlign), a new technique designed to enhance the long-context capabilities of LLMs in the phase of alignment without the need for additional efforts beyond training with original data length. SkipAlign is developed on the premise that long-range dependencies are fundamental to enhancing an LLM's capacity of long context. Departing from merely expanding the length of input samples, SkipAlign synthesizes long-range dependencies from the aspect of positions indices. This is achieved by the strategic insertion of skipped positions within instruction-following samples, which utilizes the semantic structure of the data to effectively expand the context. Through extensive experiments on base models with a variety of context window sizes, SkipAlign demonstrates its effectiveness across a spectrum of long-context tasks. Particularly noteworthy is that with a careful selection of the base model and alignment datasets, SkipAlign with only 6B parameters achieves it's best performance and comparable with strong baselines like GPT-3.5-Turbo-16K on LongBench.
21.2CVOct 17, 2024
Harnessing Webpage UIs for Text-Rich Visual UnderstandingJunpeng Liu, Tianyue Ou, Yifan Song et al.
Text-rich visual understanding-the ability to process environments where dense textual content is integrated with visuals-is crucial for multimodal large language models (MLLMs) to interact effectively with structured environments. To enhance this capability, we propose synthesizing general multimodal instructions from webpage UIs using text-based large language models (LLMs). Despite lacking direct visual input, text-based LLMs are able to process structured text representations from webpage accessibility trees. These instructions are then paired with UI screenshots to train multimodal models. We introduce MultiUI, a dataset containing 7.3 million samples from 1 million websites, covering diverse multimodal tasks and UI layouts. Models trained on MultiUI not only excel in web UI tasks-achieving up to a 48% improvement on VisualWebBench and a 19.1% boost in element accuracy on a web agent dataset Mind2Web-but also generalize surprisingly well to non-web UI tasks and even to non-UI domains, such as document understanding, OCR, and chart interpretation. These results highlight the broad applicability of web UI data for advancing text-rich visual understanding across various scenarios.
AttributionBench: How Hard is Automatic Attribution Evaluation?Yifei Li, Xiang Yue, Zeyi Liao et al.
Modern generative search engines enhance the reliability of large language model (LLM) responses by providing cited evidence. However, evaluating the answer's attribution, i.e., whether every claim within the generated responses is fully supported by its cited evidence, remains an open problem. This verification, traditionally dependent on costly human evaluation, underscores the urgent need for automatic attribution evaluation methods. To bridge the gap in the absence of standardized benchmarks for these methods, we present AttributionBench, a comprehensive benchmark compiled from various existing attribution datasets. Our extensive experiments on AttributionBench reveal the challenges of automatic attribution evaluation, even for state-of-the-art LLMs. Specifically, our findings show that even a fine-tuned GPT-3.5 only achieves around 80% macro-F1 under a binary classification formulation. A detailed analysis of more than 300 error cases indicates that a majority of failures stem from the model's inability to process nuanced information, and the discrepancy between the information the model has access to and that human annotators do.
26.6CLApr 14, 2025
VisualPuzzles: Decoupling Multimodal Reasoning Evaluation from Domain KnowledgeYueqi Song, Tianyue Ou, Yibo Kong et al.
Current multimodal benchmarks often conflate reasoning with domain-specific knowledge, making it difficult to isolate and evaluate general reasoning abilities in non-expert settings. To address this, we introduce VisualPuzzles, a benchmark that targets visual reasoning while deliberately minimizing reliance on specialized knowledge. VisualPuzzles consists of diverse questions spanning five categories: algorithmic, analogical, deductive, inductive, and spatial reasoning. One major source of our questions is manually translated logical reasoning questions from the Chinese Civil Service Examination. Experiments show that VisualPuzzles requires significantly less intensive domain-specific knowledge and more complex reasoning compared to benchmarks like MMMU, enabling us to better evaluate genuine multimodal reasoning. Evaluations show that state-of-the-art multimodal large language models consistently lag behind human performance on VisualPuzzles, and that strong performance on knowledge-intensive benchmarks does not necessarily translate to success on reasoning-focused, knowledge-light tasks. Additionally, reasoning enhancements such as scaling up inference compute (with "thinking" modes) yield inconsistent gains across models and task types, and we observe no clear correlation between model size and performance. We also found that models exhibit different reasoning and answering patterns on VisualPuzzles compared to benchmarks with heavier emphasis on knowledge. VisualPuzzles offers a clearer lens through which to evaluate reasoning capabilities beyond factual recall and domain knowledge.
14.6CLOct 22, 2024
JMMMU: A Japanese Massive Multi-discipline Multimodal Understanding Benchmark for Culture-aware EvaluationShota Onohara, Atsuyuki Miyai, Yuki Imajuku et al.
Accelerating research on Large Multimodal Models (LMMs) in non-English languages is crucial for enhancing user experiences across broader populations. In this paper, we introduce JMMMU (Japanese MMMU), the first large-scale Japanese benchmark designed to evaluate LMMs on expert-level tasks based on the Japanese cultural context. To facilitate comprehensive culture-aware evaluation, JMMMU features two complementary subsets: (i) culture-agnostic (CA) subset, where the culture-independent subjects (e.g., Math) are selected and translated into Japanese, enabling one-to-one comparison with its English counterpart MMMU; and (ii) culture-specific (CS) subset, comprising newly crafted subjects that reflect Japanese cultural context. Using the CA subset, we observe performance drop in many LMMs when evaluated in Japanese, which is purely attributable to language variation. Using the CS subset, we reveal their inadequate Japanese cultural understanding. Further, by combining both subsets, we identify that some LMMs perform well on the CA subset but not on the CS subset, exposing a shallow understanding of the Japanese language that lacks depth in cultural understanding. We hope this work will not only help advance LMM performance in Japanese but also serve as a guideline to create high-standard, culturally diverse benchmarks for multilingual LMM development. The project page is https://mmmu-japanese-benchmark.github.io/JMMMU/.
12.0CLMay 15, 2025
The CoT Encyclopedia: Analyzing, Predicting, and Controlling how a Reasoning Model will ThinkSeongyun Lee, Seungone Kim, Minju Seo et al. · cmu
Long chain-of-thought (CoT) is an essential ingredient in effective usage of modern large language models, but our understanding of the reasoning strategies underlying these capabilities remains limited. While some prior works have attempted to categorize CoTs using predefined strategy types, such approaches are constrained by human intuition and fail to capture the full diversity of model behaviors. In this work, we introduce the CoT Encyclopedia, a bottom-up framework for analyzing and steering model reasoning. Our method automatically extracts diverse reasoning criteria from model-generated CoTs, embeds them into a semantic space, clusters them into representative categories, and derives contrastive rubrics to interpret reasoning behavior. Human evaluations show that this framework produces more interpretable and comprehensive analyses than existing methods. Moreover, we demonstrate that this understanding enables performance gains: we can predict which strategy a model is likely to use and guide it toward more effective alternatives. Finally, we provide practical insights, such as that training data format (e.g., free-form vs. multiple-choice) has a far greater impact on reasoning behavior than data domain, underscoring the importance of format-aware model design.
12.5LGDec 11, 2024
Underestimated Privacy Risks for Minority Populations in Large Language Model UnlearningRongzhe Wei, Mufei Li, Mohsen Ghassemi et al. · gatech
Large Language Models (LLMs) embed sensitive, human-generated data, prompting the need for unlearning methods. Although certified unlearning offers strong privacy guarantees, its restrictive assumptions make it unsuitable for LLMs, giving rise to various heuristic approaches typically assessed through empirical evaluations. These standard evaluations randomly select data for removal, apply unlearning techniques, and use membership inference attacks (MIAs) to compare unlearned models against models retrained without the removed data. However, to ensure robust privacy protections for every data point, it is essential to account for scenarios in which certain data subsets face elevated risks. Prior research suggests that outliers, particularly including data tied to minority groups, often exhibit higher memorization propensity which indicates they may be more difficult to unlearn. Building on these insights, we introduce a complementary, minority-aware evaluation framework to highlight blind spots in existing frameworks. We substantiate our findings with carefully designed experiments, using canaries with personally identifiable information (PII) to represent these minority subsets and demonstrate that they suffer at least 20% higher privacy leakage across various unlearning methods, MIAs, datasets, and LLM scales. Our proposed minority-aware evaluation framework marks an essential step toward more equitable and comprehensive assessments of LLM unlearning efficacy.
22.9CLJun 3, 2024
MixEval: Deriving Wisdom of the Crowd from LLM Benchmark MixturesJinjie Ni, Fuzhao Xue, Xiang Yue et al.
Evaluating large language models (LLMs) is challenging. Traditional ground-truth-based benchmarks fail to capture the comprehensiveness and nuance of real-world queries, while LLM-as-judge benchmarks suffer from grading biases and limited query quantity. Both of them may also become contaminated over time. User-facing evaluation, such as Chatbot Arena, provides reliable signals but is costly and slow. In this work, we propose MixEval, a new paradigm for establishing efficient, gold-standard LLM evaluation by strategically mixing off-the-shelf benchmarks. It bridges (1) comprehensive and well-distributed real-world user queries and (2) efficient and fairly-graded ground-truth-based benchmarks, by matching queries mined from the web with similar queries from existing benchmarks. Based on MixEval, we further build MixEval-Hard, which offers more room for model improvement. Our benchmarks' advantages lie in (1) a 0.96 model ranking correlation with Chatbot Arena arising from the highly impartial query distribution and grading mechanism, (2) fast, cheap, and reproducible execution (6% of the time and cost of MMLU), and (3) dynamic evaluation enabled by the rapid and stable data update pipeline. We provide extensive meta-evaluation and analysis for our and existing LLM benchmarks to deepen the community's understanding of LLM evaluation and guide future research directions.
26.6CLMay 22, 2023
Can ChatGPT Defend its Belief in Truth? Evaluating LLM Reasoning via DebateBoshi Wang, Xiang Yue, Huan Sun
Large language models (LLMs) such as ChatGPT and GPT-4 have shown impressive performance in complex reasoning tasks. However, it is difficult to know whether the models are reasoning based on deep understandings of truth and logic, or leveraging their memorized patterns in a relatively superficial way. In this work, we explore testing LLMs' reasoning by engaging with them in a debate-like conversation, where given a question, the LLM and the user need to discuss to make the correct decision starting from opposing arguments. Upon mitigating the Clever Hans effect, our task requires the LLM to not only achieve the correct answer on its own, but also be able to hold and defend its belief instead of blindly believing or getting misled by the user's (invalid) arguments and critiques, thus testing in greater depth whether the LLM grasps the essence of the reasoning required to solve the problem. Across a range of complex reasoning benchmarks spanning math, commonsense, logic and BIG-Bench tasks, we find that despite their impressive performance as reported in existing work on generating correct step-by-step solutions in the beginning, LLMs like ChatGPT cannot maintain their beliefs in truth for a significant portion of examples when challenged by oftentimes absurdly invalid arguments. Our work points to danger zones of model alignment, and also suggests more careful treatments and interpretations of the recent findings that LLMs can improve their responses based on feedback.
Automatic Evaluation of Attribution by Large Language ModelsXiang Yue, Boshi Wang, Ziru Chen et al.
A recent focus of large language model (LLM) development, as exemplified by generative search engines, is to incorporate external references to generate and support its claims. However, evaluating the attribution, i.e., verifying whether the generated statement is fully supported by the cited reference, remains an open problem. Although human evaluation is common practice, it is costly and time-consuming. In this paper, we investigate the automatic evaluation of attribution given by LLMs. We begin by defining different types of attribution errors, and then explore two approaches for automatic evaluation: prompting LLMs and fine-tuning smaller LMs. The fine-tuning data is repurposed from related tasks such as question answering, fact-checking, natural language inference, and summarization. We manually curate a set of test examples covering 12 domains from a generative search engine, New Bing. Our results on this curated test set and simulated examples from existing benchmarks highlight both promising signals and challenges. We hope our problem formulation, testbeds, and findings will help lay the foundation for future studies on this important problem.
Differential Privacy for Text Analytics via Natural Text SanitizationXiang Yue, Minxin Du, Tianhao Wang et al.
Texts convey sophisticated knowledge. However, texts also convey sensitive information. Despite the success of general-purpose language models and domain-specific mechanisms with differential privacy (DP), existing text sanitization mechanisms still provide low utility, as cursed by the high-dimensional text representation. The companion issue of utilizing sanitized texts for downstream analytics is also under-explored. This paper takes a direct approach to text sanitization. Our insight is to consider both sensitivity and similarity via our new local DP notion. The sanitized texts also contribute to our sanitization-aware pretraining and fine-tuning, enabling privacy-preserving natural language processing over the BERT language model with promising utility. Surprisingly, the high utility does not boost up the success rate of inference attacks.
CliniQG4QA: Generating Diverse Questions for Domain Adaptation of Clinical Question AnsweringXiang Yue, Xinliang Frederick Zhang, Ziyu Yao et al.
Clinical question answering (QA) aims to automatically answer questions from medical professionals based on clinical texts. Studies show that neural QA models trained on one corpus may not generalize well to new clinical texts from a different institute or a different patient group, where large-scale QA pairs are not readily available for model retraining. To address this challenge, we propose a simple yet effective framework, CliniQG4QA, which leverages question generation (QG) to synthesize QA pairs on new clinical contexts and boosts QA models without requiring manual annotations. In order to generate diverse types of questions that are essential for training QA models, we further introduce a seq2seq-based question phrase prediction (QPP) module that can be used together with most existing QG models to diversify the generation. Our comprehensive experiment results show that the QA corpus generated by our framework can improve QA models on the new contexts (up to 8% absolute gain in terms of Exact Match), and that the QPP module plays a crucial role in achieving the gain.
PHICON: Improving Generalization of Clinical Text De-identification Models via Data AugmentationXiang Yue, Shuang Zhou
De-identification is the task of identifying protected health information (PHI) in the clinical text. Existing neural de-identification models often fail to generalize to a new dataset. We propose a simple yet effective data augmentation method PHICON to alleviate the generalization issue. PHICON consists of PHI augmentation and Context augmentation, which creates augmented training corpora by replacing PHI entities with named-entities sampled from external sources, and by changing background context with synonym replacement or random word insertion, respectively. Experimental results on the i2b2 2006 and 2014 de-identification challenge datasets show that PHICON can help three selected de-identification models boost F1-score (by at most 8.6%) on cross-dataset test setting. We also discuss how much augmentation to use and how each augmentation method influences the performance.
Clinical Reading Comprehension: A Thorough Analysis of the emrQA DatasetXiang Yue, Bernal Jimenez Gutierrez, Huan Sun
Machine reading comprehension has made great progress in recent years owing to large-scale annotated datasets. In the clinical domain, however, creating such datasets is quite difficult due to the domain expertise required for annotation. Recently, Pampari et al. (EMNLP'18) tackled this issue by using expert-annotated question templates and existing i2b2 annotations to create emrQA, the first large-scale dataset for question answering (QA) based on clinical notes. In this paper, we provide an in-depth analysis of this dataset and the clinical reading comprehension (CliniRC) task. From our qualitative analysis, we find that (i) emrQA answers are often incomplete, and (ii) emrQA questions are often answerable without using domain knowledge. From our quantitative experiments, surprising results include that (iii) using a small sampled subset (5%-20%), we can obtain roughly equal performance compared to the model trained on the entire dataset, (iv) this performance is close to human expert's performance, and (v) BERT models do not beat the best performing base model. Following our analysis of the emrQA, we further explore two desired aspects of CliniRC systems: the ability to utilize clinical domain knowledge and to generalize to unseen questions and contexts. We argue that both should be considered when creating future datasets.
0.2CLMar 6, 2020
Practical Annotation Strategies for Question Answering DatasetsBernhard Kratzwald, Xiang Yue, Huan Sun et al.
Annotating datasets for question answering (QA) tasks is very costly, as it requires intensive manual labor and often domain-specific knowledge. Yet strategies for annotating QA datasets in a cost-effective manner are scarce. To provide a remedy for practitioners, our objective is to develop heuristic rules for annotating a subset of questions, so that the annotation cost is reduced while maintaining both in- and out-of-domain performance. For this, we conduct a large-scale analysis in order to derive practical recommendations. First, we demonstrate experimentally that more training samples contribute often only to a higher in-domain test-set performance, but do not help the model in generalizing to unseen datasets. Second, we develop a model-guided annotation strategy: it makes a recommendation with regard to which subset of samples should be annotated. Its effectiveness is demonstrated in a case study based on domain customization of QA to a clinical setting. Here, remarkably, annotating a stratified subset with only 1.2% of the original training set achieves 97.7% of the performance as if the complete dataset was annotated. Hence, the labeling effort can be reduced immensely. Altogether, our work fulfills a demand in practice when labeling budgets are limited and where thus recommendations are needed for annotating QA datasets more cost-effectively.
Towards Making the Most of Context in Neural Machine TranslationZaixiang Zheng, Xiang Yue, Shujian Huang et al.
Document-level machine translation manages to outperform sentence level models by a small margin, but have failed to be widely adopted. We argue that previous research did not make a clear use of the global context, and propose a new document-level NMT framework that deliberately models the local context of each sentence with the awareness of the global context of the document in both source and target languages. We specifically design the model to be able to deal with documents containing any number of sentences, including single sentences. This unified approach allows our model to be trained elegantly on standard datasets without needing to train on sentence and document level data separately. Experimental results demonstrate that our model outperforms Transformer baselines and previous document-level NMT models with substantial margins of up to 2.1 BLEU on state-of-the-art baselines. We also provide analyses which show the benefit of context far beyond the neighboring two or three sentences, which previous studies have typically incorporated.
Graph Embedding on Biomedical Networks: Methods, Applications, and EvaluationsXiang Yue, Zhen Wang, Jingong Huang et al.
Graph embedding learning that aims to automatically learn low-dimensional node representations, has drawn increasing attention in recent years. To date, most recent graph embedding methods are evaluated on social and information networks and are not comprehensively studied on biomedical networks under systematic experiments and analyses. On the other hand, for a variety of biomedical network analysis tasks, traditional techniques such as matrix factorization (which can be seen as a type of graph embedding methods) have shown promising results, and hence there is a need to systematically evaluate the more recent graph embedding methods (e.g. random walk-based and neural network-based) in terms of their usability and potential to further the state-of-the-art. We select 11 representative graph embedding methods and conduct a systematic comparison on 3 important biomedical link prediction tasks: drug-disease association (DDA) prediction, drug-drug interaction (DDI) prediction, protein-protein interaction (PPI) prediction; and 2 node classification tasks: medical term semantic type classification, protein function prediction. Our experimental results demonstrate that the recent graph embedding methods achieve promising results and deserve more attention in the future biomedical graph analysis. Compared with three state-of-the-art methods for DDAs, DDIs and protein function predictions, the recent graph embedding methods achieve competitive performance without using any biological features and the learned embeddings can be treated as complementary representations for the biological features. By summarizing the experimental results, we provide general guidelines for properly selecting graph embedding methods and setting their hyper-parameters for different biomedical tasks.