MVKTrans: Multi-View Knowledge Transfer for Robust Multiomics Classification

The distinct characteristics of multiomics data, including complex interactions within and across biological layers and disease heterogeneity (e.g., heterogeneity in etiology and clinical symptoms), drive us to develop novel designs to address unique challenges in multiomics prediction. In this paper, we propose the multi-view knowledge transfer learning (MVKTrans) framework, which transfers intra- and inter-omics knowledge in an adaptive manner by reviewing data heterogeneity and suppressing bias transfer, thereby enhancing classification performance. Specifically, we design a graph contrastive module that is trained on unlabeled data to effectively learn and transfer the underlying intra-omics patterns to the supervised task. This unsupervised pretraining promotes learning general and unbiased representations for each modality, regardless of the downstream tasks. In light of the varying discriminative capacities of modalities across different diseases and/or samples, we introduce an adaptive and bi-directional cross-omics distillation module. This module automatically identifies richer modalities and facilitates dynamic knowledge transfer from more informative to less informative omics, thereby enabling a more robust and generalized integration. Extensive experiments on four real biomedical datasets demonstrate the superior performance and robustness of MVKTrans compared to the state-of-the-art. Code and data are available at https://github.com/Yaolab-fantastic/MVKTrans.

CP-Prompt: Composition-Based Cross-modal Prompting for Domain-Incremental Continual Learning

The key challenge of cross-modal domain-incremental learning (DIL) is to enable the learning model to continuously learn from novel data with different feature distributions under the same task without forgetting old ones. However, existing top-performing methods still cause high forgetting rates, by lacking intra-domain knowledge extraction and inter-domain common prompting strategy. In this paper, we propose a simple yet effective framework, CP-Prompt, by training limited parameters to instruct a pre-trained model to learn new domains and avoid forgetting existing feature distributions. CP-Prompt captures intra-domain knowledge by compositionally inserting personalized prompts on multi-head self-attention layers and then learns the inter-domain knowledge with a common prompting strategy. CP-Prompt shows superiority compared with state-of-the-art baselines among three widely evaluated DIL tasks. The source code is available at https://github.com/dannis97500/CP_Prompt.

Trustworthy Enhanced Multi-view Multi-modal Alzheimer's Disease Prediction with Brain-wide Imaging Transcriptomics Data

Brain transcriptomics provides insights into the molecular mechanisms by which the brain coordinates its functions and processes. However, existing multimodal methods for predicting Alzheimer's disease (AD) primarily rely on imaging and sometimes genetic data, often neglecting the transcriptomic basis of brain. Furthermore, while striving to integrate complementary information between modalities, most studies overlook the informativeness disparities between modalities. Here, we propose TMM, a trusted multiview multimodal graph attention framework for AD diagnosis, using extensive brain-wide transcriptomics and imaging data. First, we construct view-specific brain regional co-function networks (RRIs) from transcriptomics and multimodal radiomics data to incorporate interaction information from both biomolecular and imaging perspectives. Next, we apply graph attention (GAT) processing to each RRI network to produce graph embeddings and employ cross-modal attention to fuse transcriptomics-derived embedding with each imagingderived embedding. Finally, a novel true-false-harmonized class probability (TFCP) strategy is designed to assess and adaptively adjust the prediction confidence of each modality for AD diagnosis. We evaluate TMM using the AHBA database with brain-wide transcriptomics data and the ADNI database with three imaging modalities (AV45-PET, FDG-PET, and VBM-MRI). The results demonstrate the superiority of our method in identifying AD, EMCI, and LMCI compared to state-of-the-arts. Code and data are available at https://github.com/Yaolab-fantastic/TMM.

CRE-LLM: A Domain-Specific Chinese Relation Extraction Framework with Fine-tuned Large Language Model

Domain-Specific Chinese Relation Extraction (DSCRE) aims to extract relations between entities from domain-specific Chinese text. Despite the rapid development of PLMs in recent years, especially LLMs, DSCRE still faces three core challenges: complex network structure design, poor awareness, and high consumption of fine-tuning. Given the impressive performance of large language models (LLMs) in natural language processing, we propose a new framework called CRE-LLM. This framework is based on fine-tuning open-source LLMs, such as Llama-2, ChatGLM2, and Baichuan2. CRE-LLM enhances the logic-awareness and generative capabilities of the model by constructing an appropriate prompt and utilizing open-source LLMs for instruction-supervised fine-tuning. And then it directly extracts the relations of the given entities in the input textual data, which improving the CRE approach. To demonstrate the effectiveness of the proposed framework, we conducted extensive experiments on two domain-specific CRE datasets, FinRE and SanWen. The experimental results show that CRE-LLM is significantly superior and robust, achieving state-of-the-art (SOTA) performance on the FinRE dataset. This paper introduces a novel approach to domain-specific relation extraction (DSCRE) tasks that are semantically more complex by combining LLMs with triples. Our code is publicly available.

ChatKBQA: A Generate-then-Retrieve Framework for Knowledge Base Question Answering with Fine-tuned Large Language Models

Knowledge Base Question Answering (KBQA) aims to derive answers to natural language questions over large-scale knowledge bases (KBs), which are generally divided into two research components: knowledge retrieval and semantic parsing. However, three core challenges remain, including inefficient knowledge retrieval, retrieval errors adversely affecting semantic parsing, and the complexity of previous KBQA methods. In the era of large language models (LLMs), we introduce ChatKBQA, a novel generate-then-retrieve KBQA framework built on fine-tuning open-source LLMs such as Llama-2, ChatGLM2 and Baichuan2. ChatKBQA proposes generating the logical form with fine-tuned LLMs first, then retrieving and replacing entities and relations through an unsupervised retrieval method, which improves both generation and retrieval more straightforwardly. Experimental results reveal that ChatKBQA achieves new state-of-the-art performance on standard KBQA datasets, WebQSP, and ComplexWebQuestions (CWQ). This work also provides a new paradigm for combining LLMs with knowledge graphs (KGs) for interpretable and knowledge-required question answering. Our code is publicly available.

Text2NKG: Fine-Grained N-ary Relation Extraction for N-ary relational Knowledge Graph Construction

Beyond traditional binary relational facts, n-ary relational knowledge graphs (NKGs) are comprised of n-ary relational facts containing more than two entities, which are closer to real-world facts with broader applications. However, the construction of NKGs still significantly relies on manual labor, and n-ary relation extraction still remains at a course-grained level, which is always in a single schema and fixed arity of entities. To address these restrictions, we propose Text2NKG, a novel fine-grained n-ary relation extraction framework for n-ary relational knowledge graph construction. We introduce a span-tuple classification approach with hetero-ordered merging to accomplish fine-grained n-ary relation extraction in different arity. Furthermore, Text2NKG supports four typical NKG schemas: hyper-relational schema, event-based schema, role-based schema, and hypergraph-based schema, with high flexibility and practicality. Experimental results demonstrate that Text2NKG outperforms the previous state-of-the-art model by nearly 20\% points in the $F_1$ scores on the fine-grained n-ary relation extraction benchmark in the hyper-relational schema. Our code and datasets are publicly available.

HAHE: Hierarchical Attention for Hyper-Relational Knowledge Graphs in Global and Local Level

Link Prediction on Hyper-relational Knowledge Graphs (HKG) is a worthwhile endeavor. HKG consists of hyper-relational facts (H-Facts), composed of a main triple and several auxiliary attribute-value qualifiers, which can effectively represent factually comprehensive information. The internal structure of HKG can be represented as a hypergraph-based representation globally and a semantic sequence-based representation locally. However, existing research seldom simultaneously models the graphical and sequential structure of HKGs, limiting HKGs' representation. To overcome this limitation, we propose a novel Hierarchical Attention model for HKG Embedding (HAHE), including global-level and local-level attention. The global-level attention can model the graphical structure of HKG using hypergraph dual-attention layers, while the local-level attention can learn the sequential structure inside H-Facts via heterogeneous self-attention layers. Experiment results indicate that HAHE achieves state-of-the-art performance in link prediction tasks on HKG standard datasets. In addition, HAHE addresses the issue of HKG multi-position prediction for the first time, increasing the applicability of the HKG link prediction task. Our code is publicly available.

NQE: N-ary Query Embedding for Complex Query Answering over Hyper-relational Knowledge Graphs

Complex query answering (CQA) is an essential task for multi-hop and logical reasoning on knowledge graphs (KGs). Currently, most approaches are limited to queries among binary relational facts and pay less attention to n-ary facts (n>=2) containing more than two entities, which are more prevalent in the real world. Moreover, previous CQA methods can only make predictions for a few given types of queries and cannot be flexibly extended to more complex logical queries, which significantly limits their applications. To overcome these challenges, in this work, we propose a novel N-ary Query Embedding (NQE) model for CQA over hyper-relational knowledge graphs (HKGs), which include massive n-ary facts. The NQE utilizes a dual-heterogeneous Transformer encoder and fuzzy logic theory to satisfy all n-ary FOL queries, including existential quantifiers, conjunction, disjunction, and negation. We also propose a parallel processing algorithm that can train or predict arbitrary n-ary FOL queries in a single batch, regardless of the kind of each query, with good flexibility and extensibility. In addition, we generate a new CQA dataset WD50K-NFOL, including diverse n-ary FOL queries over WD50K. Experimental results on WD50K-NFOL and other standard CQA datasets show that NQE is the state-of-the-art CQA method over HKGs with good generalization capability. Our code and dataset are publicly available.

DHGE: Dual-view Hyper-Relational Knowledge Graph Embedding for Link Prediction and Entity Typing

In the field of representation learning on knowledge graphs (KGs), a hyper-relational fact consists of a main triple and several auxiliary attribute value descriptions, which is considered to be more comprehensive and specific than a triple-based fact. However, the existing hyper-relational KG embedding methods in a single view are limited in application due to weakening the hierarchical structure representing the affiliation between entities. To break this limitation, we propose a dual-view hyper-relational KG (DH-KG) structure which contains a hyper-relational instance view for entities and a hyper-relational ontology view for concepts abstracted hierarchically from entities to jointly model hyper-relational and hierarchical information. In this paper, we first define link prediction and entity typing tasks on DH-KG and construct two DH-KG datasets, JW44K-6K extracted from Wikidata and HTDM based on medical data. Furthermore, We propose a DH-KG embedding model DHGE, based on GRAN encoder, HGNN, and joint learning. Experimental results show that DHGE outperforms baseline models on DH-KG. We also provide an example of the application of this technology in the field of hypertension medication. Our model and datasets are publicly available.

TFLEX: Temporal Feature-Logic Embedding Framework for Complex Reasoning over Temporal Knowledge Graph

Multi-hop logical reasoning over knowledge graph (KG) plays a fundamental role in many artificial intelligence tasks. Recent complex query embedding (CQE) methods for reasoning focus on static KGs, while temporal knowledge graphs (TKGs) have not been fully explored. Reasoning over TKGs has two challenges: 1. The query should answer entities or timestamps; 2. The operators should consider both set logic on entity set and temporal logic on timestamp set. To bridge this gap, we define the multi-hop logical reasoning problem on TKGs. With generated three datasets, we propose the first temporal CQE named Temporal Feature-Logic Embedding framework (TFLEX) to answer the temporal complex queries. We utilize vector logic to compute the logic part of Temporal Feature-Logic embeddings, thus naturally modeling all First-Order Logic (FOL) operations on entity set. In addition, our framework extends vector logic on timestamp set to cope with three extra temporal operators (After, Before and Between). Experiments on numerous query patterns demonstrate the effectiveness of our method.