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Jan 2

Integration of Domain Knowledge using Medical Knowledge Graph Deep Learning for Cancer Phenotyping

A key component of deep learning (DL) for natural language processing (NLP) is word embeddings. Word embeddings that effectively capture the meaning and context of the word that they represent can significantly improve the performance of downstream DL models for various NLP tasks. Many existing word embeddings techniques capture the context of words based on word co-occurrence in documents and text; however, they often cannot capture broader domain-specific relationships between concepts that may be crucial for the NLP task at hand. In this paper, we propose a method to integrate external knowledge from medical terminology ontologies into the context captured by word embeddings. Specifically, we use a medical knowledge graph, such as the unified medical language system (UMLS), to find connections between clinical terms in cancer pathology reports. This approach aims to minimize the distance between connected clinical concepts. We evaluate the proposed approach using a Multitask Convolutional Neural Network (MT-CNN) to extract six cancer characteristics -- site, subsite, laterality, behavior, histology, and grade -- from a dataset of ~900K cancer pathology reports. The results show that the MT-CNN model which uses our domain informed embeddings outperforms the same MT-CNN using standard word2vec embeddings across all tasks, with an improvement in the overall micro- and macro-F1 scores by 4.97\%and 22.5\%, respectively.

  • 12 authors
·
Jan 4, 2021

EXplainable Neural-Symbolic Learning (X-NeSyL) methodology to fuse deep learning representations with expert knowledge graphs: the MonuMAI cultural heritage use case

The latest Deep Learning (DL) models for detection and classification have achieved an unprecedented performance over classical machine learning algorithms. However, DL models are black-box methods hard to debug, interpret, and certify. DL alone cannot provide explanations that can be validated by a non technical audience. In contrast, symbolic AI systems that convert concepts into rules or symbols -- such as knowledge graphs -- are easier to explain. However, they present lower generalisation and scaling capabilities. A very important challenge is to fuse DL representations with expert knowledge. One way to address this challenge, as well as the performance-explainability trade-off is by leveraging the best of both streams without obviating domain expert knowledge. We tackle such problem by considering the symbolic knowledge is expressed in form of a domain expert knowledge graph. We present the eXplainable Neural-symbolic learning (X-NeSyL) methodology, designed to learn both symbolic and deep representations, together with an explainability metric to assess the level of alignment of machine and human expert explanations. The ultimate objective is to fuse DL representations with expert domain knowledge during the learning process to serve as a sound basis for explainability. X-NeSyL methodology involves the concrete use of two notions of explanation at inference and training time respectively: 1) EXPLANet: Expert-aligned eXplainable Part-based cLAssifier NETwork Architecture, a compositional CNN that makes use of symbolic representations, and 2) SHAP-Backprop, an explainable AI-informed training procedure that guides the DL process to align with such symbolic representations in form of knowledge graphs. We showcase X-NeSyL methodology using MonuMAI dataset for monument facade image classification, and demonstrate that our approach improves explainability and performance.

  • 10 authors
·
Apr 24, 2021

MedReseacher-R1: Expert-Level Medical Deep Researcher via A Knowledge-Informed Trajectory Synthesis Framework

Recent developments in Large Language Model (LLM)-based agents have shown impressive capabilities spanning multiple domains, exemplified by deep research systems that demonstrate superior performance on complex information-seeking and synthesis tasks. While general-purpose deep research agents have shown impressive capabilities, they struggle significantly with medical domain challenges, as evidenced by leading proprietary systems achieving limited accuracy on complex medical benchmarks. The key limitations are: (1) the model lacks sufficient dense medical knowledge for clinical reasoning, and (2) the framework is constrained by the absence of specialized retrieval tools tailored for medical contexts.We present a medical deep research agent that addresses these challenges through two core innovations. First, we develop a novel data synthesis framework using medical knowledge graphs, extracting the longest chains from subgraphs around rare medical entities to generate complex multi-hop question-answer pairs. Second, we integrate a custom-built private medical retrieval engine alongside general-purpose tools, enabling accurate medical information synthesis. Our approach generates 2100+ diverse trajectories across 12 medical specialties, each averaging 4.2 tool interactions.Through a two-stage training paradigm combining supervised fine-tuning and online reinforcement learning with composite rewards, our MedResearcher-R1-32B model demonstrates exceptional performance, establishing new state-of-the-art results on medical benchmarks while maintaining competitive performance on general deep research tasks. Our work demonstrates that strategic domain-specific innovations in architecture, tool design, and training data construction can enable smaller open-source models to outperform much larger proprietary systems in specialized domains.

  • 15 authors
·
Aug 20, 2025 2

Knowledge-Aware Prompt Tuning for Generalizable Vision-Language Models

Pre-trained vision-language models, e.g., CLIP, working with manually designed prompts have demonstrated great capacity of transfer learning. Recently, learnable prompts achieve state-of-the-art performance, which however are prone to overfit to seen classes, failing to generalize to unseen classes. In this paper, we propose a Knowledge-Aware Prompt Tuning (KAPT) framework for vision-language models. Our approach takes inspiration from human intelligence in which external knowledge is usually incorporated into recognizing novel categories of objects. Specifically, we design two complementary types of knowledge-aware prompts for the text encoder to leverage the distinctive characteristics of category-related external knowledge. The discrete prompt extracts the key information from descriptions of an object category, and the learned continuous prompt captures overall contexts. We further design an adaptation head for the visual encoder to aggregate salient attentive visual cues, which establishes discriminative and task-aware visual representations. We conduct extensive experiments on 11 widely-used benchmark datasets and the results verify the effectiveness in few-shot image classification, especially in generalizing to unseen categories. Compared with the state-of-the-art CoCoOp method, KAPT exhibits favorable performance and achieves an absolute gain of 3.22% on new classes and 2.57% in terms of harmonic mean.

  • 6 authors
·
Aug 22, 2023

DKPLM: Decomposable Knowledge-enhanced Pre-trained Language Model for Natural Language Understanding

Knowledge-Enhanced Pre-trained Language Models (KEPLMs) are pre-trained models with relation triples injecting from knowledge graphs to improve language understanding abilities. To guarantee effective knowledge injection, previous studies integrate models with knowledge encoders for representing knowledge retrieved from knowledge graphs. The operations for knowledge retrieval and encoding bring significant computational burdens, restricting the usage of such models in real-world applications that require high inference speed. In this paper, we propose a novel KEPLM named DKPLM that Decomposes Knowledge injection process of the Pre-trained Language Models in pre-training, fine-tuning and inference stages, which facilitates the applications of KEPLMs in real-world scenarios. Specifically, we first detect knowledge-aware long-tail entities as the target for knowledge injection, enhancing the KEPLMs' semantic understanding abilities and avoiding injecting redundant information. The embeddings of long-tail entities are replaced by "pseudo token representations" formed by relevant knowledge triples. We further design the relational knowledge decoding task for pre-training to force the models to truly understand the injected knowledge by relation triple reconstruction. Experiments show that our model outperforms other KEPLMs significantly over zero-shot knowledge probing tasks and multiple knowledge-aware language understanding tasks. We further show that DKPLM has a higher inference speed than other competing models due to the decomposing mechanism.

  • 7 authors
·
Dec 2, 2021

Physics of Language Models: Part 3.3, Knowledge Capacity Scaling Laws

Scaling laws describe the relationship between the size of language models and their capabilities. Unlike prior studies that evaluate a model's capability via loss or benchmarks, we estimate the number of knowledge bits a model stores. We focus on factual knowledge represented as tuples, such as (USA, capital, Washington D.C.) from a Wikipedia page. Through multiple controlled datasets, we establish that language models can and only can store 2 bits of knowledge per parameter, even when quantized to int8, and such knowledge can be flexibly extracted for downstream applications. Consequently, a 7B model can store 14B bits of knowledge, surpassing the English Wikipedia and textbooks combined based on our estimation. More broadly, we present 12 results on how (1) training duration, (2) model architecture, (3) quantization, (4) sparsity constraints such as MoE, and (5) data signal-to-noise ratio affect a model's knowledge storage capacity. Notable insights include: * The GPT-2 architecture, with rotary embedding, matches or even surpasses LLaMA/Mistral architectures in knowledge storage, particularly over shorter training durations. This arises because LLaMA/Mistral uses GatedMLP, which is less stable and harder to train. * Prepending training data with domain names (e.g., wikipedia.org) significantly increases a model's knowledge capacity. Language models can autonomously identify and prioritize domains rich in knowledge, optimizing their storage capacity.

  • 2 authors
·
Apr 8, 2024

Know2Vec: A Black-Box Proxy for Neural Network Retrieval

For general users, training a neural network from scratch is usually challenging and labor-intensive. Fortunately, neural network zoos enable them to find a well-performing model for directly use or fine-tuning it in their local environments. Although current model retrieval solutions attempt to convert neural network models into vectors to avoid complex multiple inference processes required for model selection, it is still difficult to choose a suitable model due to inaccurate vectorization and biased correlation alignment between the query dataset and models. From the perspective of knowledge consistency, i.e., whether the knowledge possessed by the model can meet the needs of query tasks, we propose a model retrieval scheme, named Know2Vec, that acts as a black-box retrieval proxy for model zoo. Know2Vec first accesses to models via a black-box interface in advance, capturing vital decision knowledge from models while ensuring their privacy. Next, it employs an effective encoding technique to transform the knowledge into precise model vectors. Secondly, it maps the user's query task to a knowledge vector by probing the semantic relationships within query samples. Furthermore, the proxy ensures the knowledge-consistency between query vector and model vectors within their alignment space, which is optimized through the supervised learning with diverse loss functions, and finally it can identify the most suitable model for a given task during the inference stage. Extensive experiments show that our Know2Vec achieves superior retrieval accuracy against the state-of-the-art methods in diverse neural network retrieval tasks.

  • 6 authors
·
Dec 19, 2024

Zero-shot and Few-shot Learning with Knowledge Graphs: A Comprehensive Survey

Machine learning especially deep neural networks have achieved great success but many of them often rely on a number of labeled samples for supervision. As sufficient labeled training data are not always ready due to e.g., continuously emerging prediction targets and costly sample annotation in real world applications, machine learning with sample shortage is now being widely investigated. Among all these studies, many prefer to utilize auxiliary information including those in the form of Knowledge Graph (KG) to reduce the reliance on labeled samples. In this survey, we have comprehensively reviewed over 90 papers about KG-aware research for two major sample shortage settings -- zero-shot learning (ZSL) where some classes to be predicted have no labeled samples, and few-shot learning (FSL) where some classes to be predicted have only a small number of labeled samples that are available. We first introduce KGs used in ZSL and FSL as well as their construction methods, and then systematically categorize and summarize KG-aware ZSL and FSL methods, dividing them into different paradigms such as the mapping-based, the data augmentation, the propagation-based and the optimization-based. We next present different applications, including not only KG augmented prediction tasks such as image classification, question answering, text classification and knowledge extraction, but also KG completion tasks, and some typical evaluation resources for each task. We eventually discuss some challenges and open problems from different perspectives.

  • 8 authors
·
Dec 18, 2021

Correlation and Navigation in the Vocabulary Key Representation Space of Language Models

Language model (LM) decoding is based on the next-token prediction (NTP) probability distribution. For neural LMs (e.g., Transformer-based), NTP distribution is essentially a softmax-regularized dot product between an encoded input context (query) and fixed vocabulary representations (keys). In this paper, we study the effect of the key distribution on the NTP distribution, with a focus on whether the similarity between keys will trigger spurious correlations in NTP. Through knowledge-probing tasks, we show that in the NTP distribution, the few top-ranked tokens are typically accurate. However, the middle-ranked prediction is highly biased towards the tokens that are distributionally (not necessarily semantically) similar to these top ones. For instance, if "P" is predicted as the top-1 token, "A"-"Z" will all be ranked high in NTP, no matter whether they can lead to correct decoding results. This hurts the sampling diversity and makes the sampling of correct, long-tail results hopeless and noisy. We attempt to alleviate this issue via a novel in-context method that iteratively pushes the query representation away from explored regions. Specifically, we include the explored decoding results in the context and prompt the LM to generate something else, which encourages the LM to produce a query representation that has small dot products with explored keys. Experiments on knowledge-probing tasks show that our method leads to efficient navigation away from explored keys to correct new keys. We further extend our method to open-ended and chain-of-thought (for reasoning) generation. Experiment results show that ICN contributes to better generation diversity and improved self-consistency voting performance. Finally, we discuss potential training issues caused by the fixed key space together with the challenges and possible ways to address them in future research.

  • 3 authors
·
Oct 3, 2024

Knowledge Solver: Teaching LLMs to Search for Domain Knowledge from Knowledge Graphs

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.

  • 3 authors
·
Sep 6, 2023

KnowPO: Knowledge-aware Preference Optimization for Controllable Knowledge Selection in Retrieval-Augmented Language Models

By integrating external knowledge, Retrieval-Augmented Generation (RAG) has become an effective strategy for mitigating the hallucination problems that large language models (LLMs) encounter when dealing with knowledge-intensive tasks. However, in the process of integrating external non-parametric supporting evidence with internal parametric knowledge, inevitable knowledge conflicts may arise, leading to confusion in the model's responses. To enhance the knowledge selection of LLMs in various contexts, some research has focused on refining their behavior patterns through instruction-tuning. Nonetheless, due to the absence of explicit negative signals and comparative objectives, models fine-tuned in this manner may still exhibit undesirable behaviors such as contextual ignorance and contextual overinclusion. To this end, we propose a Knowledge-aware Preference Optimization strategy, dubbed KnowPO, aimed at achieving adaptive knowledge selection based on contextual relevance in real retrieval scenarios. Concretely, we proposed a general paradigm for constructing knowledge conflict datasets, which comprehensively cover various error types and learn how to avoid these negative signals through preference optimization methods. Simultaneously, we proposed a rewriting strategy and data ratio optimization strategy to address preference imbalances. Experimental results show that KnowPO outperforms previous methods for handling knowledge conflicts by over 37\%, while also exhibiting robust generalization across various out-of-distribution datasets.

  • 8 authors
·
Aug 6, 2024

Knowledge Infused Decoding

Pre-trained language models (LMs) have been shown to memorize a substantial amount of knowledge from the pre-training corpora; however, they are still limited in recalling factually correct knowledge given a certain context. Hence, they tend to suffer from counterfactual or hallucinatory generation when used in knowledge-intensive natural language generation (NLG) tasks. Recent remedies to this problem focus on modifying either the pre-training or task fine-tuning objectives to incorporate knowledge, which normally require additional costly training or architecture modification of LMs for practical applications. We present Knowledge Infused Decoding (KID) -- a novel decoding algorithm for generative LMs, which dynamically infuses external knowledge into each step of the LM decoding. Specifically, we maintain a local knowledge memory based on the current context, interacting with a dynamically created external knowledge trie, and continuously update the local memory as a knowledge-aware constraint to guide decoding via reinforcement learning. On six diverse knowledge-intensive NLG tasks, task-agnostic LMs (e.g., GPT-2 and BART) armed with KID outperform many task-optimized state-of-the-art models, and show particularly strong performance in few-shot scenarios over seven related knowledge-infusion techniques. Human evaluation confirms KID's ability to generate more relevant and factual language for the input context when compared with multiple baselines. Finally, KID also alleviates exposure bias and provides stable generation quality when generating longer sequences. Code for KID is available at https://github.com/microsoft/KID.

  • 8 authors
·
Apr 6, 2022

BertNet: Harvesting Knowledge Graphs with Arbitrary Relations from Pretrained Language Models

It is crucial to automatically construct knowledge graphs (KGs) of diverse new relations to support knowledge discovery and broad applications. Previous KG construction methods, based on either crowdsourcing or text mining, are often limited to a small predefined set of relations due to manual cost or restrictions in text corpus. Recent research proposed to use pretrained language models (LMs) as implicit knowledge bases that accept knowledge queries with prompts. Yet, the implicit knowledge lacks many desirable properties of a full-scale symbolic KG, such as easy access, navigation, editing, and quality assurance. In this paper, we propose a new approach of harvesting massive KGs of arbitrary relations from pretrained LMs. With minimal input of a relation definition (a prompt and a few shot of example entity pairs), the approach efficiently searches in the vast entity pair space to extract diverse accurate knowledge of the desired relation. We develop an effective search-and-rescore mechanism for improved efficiency and accuracy. We deploy the approach to harvest KGs of over 400 new relations from different LMs. Extensive human and automatic evaluations show our approach manages to extract diverse accurate knowledge, including tuples of complex relations (e.g., "A is capable of but not good at B"). The resulting KGs as a symbolic interpretation of the source LMs also reveal new insights into the LMs' knowledge capacities.

  • 8 authors
·
Jun 28, 2022

Fantastic Gains and Where to Find Them: On the Existence and Prospect of General Knowledge Transfer between Any Pretrained Model

Training deep networks requires various design decisions regarding for instance their architecture, data augmentation, or optimization. In this work, we find these training variations to result in networks learning unique feature sets from the data. Using public model libraries comprising thousands of models trained on canonical datasets like ImageNet, we observe that for arbitrary pairings of pretrained models, one model extracts significant data context unavailable in the other -- independent of overall performance. Given any arbitrary pairing of pretrained models and no external rankings (such as separate test sets, e.g. due to data privacy), we investigate if it is possible to transfer such "complementary" knowledge from one model to another without performance degradation -- a task made particularly difficult as additional knowledge can be contained in stronger, equiperformant or weaker models. Yet facilitating robust transfer in scenarios agnostic to pretrained model pairings would unlock auxiliary gains and knowledge fusion from any model repository without restrictions on model and problem specifics - including from weaker, lower-performance models. This work therefore provides an initial, in-depth exploration on the viability of such general-purpose knowledge transfer. Across large-scale experiments, we first reveal the shortcomings of standard knowledge distillation techniques, and then propose a much more general extension through data partitioning for successful transfer between nearly all pretrained models, which we show can also be done unsupervised. Finally, we assess both the scalability and impact of fundamental model properties on successful model-agnostic knowledge transfer.

  • 6 authors
·
Oct 26, 2023

Augmenting Pre-trained Language Models with QA-Memory for Open-Domain Question Answering

Retrieval augmented language models have recently become the standard for knowledge intensive tasks. Rather than relying purely on latent semantics within the parameters of large neural models, these methods enlist a semi-parametric memory to encode an index of knowledge for the model to retrieve over. Most prior work has employed text passages as the unit of knowledge, which has high coverage at the cost of interpretability, controllability, and efficiency. The opposite properties arise in other methods which have instead relied on knowledge base (KB) facts. At the same time, more recent work has demonstrated the effectiveness of storing and retrieving from an index of Q-A pairs derived from text lewis2021paq. This approach yields a high coverage knowledge representation that maintains KB-like properties due to its representations being more atomic units of information. In this work we push this line of research further by proposing a question-answer augmented encoder-decoder model and accompanying pretraining strategy. This yields an end-to-end system that not only outperforms prior QA retrieval methods on single-hop QA tasks but also enables compositional reasoning, as demonstrated by strong performance on two multi-hop QA datasets. Together, these methods improve the ability to interpret and control the model while narrowing the performance gap with passage retrieval systems.

  • 5 authors
·
Apr 9, 2022

FaithfulRAG: Fact-Level Conflict Modeling for Context-Faithful Retrieval-Augmented Generation

Large language models (LLMs) augmented with retrieval systems have demonstrated significant potential in handling knowledge-intensive tasks. However, these models often struggle with unfaithfulness issues, generating outputs that either ignore the retrieved context or inconsistently blend it with the LLM`s parametric knowledge. This issue is particularly severe in cases of knowledge conflict, where the retrieved context conflicts with the model`s parametric knowledge. While existing faithful RAG approaches enforce strict context adherence through well-designed prompts or modified decoding strategies, our analysis reveals a critical limitation: they achieve faithfulness by forcibly suppressing the model`s parametric knowledge, which undermines the model`s internal knowledge structure and increases the risk of misinterpreting the context. To this end, this paper proposes FaithfulRAG, a novel framework that resolves knowledge conflicts by explicitly modeling discrepancies between the model`s parametric knowledge and retrieved context. Specifically, FaithfulRAG identifies conflicting knowledge at the fact level and designs a self-thinking process, allowing LLMs to reason about and integrate conflicting facts before generating responses. Extensive experiments demonstrate that our method outperforms state-of-the-art methods. The code is available at https:// github.com/DeepLearnXMU/Faithful-RAG

  • 7 authors
·
Jun 10, 2025

A Comprehensive Study of Knowledge Editing for Large Language Models

Large Language Models (LLMs) have shown extraordinary capabilities in understanding and generating text that closely mirrors human communication. However, a primary limitation lies in the significant computational demands during training, arising from their extensive parameterization. This challenge is further intensified by the dynamic nature of the world, necessitating frequent updates to LLMs to correct outdated information or integrate new knowledge, thereby ensuring their continued relevance. Note that many applications demand continual model adjustments post-training to address deficiencies or undesirable behaviors. There is an increasing interest in efficient, lightweight methods for on-the-fly model modifications. To this end, recent years have seen a burgeoning in the techniques of knowledge editing for LLMs, which aim to efficiently modify LLMs' behaviors within specific domains while preserving overall performance across various inputs. In this paper, we first define the knowledge editing problem and then provide a comprehensive review of cutting-edge approaches. Drawing inspiration from educational and cognitive research theories, we propose a unified categorization criterion that classifies knowledge editing methods into three groups: resorting to external knowledge, merging knowledge into the model, and editing intrinsic knowledge. Furthermore, we introduce a new benchmark, KnowEdit, for a comprehensive empirical evaluation of representative knowledge editing approaches. Additionally, we provide an in-depth analysis of knowledge location, which can provide a deeper understanding of the knowledge structures inherent within LLMs. Finally, we discuss several potential applications of knowledge editing, outlining its broad and impactful implications.

  • 22 authors
·
Jan 2, 2024

Augmenting LLMs with Knowledge: A survey on hallucination prevention

Large pre-trained language models have demonstrated their proficiency in storing factual knowledge within their parameters and achieving remarkable results when fine-tuned for downstream natural language processing tasks. Nonetheless, their capacity to access and manipulate knowledge with precision remains constrained, resulting in performance disparities on knowledge-intensive tasks when compared to task-specific architectures. Additionally, the challenges of providing provenance for model decisions and maintaining up-to-date world knowledge persist as open research frontiers. To address these limitations, the integration of pre-trained models with differentiable access mechanisms to explicit non-parametric memory emerges as a promising solution. This survey delves into the realm of language models (LMs) augmented with the ability to tap into external knowledge sources, including external knowledge bases and search engines. While adhering to the standard objective of predicting missing tokens, these augmented LMs leverage diverse, possibly non-parametric external modules to augment their contextual processing capabilities, departing from the conventional language modeling paradigm. Through an exploration of current advancements in augmenting large language models with knowledge, this work concludes that this emerging research direction holds the potential to address prevalent issues in traditional LMs, such as hallucinations, un-grounded responses, and scalability challenges.

  • 2 authors
·
Sep 28, 2023

NLKI: A lightweight Natural Language Knowledge Integration Framework for Improving Small VLMs in Commonsense VQA Tasks

Commonsense visual-question answering often hinges on knowledge that is missing from the image or the question. Small vision-language models (sVLMs) such as ViLT, VisualBERT and FLAVA therefore lag behind their larger generative counterparts. To study the effect of careful commonsense knowledge integration on sVLMs, we present an end-to-end framework (NLKI) that (i) retrieves natural language facts, (ii) prompts an LLM to craft natural language explanations, and (iii) feeds both signals to sVLMs respectively across two commonsense VQA datasets (CRIC, AOKVQA) and a visual-entailment dataset (e-SNLI-VE). Facts retrieved using a fine-tuned ColBERTv2 and an object information-enriched prompt yield explanations that largely cut down hallucinations, while lifting the end-to-end answer accuracy by up to 7% (across 3 datasets), making FLAVA and other models in NLKI match or exceed medium-sized VLMs such as Qwen-2 VL-2B and SmolVLM-2.5B. As these benchmarks contain 10-25% label noise, additional finetuning using noise-robust losses (such as symmetric cross entropy and generalised cross entropy) adds another 2.5% in CRIC, and 5.5% in AOKVQA. Our findings expose when LLM-based commonsense knowledge beats retrieval from commonsense knowledge bases, how noise-aware training stabilises small models in the context of external knowledge augmentation, and why parameter-efficient commonsense reasoning is now within reach for 250M models.

  • 4 authors
·
Aug 27, 2025

LFD: Layer Fused Decoding to Exploit External Knowledge in Retrieval-Augmented Generation

Retrieval-augmented generation (RAG) incorporates external knowledge into large language models (LLMs), improving their adaptability to downstream tasks and enabling information updates. Surprisingly, recent empirical evidence demonstrates that injecting noise into retrieved relevant documents paradoxically facilitates exploitation of external knowledge and improves generation quality. Although counterintuitive and challenging to apply in practice, this phenomenon enables granular control and rigorous analysis of how LLMs integrate external knowledge. Therefore, in this paper, we intervene on noise injection and establish a layer-specific functional demarcation within the LLM: shallow layers specialize in local context modeling, intermediate layers focus on integrating long-range external factual knowledge, and deeper layers primarily rely on parametric internal knowledge. Building on this insight, we propose Layer Fused Decoding (LFD), a simple decoding strategy that directly combines representations from an intermediate layer with final-layer decoding outputs to fully exploit the external factual knowledge. To identify the optimal intermediate layer, we introduce an internal knowledge score (IKS) criterion that selects the layer with the lowest IKS value in the latter half of layers. Experimental results across multiple benchmarks demonstrate that LFD helps RAG systems more effectively surface retrieved context knowledge with minimal cost.

  • 10 authors
·
Aug 27, 2025

Semantic Representation and Inference for NLP

Semantic representation and inference is essential for Natural Language Processing (NLP). The state of the art for semantic representation and inference is deep learning, and particularly Recurrent Neural Networks (RNNs), Convolutional Neural Networks (CNNs), and transformer Self-Attention models. This thesis investigates the use of deep learning for novel semantic representation and inference, and makes contributions in the following three areas: creating training data, improving semantic representations and extending inference learning. In terms of creating training data, we contribute the largest publicly available dataset of real-life factual claims for the purpose of automatic claim verification (MultiFC), and we present a novel inference model composed of multi-scale CNNs with different kernel sizes that learn from external sources to infer fact checking labels. In terms of improving semantic representations, we contribute a novel model that captures non-compositional semantic indicators. By definition, the meaning of a non-compositional phrase cannot be inferred from the individual meanings of its composing words (e.g., hot dog). Motivated by this, we operationalize the compositionality of a phrase contextually by enriching the phrase representation with external word embeddings and knowledge graphs. Finally, in terms of inference learning, we propose a series of novel deep learning architectures that improve inference by using syntactic dependencies, by ensembling role guided attention heads, incorporating gating layers, and concatenating multiple heads in novel and effective ways. This thesis consists of seven publications (five published and two under review).

  • 1 authors
·
Jun 15, 2021

A Textbook Remedy for Domain Shifts: Knowledge Priors for Medical Image Analysis

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.

  • 8 authors
·
May 23, 2024

PIKE-RAG: sPecIalized KnowledgE and Rationale Augmented Generation

Despite notable advancements in Retrieval-Augmented Generation (RAG) systems that expand large language model (LLM) capabilities through external retrieval, these systems often struggle to meet the complex and diverse needs of real-world industrial applications. The reliance on retrieval alone proves insufficient for extracting deep, domain-specific knowledge performing in logical reasoning from specialized corpora. To address this, we introduce sPecIalized KnowledgE and Rationale Augmentation Generation (PIKE-RAG), focusing on extracting, understanding, and applying specialized knowledge, while constructing coherent rationale to incrementally steer LLMs toward accurate responses. Recognizing the diverse challenges of industrial tasks, we introduce a new paradigm that classifies tasks based on their complexity in knowledge extraction and application, allowing for a systematic evaluation of RAG systems' problem-solving capabilities. This strategic approach offers a roadmap for the phased development and enhancement of RAG systems, tailored to meet the evolving demands of industrial applications. Furthermore, we propose knowledge atomizing and knowledge-aware task decomposition to effectively extract multifaceted knowledge from the data chunks and iteratively construct the rationale based on original query and the accumulated knowledge, respectively, showcasing exceptional performance across various benchmarks.

  • 5 authors
·
Jan 20, 2025

Leveraging Open Knowledge for Advancing Task Expertise in Large Language Models

The cultivation of expertise for large language models (LLMs) to solve tasks of specific areas often requires special-purpose tuning with calibrated behaviors on the expected stable outputs. To avoid huge cost brought by manual preparation of instruction datasets and training resources up to hundreds of hours, the exploitation of open knowledge including a wealth of low rank adaptation (LoRA) models and instruction datasets serves as a good starting point. However, existing methods on model and data selection focus on the performance of general-purpose capabilities while neglecting the knowledge gap exposed in domain-specific deployment. In the present study, we propose to bridge such gap by introducing few human-annotated samples (i.e., K-shot) for advancing task expertise of LLMs with open knowledge. Specifically, we develop an efficient and scalable pipeline to cost-efficiently produce task experts where K-shot data intervene in selecting the most promising expert candidates and the task-relevant instructions. A mixture-of-expert (MoE) system is built to make the best use of individual-yet-complementary knowledge between multiple experts. We unveil the two keys to the success of a MoE system, 1) the abidance by K-shot, and 2) the insistence on diversity. For the former, we ensure that models that truly possess problem-solving abilities on K-shot are selected rather than those blind guessers. Besides, during data selection, instructions that share task-relevant contexts with K-shot are prioritized. For the latter, we highlight the diversity of constituting experts and that of the fine-tuning instructions throughout the model and data selection process. Extensive experimental results confirm the superiority of our approach over existing methods on utilization of open knowledge across various tasks. Codes and models will be released later.

  • 12 authors
·
Aug 28, 2024 4

CooK: Empowering General-Purpose Language Models with Modular and Collaborative Knowledge

Large language models (LLMs) are increasingly adopted for knowledge-intensive tasks and contexts. Existing approaches improve the knowledge capabilities of general-purpose LLMs through retrieval or generated knowledge prompting, but they fall short of reflecting two key properties of knowledge-rich models: knowledge should be modular, ever-growing, sourced from diverse domains; knowledge acquisition and production should be a collaborative process, where diverse stakeholders contribute new information. To this end, we propose CooK, a novel framework to empower general-purpose large language models with modular and collaboratively sourced knowledge. We first introduce specialized language models, autoregressive models trained on corpora from a wide range of domains and sources. These specialized LMs serve as parametric knowledge repositories that are later prompted to generate background knowledge for general-purpose LLMs. We then propose three knowledge filters to dynamically select and retain information in generated documents by controlling for relevance, brevity, and factuality. Finally, we propose bottom-up and top-down knowledge integration approaches to augment general-purpose LLMs with the curated (relevant, factual) knowledge from community-driven specialized LMs that enable multi-domain knowledge synthesis and on-demand knowledge requests. Through extensive experiments, we demonstrate that CooK achieves state-of-the-art performance on six benchmark datasets. Our results highlight the potential of enriching general-purpose LLMs with evolving and modular knowledge -- relevant knowledge that can be continuously updated through the collective efforts of the research community.

  • 6 authors
·
May 17, 2023

Prompting Large Language Models with Answer Heuristics for Knowledge-based Visual Question Answering

Knowledge-based visual question answering (VQA) requires external knowledge beyond the image to answer the question. Early studies retrieve required knowledge from explicit knowledge bases (KBs), which often introduces irrelevant information to the question, hence restricting the performance of their models. Recent works have sought to use a large language model (i.e., GPT-3) as an implicit knowledge engine to acquire the necessary knowledge for answering. Despite the encouraging results achieved by these methods, we argue that they have not fully activated the capacity of GPT-3 as the provided input information is insufficient. In this paper, we present Prophet -- a conceptually simple framework designed to prompt GPT-3 with answer heuristics for knowledge-based VQA. Specifically, we first train a vanilla VQA model on a specific knowledge-based VQA dataset without external knowledge. After that, we extract two types of complementary answer heuristics from the model: answer candidates and answer-aware examples. Finally, the two types of answer heuristics are encoded into the prompts to enable GPT-3 to better comprehend the task thus enhancing its capacity. Prophet significantly outperforms all existing state-of-the-art methods on two challenging knowledge-based VQA datasets, OK-VQA and A-OKVQA, delivering 61.1% and 55.7% accuracies on their testing sets, respectively.

  • 4 authors
·
Mar 3, 2023

Establishing Knowledge Preference in Language Models

Language models are known to encode a great amount of factual knowledge through pretraining. However, such knowledge might be insufficient to cater to user requests, requiring the model to integrate external knowledge sources and adhere to user-provided specifications. When answering questions about ongoing events, the model should use recent news articles to update its response; when asked to provide recommendations, the model should prioritize user specifications over retrieved product reviews; when some facts are edited in the model, the updated facts should override all prior knowledge learned by the model even if they are conflicting. In all of the cases above, the model faces a decision between its own parametric knowledge, (retrieved) contextual knowledge, and user instruction knowledge. In this paper, we (1) unify such settings into the problem of knowledge preference and define a three-level preference hierarchy over these knowledge sources; (2) compile a collection of existing datasets IfQA, MQuAKE, and MRQA covering a combination of settings (with/without user specifications, with/without context documents) to systematically evaluate how well models obey the intended knowledge preference; and (3) propose a dataset synthesis method that composes diverse question-answer pairs with user assumptions and related context to directly fine-tune LMs for instilling the hierarchy of knowledge. We demonstrate that a 7B model, fine-tuned on only a few thousand examples automatically generated by our proposed method, effectively achieves superior performance (more than 18% improvement across all evaluation benchmarks) in adhering to the desired knowledge preference hierarchy.

  • 6 authors
·
Jul 17, 2024

NeuroComparatives: Neuro-Symbolic Distillation of Comparative Knowledge

Comparative knowledge (e.g., steel is stronger and heavier than styrofoam) is an essential component of our world knowledge, yet understudied in prior literature. In this paper, we harvest the dramatic improvements in knowledge capabilities of language models into a large-scale comparative knowledge base. While the ease of acquisition of such comparative knowledge is much higher from extreme-scale models like GPT-4, compared to their considerably smaller and weaker counterparts such as GPT-2, not even the most powerful models are exempt from making errors. We thus ask: to what extent are models at different scales able to generate valid and diverse comparative knowledge? We introduce NeuroComparatives, a novel framework for comparative knowledge distillation overgenerated from language models such as GPT-variants and LLaMA, followed by stringent filtering of the generated knowledge. Our framework acquires comparative knowledge between everyday objects, producing a corpus of up to 8.8M comparisons over 1.74M entity pairs - 10X larger and 30% more diverse than existing resources. Moreover, human evaluations show that NeuroComparatives outperform existing resources in terms of validity (up to 32% absolute improvement). Our acquired NeuroComparatives leads to performance improvements on five downstream tasks. We find that neuro-symbolic manipulation of smaller models offers complementary benefits to the currently dominant practice of prompting extreme-scale language models for knowledge distillation.

  • 6 authors
·
May 8, 2023

SKA-Bench: A Fine-Grained Benchmark for Evaluating Structured Knowledge Understanding of LLMs

Although large language models (LLMs) have made significant progress in understanding Structured Knowledge (SK) like KG and Table, existing evaluations for SK understanding are non-rigorous (i.e., lacking evaluations of specific capabilities) and focus on a single type of SK. Therefore, we aim to propose a more comprehensive and rigorous structured knowledge understanding benchmark to diagnose the shortcomings of LLMs. In this paper, we introduce SKA-Bench, a Structured Knowledge Augmented QA Benchmark that encompasses four widely used structured knowledge forms: KG, Table, KG+Text, and Table+Text. We utilize a three-stage pipeline to construct SKA-Bench instances, which includes a question, an answer, positive knowledge units, and noisy knowledge units. To evaluate the SK understanding capabilities of LLMs in a fine-grained manner, we expand the instances into four fundamental ability testbeds: Noise Robustness, Order Insensitivity, Information Integration, and Negative Rejection. Empirical evaluations on 8 representative LLMs, including the advanced DeepSeek-R1, indicate that existing LLMs still face significant challenges in understanding structured knowledge, and their performance is influenced by factors such as the amount of noise, the order of knowledge units, and hallucination phenomenon. Our dataset and code are available at https://github.com/Lza12a/SKA-Bench.

  • 7 authors
·
Jul 22, 2025

Harnessing Large Language Models for Knowledge Graph Question Answering via Adaptive Multi-Aspect Retrieval-Augmentation

Large Language Models (LLMs) demonstrate remarkable capabilities, yet struggle with hallucination and outdated knowledge when tasked with complex knowledge reasoning, resulting in factually incorrect outputs. Previous studies have attempted to mitigate it by retrieving factual knowledge from large-scale knowledge graphs (KGs) to assist LLMs in logical reasoning and prediction of answers. However, this kind of approach often introduces noise and irrelevant data, especially in situations with extensive context from multiple knowledge aspects. In this way, LLM attention can be potentially mislead from question and relevant information. In our study, we introduce an Adaptive Multi-Aspect Retrieval-augmented over KGs (Amar) framework. This method retrieves knowledge including entities, relations, and subgraphs, and converts each piece of retrieved text into prompt embeddings. The Amar framework comprises two key sub-components: 1) a self-alignment module that aligns commonalities among entities, relations, and subgraphs to enhance retrieved text, thereby reducing noise interference; 2) a relevance gating module that employs a soft gate to learn the relevance score between question and multi-aspect retrieved data, to determine which information should be used to enhance LLMs' output, or even filtered altogether. Our method has achieved state-of-the-art performance on two common datasets, WebQSP and CWQ, showing a 1.9\% improvement in accuracy over its best competitor and a 6.6\% improvement in logical form generation over a method that directly uses retrieved text as context prompts. These results demonstrate the effectiveness of Amar in improving the reasoning of LLMs.

  • 10 authors
·
Dec 24, 2024

R-Tuning: Teaching Large Language Models to Refuse Unknown Questions

Large language models (LLMs) have revolutionized numerous domains with their impressive performance but still face their challenges. A predominant issue is the propensity for these models to generate non-existent facts, a concern termed hallucination. Our research is motivated by the observation that previous instruction tuning methods force the model to complete a sentence no matter whether the model knows the knowledge or not. When the question is out of the parametric knowledge, it will try to make up something and fail to indicate when it lacks knowledge. In this paper, we present a new approach called Refusal-Aware Instruction Tuning (R-Tuning). This approach is formalized by first identifying the knowledge gap between parametric knowledge and the instruction tuning data. Then, we construct the refusal-aware data based on the knowledge intersection, to tune LLMs to refrain from responding to questions beyond its parametric knowledge. Experimental results demonstrate this new instruction tuning approach effectively improves a model's ability to answer known questions and refrain from answering unknown questions. Furthermore, when tested on out-of-domain datasets, the refusal ability was found to be a meta-skill that could be generalized to other tasks. Further analysis surprisingly finds that learning the uncertainty during training displays a better ability to estimate uncertainty than uncertainty-based testing. Our code will be released at https://github.com/shizhediao/R-Tuning.

  • 9 authors
·
Nov 16, 2023

Symbolic Knowledge Distillation: from General Language Models to Commonsense Models

The common practice for training commonsense models has gone from-human-to-corpus-to-machine: humans author commonsense knowledge graphs in order to train commonsense models. In this work, we investigate an alternative, from-machine-to-corpus-to-machine: general language models author these commonsense knowledge graphs to train commonsense models. Our study leads to a new framework, Symbolic Knowledge Distillation. As with prior art in Knowledge Distillation (Hinton et al., 2015), our approach uses larger models to teach smaller models. A key difference is that we distill knowledge symbolically-as text-in addition to the neural model. We also distill only one aspect-the commonsense of a general language model teacher, allowing the student to be a different type, a commonsense model. Altogether, we show that careful prompt engineering and a separately trained critic model allow us to selectively distill high-quality causal commonsense from GPT-3, a general language model. Empirical results demonstrate that, for the first time, a human-authored commonsense knowledge graph is surpassed by our automatically distilled variant in all three criteria: quantity, quality, and diversity. In addition, it results in a neural commonsense model that surpasses the teacher model's commonsense capabilities despite its 100x smaller size. We apply this to the ATOMIC resource, and share our new symbolic knowledge graph and commonsense models.

  • 9 authors
·
Oct 14, 2021

KaSA: Knowledge-Aware Singular-Value Adaptation of Large Language Models

The increasing sizes of large language models (LLMs) result in significant computational overhead and memory usage when adapting these models to specific tasks or domains. Various parameter-efficient fine-tuning (PEFT) methods have been devised to mitigate these challenges by training a small set of parameters for the task-specific updates of the model weights. Among PEFT methods, LoRA stands out for its simplicity and efficiency, inspiring the development of a series of variants. However, LoRA and its successors disregard the knowledge that is noisy or irrelevant to the targeted task, detrimentally impacting model performance and leading to suboptimality. To address this limitation, we introduce Knowledge-aware Singular-value Adaptation (KaSA), a PEFT method that leverages singular value decomposition (SVD) with knowledge-aware singular values to dynamically activate knowledge based on its relevance to the task at hand. We conduct extensive experiments across a range of LLMs on tasks spanning natural language understanding (NLU), generation (NLG), instruction following, and commonsense reasoning. The experimental results demonstrate that KaSA consistently outperforms FFT and 14 popular PEFT baselines across 16 benchmarks and 4 synthetic datasets, underscoring our method's efficacy and adaptability. The source code of our method is available at https://github.com/juyongjiang/KaSA.

  • 5 authors
·
Dec 8, 2024 2

Robust and Scalable Model Editing for Large Language Models

Large language models (LLMs) can make predictions using parametric knowledge--knowledge encoded in the model weights--or contextual knowledge--knowledge presented in the context. In many scenarios, a desirable behavior is that LLMs give precedence to contextual knowledge when it conflicts with the parametric knowledge, and fall back to using their parametric knowledge when the context is irrelevant. This enables updating and correcting the model's knowledge by in-context editing instead of retraining. Previous works have shown that LLMs are inclined to ignore contextual knowledge and fail to reliably fall back to parametric knowledge when presented with irrelevant context. In this work, we discover that, with proper prompting methods, instruction-finetuned LLMs can be highly controllable by contextual knowledge and robust to irrelevant context. Utilizing this feature, we propose EREN (Edit models by REading Notes) to improve the scalability and robustness of LLM editing. To better evaluate the robustness of model editors, we collect a new dataset, that contains irrelevant questions that are more challenging than the ones in existing datasets. Empirical results show that our method outperforms current state-of-the-art methods by a large margin. Unlike existing techniques, it can integrate knowledge from multiple edits, and correctly respond to syntactically similar but semantically unrelated inputs (and vice versa). The source code can be found at https://github.com/thunlp/EREN.

  • 9 authors
·
Mar 26, 2024