NeurIPS 2024 Papers

While deep networks have achieved broad success in analyzing natural images, when applied to medical scans, they often fail in unexcepted situations. We investigate this challenge and focus on model sensitivity to domain shifts, such as data sampled from different hospitals or data confounded by demographic variables such as sex, race, etc, in the context of chest X-rays and skin lesion images. A key finding we show empirically is that existing visual backbones lack an appropriate prior from the architecture for reliable generalization in these settings. Taking inspiration from medical training, we propose giving deep networks a prior grounded in explicit medical knowledge communicated in natural language. To this end, we introduce Knowledge-enhanced Bottlenecks (KnoBo), a class of concept bottleneck models that incorporates knowledge priors that constrain it to reason with clinically relevant factors found in medical textbooks or PubMed. KnoBo uses retrieval-augmented language models to design an appropriate concept space paired with an automatic training procedure for recognizing the concept. We evaluate different resources of knowledge and recognition architectures on a broad range of domain shifts across 20 datasets. In our comprehensive evaluation with two imaging modalities, KnoBo outperforms fine-tuned models on confounded datasets by 32.4% on average. Finally, evaluations reveal that PubMed is a promising resource for making medical models less sensitive to domain shift, outperforming other resources on both diversity of information and final prediction performance.

Large language models (LLMs) typically utilize the top-k contexts from a retriever in retrieval-augmented generation (RAG). In this work, we propose a novel method called RankRAG, which instruction-tunes a single LLM for both context ranking and answer generation in RAG. In particular, the instruction-tuned LLMs work surprisingly well by adding a small fraction of ranking data into the training blend, and outperform existing expert ranking models, including the same LLM exclusively fine-tuned on a large amount of ranking data. For generation, we compare our model with many strong baselines, including ChatQA-1.5, an open-sourced model with the state-of-the-art performance on RAG benchmarks. Specifically, our Llama3-RankRAG-8B and Llama3-RankRAG-70B significantly outperform Llama3-ChatQA-1.5-8B and Llama3-ChatQA-1.5-70B, respectively, on nine general knowledge-intensive benchmarks for RAG. In addition, it also performs comparably to GPT-4 on five RAG benchmarks in the biomedical domain without instruction fine-tuning on biomedical data, demonstrating its superb capability for generalization to new domains.

Answering real-world complex queries, such as complex product search, often requires accurate retrieval from semi-structured knowledge bases that involve blend of unstructured (e.g., textual descriptions of products) and structured (e.g., entity relations of products) information. However, many previous works studied textual and relational retrieval tasks as separate topics. To address the gap, we develop STARK, a large-scale Semi-structure retrieval benchmark on Textual and Relational Knowledge Bases. Our benchmark covers three domains: product search, academic paper search, and queries in precision medicine. We design a novel pipeline to synthesize realistic user queries that integrate diverse relational information and complex textual properties, together with their ground-truth answers (items). We conduct rigorous human evaluation to validate the quality of our synthesized queries. We further enhance the benchmark with high-quality human-generated queries to provide an authentic reference. STARK serves as a comprehensive testbed for evaluating the performance of retrieval systems driven by large language models (LLMs). Our experiments suggest that STARK presents significant challenges to the current retrieval and LLM systems, highlighting the need for more capable semi-structured retrieval systems.

Large language models (LLMs) have rapidly advanced and demonstrated impressive capabilities. In-Context Learning (ICL) and Parameter-Efficient Fine-Tuning (PEFT) are currently two mainstream methods for augmenting LLMs to downstream tasks. ICL typically constructs a few-shot learning scenario, either manually or by setting up a Retrieval-Augmented Generation (RAG) system, helping models quickly grasp domain knowledge or question-answering patterns without changing model parameters. However, this approach involves trade-offs, such as slower inference speed and increased space occupancy. PEFT assists the model in adapting to tasks through minimal parameter modifications, but the training process still demands high hardware requirements, even with a small number of parameters involved. To address these challenges, we propose Reference Trustable Decoding (RTD), a paradigm that allows models to quickly adapt to new tasks without fine-tuning, maintaining low inference costs. RTD constructs a reference datastore from the provided training examples and optimizes the LLM's final vocabulary distribution by flexibly selecting suitable references based on the input, resulting in more trustable responses and enabling the model to adapt to downstream tasks at a low cost. Experimental evaluations on various LLMs using different benchmarks demonstrate that RTD establishes a new paradigm for augmenting models to downstream tasks. Furthermore, our method exhibits strong orthogonality with traditional methods, allowing for concurrent usage. Our code can be found at https://github.com/ShiLuohe/ReferenceTrustableDecoding.

Retrieval-Augmented Generation (RAG) has recently emerged as a promising solution to alleviate Large Language Model (LLM)’s deficiency in lack of knowledge. Existing RAG datasets, however, do not adequately represent the diverse and dynamic nature of real-world Question Answering (QA) tasks. To bridge this gap, we introduce the Comprehensive RAG Benchmark (CRAG), a factual question answering benchmark of 4,409 question-answer pairs and mock APIs to simulate web and Knowledge Graph (KG) search. CRAG is designed to encapsulate a diverse array of questions across five domains and eight question categories, reflecting varied entity popularity from popular to long-tail, and temporal dynamisms ranging from years to seconds. Our evaluation on this benchmark highlights the gap to fully trustworthy QA. Whereas most advanced LLMs achieve $\le 34\%$ accuracy on CRAG, adding RAG in a straightforward manner improves the accuracy only to 44%. State-of-the-art industry RAG solutions only answer 63% questions without any hallucination. CRAG also reveals much lower accuracy in answering questions regarding facts with higher dynamism, lower popularity, or higher complexity, suggesting future research directions. The CRAG benchmark laid the groundwork for a KDD Cup 2024 challenge, attracted thousands of participants and submissions. We commit to maintaining CRAG to serve research communities in advancing RAG solutions and general QA solutions. CRAG is available at https://github.com/facebookresearch/CRAG/.

Large Language Models (LLMs) have demonstrated remarkable capabilities in many real-world applications. Nonetheless, LLMs are often criticized for their tendency to produce hallucinations, wherein the models fabricate incorrect statements on tasks beyond their knowledge and perception. To alleviate this issue, graph retrieval-augmented generation (GraphRAG) has been extensively explored which leverages the factual knowledge in knowledge graphs (KGs) to ground the LLM's responses in established facts and principles. However, most state-of-the-art LLMs are closed-source, making it challenging to develop a prompting framework that can efficiently and effectively integrate KGs into LLMs with hard prompts only. Generally, existing KG-enhanced LLMs usually suffer from three critical issues, including huge search space, high API costs, and laborious prompt engineering, that impede their widespread application in practice. To this end, we introduce a novel **Know**ledge **Gr**aph based **P**romp**T**ing framework, namely **KnowGPT**, to enhance LLMs with domain knowledge. KnowGPT contains a knowledge extraction module to extract the most informative knowledge from KGs, and a context-aware prompt construction module to automatically convert extracted knowledge into effective prompts. Experiments on three benchmarks demonstrate that KnowGPT significantly outperforms all competitors. Notably, KnowGPT achieves a 92.6% accuracy on OpenbookQA leaderboard, comparable to human-level performance.

Enzymes are important proteins that catalyze chemical reactions. In recent years, machine learning methods have emerged to predict enzyme function from sequence; however, there are no standardized benchmarks to evaluate these methods. We introduce CARE, a benchmark and dataset suite for the Classification And Retrieval of Enzymes (CARE). CARE centers on two tasks: (1) classification of a protein sequence by its enzyme commission (EC) number and (2) retrieval of an EC number given a chemical reaction. For each task, we design train-test splits to evaluate different kinds of out-of-distribution generalization that are relevant to real use cases. For the classification task, we provide baselines for state-of-the-art methods. Because the retrieval task has not been previously formalized, we propose a method called Contrastive Reaction-EnzymE Pretraining (CREEP) as one of the first baselines for this task and compare it to the recent method, CLIPZyme. CARE is available at https://github.com/jsunn-y/CARE/.

Humans judge perceptual similarity according to diverse visual attributes, including scene layout, subject location, and camera pose. Existing vision models understand a wide range of semantic abstractions but improperly weigh these attributes and thus make inferences misaligned with human perception. While vision representations have previously benefited from human preference alignment in contexts like image generation, the utility of perceptually aligned representations in more general-purpose settings remains unclear. Here, we investigate how aligning vision model representations to human perceptual judgments impacts their usability in standard computer vision tasks. We finetune state-of-the-art models on a dataset of human similarity judgments for synthetic image triplets and evaluate them across diverse computer vision tasks. We find that aligning models to perceptual judgments yields representations that improve upon the original backbones across many downstream tasks, including counting, semantic segmentation, depth estimation, instance retrieval, and retrieval-augmented generation. In addition, we find that performance is widely preserved on other tasks, including specialized out-of-distribution domains such as in medical imaging and 3D environment frames. Our results suggest that injecting an inductive bias about human perceptual knowledge into vision models can make them better representation learners.

The use of Retrieval-Augmented Generation (RAG) has improved Large Language Models (LLMs) in collaborating with external data, yet significant challenges exist in real-world scenarios. In areas such as academic literature and finance question answering, data are often found in raw text and tables in HTML or PDF formats, which can be lengthy and highly unstructured. In this paper, we introduce a benchmark suite, namely Unstructured Document Analysis (UDA), that involves 2,965 real-world documents and 29,590 expert-annotated Q&A pairs. We revisit popular LLM- and RAG-based solutions for document analysis and evaluate the design choices and answer qualities across multiple document domains and diverse query types. Our evaluation yields interesting findings and highlights the importance of data parsing and retrieval. We hope our benchmark can shed light and better serve real-world document analysis applications. The benchmark suite and code can be found at https://github.com/qinchuanhui/UDA-Benchmark

Given a graph with textual attributes, we enable users to `chat with their graph': that is, to ask questions about the graph using a conversational interface. In response to a user's questions, our method provides textual replies and highlights the relevant parts of the graph. While existing works integrate large language models (LLMs) and graph neural networks (GNNs) in various ways, they mostly focus on either conventional graph tasks (such as node, edge, and graph classification), or on answering simple graph queries on small or synthetic graphs. In contrast, we develop a flexible question-answering framework targeting real-world textual graphs, applicable to multiple applications including scene graph understanding, common sense reasoning, and knowledge graph reasoning. Toward this goal, we first develop a Graph Question Answering (GraphQA) benchmark with data collected from different tasks. Then, we propose our \textit{G-Retriever} method, introducing the first retrieval-augmented generation (RAG) approach for general textual graphs, which can be fine-tuned to enhance graph understanding via soft prompting. To resist hallucination and to allow for textual graphs that greatly exceed the LLM's context window size, \textit{G-Retriever} performs RAG over a graph by formulating this task as a Prize-Collecting Steiner Tree optimization problem. Empirical evaluations show that our method outperforms baselines on textual graph tasks from multiple domains, scales well with larger graph sizes, and mitigates hallucination.~\footnote{Our codes and datasets are available at: \url{https://github.com/XiaoxinHe/G-Retriever}}

Addressing the challenge of effectively processing long contexts has become a critical issue for Large Language Models (LLMs). Two common strategies have emerged: 1) reducing the input length, such as retrieving relevant chunks by Retrieval-Augmented Generation (RAG), and 2) expanding the context window limit of LLMs. However, both strategies have drawbacks: input reduction has no guarantee of covering the part with needed information, while window extension struggles with focusing on the pertinent information for solving the task. To mitigate these limitations, we propose Chain-of-Agents (CoA), a novel framework that harnesses multi-agent collaboration through natural language to enable information aggregation and context reasoning across various LLMs over long-context tasks. CoA consists of multiple worker agents who sequentially communicate to handle different segmented portions of the text, followed by a manager agent who synthesizes these contributions into a coherent final output. CoA processes the entire input by interleaving reading and reasoning, and it mitigates long context focus issues by assigning each agent a short context. We perform a comprehensive evaluation of CoA on a wide range of long-context tasks in question answering, summarization, and code completion, demonstrating significant improvements by up to 10% over strong baselines of RAG, Full-Context, and multi-agent LLMs.

This study presents an Exploratory Retrieval-Augmented Planning (ExRAP) framework, designed to tackle continual instruction following tasks of embodied agents in dynamic, non-stationary environments. The framework enhances Large Language Models' (LLMs) embodied reasoning capabilities by efficiently exploring the physical environment and establishing the environmental context memory, thereby effectively grounding the task planning process in time-varying environment contexts. In ExRAP, given multiple continual instruction following tasks, each instruction is decomposed into queries on the environmental context memory and task executions conditioned on the query results. To efficiently handle these multiple tasks that are performed continuously and simultaneously, we implement an exploration-integrated task planning scheme by incorporating the information-based exploration into the LLM-based planning process. Combined with memory-augmented query evaluation, this integrated scheme not only allows for a better balance between the validity of the environmental context memory and the load of environment exploration, but also improves overall task performance. Furthermore, we devise a temporal consistency refinement scheme for query evaluation to address the inherent decay of knowledge in the memory. Through experiments with VirtualHome, ALFRED, and CARLA, our approach demonstrates robustness against a variety of embodied instruction following scenarios involving different instruction scales and types, and non-stationarity degrees, and it consistently outperforms other state-of-the-art LLM-based task planning approaches in terms of both goal success rate and execution efficiency.

Large Language Models (LLMs) are widely used for knowledge-seeking purposes yet suffer from hallucinations. The knowledge boundary of an LLM limits its factual understanding, beyond which it may begin to hallucinate. Investigating the perception of LLMs' knowledge boundary is crucial for detecting hallucinations and LLMs' reliable generation. Current studies perceive LLMs' knowledge boundary on questions with concrete answers (close-ended questions) while paying limited attention to semi-open-ended questions that correspond to many potential answers. Some researchers achieve it by judging whether the question is answerable or not. However, this paradigm is not so suitable for semi-open-ended questions, which are usually ``partially answerable questions'' containing both answerable answers and ambiguous (unanswerable) answers. Ambiguous answers are essential for knowledge-seeking, but it may go beyond the knowledge boundary of LLMs. In this paper, we perceive the LLMs' knowledge boundary with semi-open-ended questions by discovering more ambiguous answers. First, we apply an LLM-based approach to construct semi-open-ended questions and obtain answers from a target LLM. Unfortunately, the output probabilities of mainstream black-box LLMs are inaccessible to sample more low-probability ambiguous answers. Therefore, we apply an open-sourced auxiliary model to explore ambiguous answers for the target LLM. We calculate the nearest semantic representation for existing answers to estimate their probabilities, with which we reduce the generation probability of high-probability existing answers to achieve a more effective generation. Finally, we compare the results from the RAG-based evaluation and LLM self-evaluation to categorize four types of ambiguous answers that are beyond the knowledge boundary of the target LLM. Following our method, we construct a dataset to perceive the knowledge boundary for GPT-4. We find that GPT-4 performs poorly on semi-open-ended questions and is often unaware of its knowledge boundary. Besides, our auxiliary model, LLaMA-2-13B, is effective in discovering many ambiguous answers, including correct answers neglected by GPT-4 and delusive wrong answers GPT-4 struggles to identify.

Predicting the effects of protein mutations is crucial for analyzing protein functions and understanding genetic diseases. However, existing models struggle to effectively extract mutation-related local structure motifs from protein databases, which hinders their predictive accuracy and robustness. To tackle this problem, we design a novel retrieval-augmented framework for incorporating similar structure information in known protein structures. We create a vector database consisting of local structure motif embeddings from a pre-trained protein structure encoder, which allows for efficient retrieval of similar local structure motifs during mutation effect prediction. Our findings demonstrate that leveraging this method results in the SOTA performance across multiple protein mutation prediction datasets, and offers a scalable solution for studying mutation effects.

While Large Language Models (LLMs) have become immensely popular due to their outstanding performance on a broad range of tasks, these models are prone to producing hallucinations— outputs that are fallacious or fabricated yet often appear plausible or tenable at a glance. In this paper, we conduct a comprehensive investigation into the nature of hallucinations within LLMs and furthermore explore effective techniques for detecting such inaccuracies in various real-world settings. Prior approaches to detect hallucinations in LLM outputs, such as consistency checks or retrieval-based methods, typically assume access to multiple model responses or large databases. These techniques, however, tend to be computationally expensive in practice, thereby limiting their applicability to real-time analysis. In contrast, in this work, we seek to identify hallucinations within a single response in both white-box and black-box settings by analyzing the internal hidden states, attention maps, and output prediction probabilities of an auxiliary LLM. In addition, we also study hallucination detection in scenarios where ground-truth references are also available, such as in the setting of Retrieval-Augmented Generation (RAG). We demonstrate that the proposed detection methods are extremely compute-efficient, with speedups of up to 45x and 450x over other baselines, while achieving significant improvements in detection performance over diverse datasets.

Despite Retrieval-Augmented Generation (RAG) has shown promising capability in leveraging external knowledge, a comprehensive evaluation of RAG systems is still challenging due to the modular nature of RAG, evaluation of long-form responses and reliability of measurements. In this paper, we propose a fine-grained evaluation framework, RAGChecker, that incorporates a suite of diagnostic metrics for both the retrieval and generation modules. Meta evaluation verifies that RAGChecker has significantly better correlations with human judgments than other evaluation metrics. Using RAGChecker, we evaluate 8 RAG systems and conduct an in-depth analysis of their performance, revealing insightful patterns and trade-offs in the design choices of RAG architectures. The metrics of RAGChecker can guide researchers and practitioners in developing more effective RAG systems.

The rise of large language models (LLMs) has significantly transformed both the construction and application of information retrieval (IR) systems. However, current interactions between IR systems and LLMs remain limited, with LLMs merely serving as part of components within IR systems, and IR systems being constructed independently of LLMs. This separated architecture restricts knowledge sharing and deep collaboration between them. In this paper, we introduce Self-Retrieval, a novel end-to-end LLM-driven information retrieval architecture. Self-Retrieval unifies all essential IR functions within a single LLM, leveraging the inherent capabilities of LLMs throughout the IR process. Specifically, Self-Retrieval internalizes the retrieval corpus through self-supervised learning, transforms the retrieval process into sequential passage generation, and performs relevance assessment for reranking. Experimental results demonstrate that Self-Retrieval not only outperforms existing retrieval approaches by a significant margin, but also substantially enhances the performance of LLM-driven downstream applications like retrieval-augmented generation.

Forecasting future events is important for policy and decision making. In this work, we study whether language models (LMs) can forecast at the level of competitive human forecasters. Towards this goal, we develop a retrieval-augmented LM system designed to automatically search for relevant information, generate forecasts, and aggregate predictions. To facilitate our study, we collect a large dataset of questions from competitive forecasting platforms. Under a test set published after the knowledge cut-offs of our LMs, we evaluate the end-to-end performance of our system against the aggregates of human forecasts. On average, the system nears the crowd aggregate of competitive forecasters and, in a certain relaxed setting, surpasses it. Our work suggests that using LMs to forecasts the future could provide accurate predictions at scale and help to inform institutional decision making.

Graph Neural Networks (GNNs) have become essential in interpreting relational data across various domains, yet, they often struggle to generalize to unseen graph data that differs markedly from training instances. In this paper, we introduce a novel framework called General Retrieval-Augmented Graph Learning (RAGraph), which brings external graph data into the general graph foundation model to improve model generalization on unseen scenarios. On the top of our framework is a toy graph vector library that we established, which captures key attributes, such as features and task-specific label information. During inference, the RAGraph adeptly retrieves similar toy graphs based on key similarities in downstream tasks, integrating the retrieved data to enrich the learning context via the message-passing prompting mechanism. Our extensive experimental evaluations demonstrate that RAGraph significantly outperforms state-of-the-art graph learning methods in multiple tasks such as node classification, link prediction, and graph classification across both dynamic and static datasets. Furthermore, extensive testing confirms that RAGraph consistently maintains high performance without the need for task-specific fine-tuning, highlighting its adaptability, robustness, and broad applicability.