EquiFlow: Equivariant Conditional Flow Matching with Optimal Transport for 3D Molecular Conformation Prediction

Molecular 3D conformations play a key role in determining how molecules interact with other molecules or protein surfaces. Recent deep learning advancements have improved conformation prediction, but slow training speeds and difficulties in utilizing high-degree features limit performance. We propose EquiFlow, an equivariant conditional flow matching model with optimal transport. EquiFlow uniquely applies conditional flow matching in molecular 3D conformation prediction, leveraging simulation-free training to address slow training speeds. It uses a modified Equiformer model to encode Cartesian molecular conformations along with their atomic and bond properties into higher-degree embeddings. Additionally, EquiFlow employs an ODE solver, providing faster inference speeds compared to diffusion models with SDEs. Experiments on the QM9 dataset show that EquiFlow predicts small molecule conformations more accurately than current state-of-the-art models.

Graph Disentangle Causal Model: Enhancing Causal Inference in Networked Observational Data

Estimating individual treatment effects (ITE) from observational data is a critical task across various domains. However, many existing works on ITE estimation overlook the influence of hidden confounders, which remain unobserved at the individual unit level. To address this limitation, researchers have utilized graph neural networks to aggregate neighbors' features to capture the hidden confounders and mitigate confounding bias by minimizing the discrepancy of confounder representations between the treated and control groups. Despite the success of these approaches, practical scenarios often treat all features as confounders and involve substantial differences in feature distributions between the treated and control groups. Confusing the adjustment and confounder and enforcing strict balance on the confounder representations could potentially undermine the effectiveness of outcome prediction. To mitigate this issue, we propose a novel framework called the \textit{Graph Disentangle Causal model} (GDC) to conduct ITE estimation in the network setting. GDC utilizes a causal disentangle module to separate unit features into adjustment and confounder representations. Then we design a graph aggregation module consisting of three distinct graph aggregators to obtain adjustment, confounder, and counterfactual confounder representations. Finally, a causal constraint module is employed to enforce the disentangled representations as true causal factors. The effectiveness of our proposed method is demonstrated by conducting comprehensive experiments on two networked datasets.

UniHR: Hierarchical Representation Learning for Unified Knowledge Graph Link Prediction

Beyond-triple fact representations including hyper-relational facts with auxiliary key-value pairs, temporal facts with additional timestamps, and nested facts implying relationships between facts, are gaining significant attention. However, existing link prediction models are usually designed for one specific type of facts, making it difficult to generalize to other fact representations. To overcome this limitation, we propose a Unified Hierarchical Representation learning framework (UniHR) for unified knowledge graph link prediction. It consists of a unified Hierarchical Data Representation (HiDR) module and a unified Hierarchical Structure Learning (HiSL) module as graph encoder. The HiDR module unifies hyper-relational KGs, temporal KGs, and nested factual KGs into triple-based representations. Then HiSL incorporates intra-fact and inter-fact message passing, focusing on enhancing the semantic information within individual facts and enriching the structural information between facts. Experimental results across 7 datasets from 3 types of KGs demonstrate that our UniHR outperforms baselines designed for one specific kind of KG, indicating strong generalization capability of HiDR form and the effectiveness of HiSL module. Code and data are available at https://github.com/Lza12a/UniHR.

The Devil is in the Sources! Knowledge Enhanced Cross-Domain Recommendation in an Information Bottleneck Perspective

Cross-domain Recommendation (CDR) aims to alleviate the data sparsity and the cold-start problems in traditional recommender systems by leveraging knowledge from an informative source domain. However, previously proposed CDR models pursue an imprudent assumption that the entire information from the source domain is equally contributed to the target domain, neglecting the evil part that is completely irrelevant to users' intrinsic interest. To address this concern, in this paper, we propose a novel knowledge enhanced cross-domain recommendation framework named CoTrans, which remolds the core procedures of CDR models with: Compression on the knowledge from the source domain and Transfer of the purity to the target domain. Specifically, following the theory of Graph Information Bottleneck, CoTrans first compresses the source behaviors with the perception of information from the target domain. Then to preserve all the important information for the CDR task, the feedback signals from both domains are utilized to promote the effectiveness of the transfer procedure. Additionally, a knowledge-enhanced encoder is employed to narrow gaps caused by the non-overlapped items across separate domains. Comprehensive experiments on three widely used cross-domain datasets demonstrate that CoTrans significantly outperforms both single-domain and state-of-the-art cross-domain recommendation approaches.

Learning to Plan for Retrieval-Augmented Large Language Models from Knowledge Graphs

Improving the performance of large language models (LLMs) in complex question-answering (QA) scenarios has always been a research focal point. Recent studies have attempted to enhance LLMs' performance by combining step-wise planning with external retrieval. While effective for advanced models like GPT-3.5, smaller LLMs face challenges in decomposing complex questions, necessitating supervised fine-tuning. Previous work has relied on manual annotation and knowledge distillation from teacher LLMs, which are time-consuming and not accurate enough. In this paper, we introduce a novel framework for enhancing LLMs' planning capabilities by using planning data derived from knowledge graphs (KGs). LLMs fine-tuned with this data have improved planning capabilities, better equipping them to handle complex QA tasks that involve retrieval. Evaluations on multiple datasets, including our newly proposed benchmark, highlight the effectiveness of our framework and the benefits of KG-derived planning data.

Personalized Binomial DAGs Learning with Network Structured Covariates

The causal dependence in data is often characterized by Directed Acyclic Graphical (DAG) models, widely used in many areas. Causal discovery aims to recover the DAG structure using observational data. This paper focuses on causal discovery with multi-variate count data. We are motivated by real-world web visit data, recording individual user visits to multiple websites. Building a causal diagram can help understand user behavior in transitioning between websites, inspiring operational strategy. A challenge in modeling is user heterogeneity, as users with different backgrounds exhibit varied behaviors. Additionally, social network connections can result in similar behaviors among friends. We introduce personalized Binomial DAG models to address heterogeneity and network dependency between observations, which are common in real-world applications. To learn the proposed DAG model, we develop an algorithm that embeds the network structure into a dimension-reduced covariate, learns each node's neighborhood to reduce the DAG search space, and explores the variance-mean relation to determine the ordering. Simulations show our algorithm outperforms state-of-the-art competitors in heterogeneous data. We demonstrate its practical usefulness on a real-world web visit dataset.

Similarity is Not All You Need: Endowing Retrieval Augmented Generation with Multi Layered Thoughts

In recent years, large language models (LLMs) have made remarkable achievements in various domains. However, the untimeliness and cost of knowledge updates coupled with hallucination issues of LLMs have curtailed their applications in knowledge intensive tasks, where retrieval augmented generation (RAG) can be of help. Nevertheless, existing retrieval augmented models typically use similarity as a bridge between queries and documents and follow a retrieve then read procedure. In this work, we argue that similarity is not always the panacea and totally relying on similarity would sometimes degrade the performance of retrieval augmented generation. To this end, we propose MetRag, a Multi layEred Thoughts enhanced Retrieval Augmented Generation framework. To begin with, beyond existing similarity oriented thought, we embrace a small scale utility model that draws supervision from an LLM for utility oriented thought and further come up with a smarter model by comprehensively combining the similarity and utility oriented thoughts. Furthermore, given the fact that the retrieved document set tends to be huge and using them in isolation makes it difficult to capture the commonalities and characteristics among them, we propose to make an LLM as a task adaptive summarizer to endow retrieval augmented generation with compactness-oriented thought. Finally, with multi layered thoughts from the precedent stages, an LLM is called for knowledge augmented generation. Extensive experiments on knowledge-intensive tasks have demonstrated the superiority of MetRag.

Mixture of Modality Knowledge Experts for Robust Multi-modal Knowledge Graph Completion

Multi-modal knowledge graph completion (MMKGC) aims to automatically discover new knowledge triples in the given multi-modal knowledge graphs (MMKGs), which is achieved by collaborative modeling the structural information concealed in massive triples and the multi-modal features of the entities. Existing methods tend to focus on crafting elegant entity-wise multi-modal fusion strategies, yet they overlook the utilization of multi-perspective features concealed within the modalities under diverse relational contexts. To address this issue, we introduce a novel MMKGC framework with Mixture of Modality Knowledge experts (MoMoK for short) to learn adaptive multi-modal embedding under intricate relational contexts. We design relation-guided modality knowledge experts to acquire relation-aware modality embeddings and integrate the predictions from multi-modalities to achieve comprehensive decisions. Additionally, we disentangle the experts by minimizing their mutual information. Experiments on four public MMKG benchmarks demonstrate the outstanding performance of MoMoK under complex scenarios.

Your decision path does matter in pre-training industrial recommenders with multi-source behaviors

Online service platforms offering a wide range of services through miniapps have become crucial for users who visit these platforms with clear intentions to find services they are interested in. Aiming at effective content delivery, cross-domain recommendation are introduced to learn high-quality representations by transferring behaviors from data-rich scenarios. However, these methods overlook the impact of the decision path that users take when conduct behaviors, that is, users ultimately exhibit different behaviors based on various intents. To this end, we propose HIER, a novel Hierarchical decIsion path Enhanced Representation learning for cross-domain recommendation. With the help of graph neural networks for high-order topological information of the knowledge graph between multi-source behaviors, we further adaptively learn decision paths through well-designed exemplar-level and information bottleneck based contrastive learning. Extensive experiments in online and offline environments show the superiority of HIER.

Multi-domain Knowledge Graph Collaborative Pre-training and Prompt Tuning for Diverse Downstream Tasks

Knowledge graphs (KGs) provide reliable external knowledge for a wide variety of AI tasks in the form of structured triples. Knowledge graph pre-training (KGP) aims to pre-train neural networks on large-scale KGs and provide unified interfaces to enhance different downstream tasks, which is a key direction for KG management, maintenance, and applications. Existing works often focus on purely research questions in open domains, or they are not open source due to data security and privacy in real scenarios. Meanwhile, existing studies have not explored the training efficiency and transferability of KGP models in depth. To address these problems, We propose a framework MuDoK to achieve multi-domain collaborative pre-training and efficient prefix prompt tuning to serve diverse downstream tasks like recommendation and text understanding. Our design is a plug-and-play prompt learning approach that can be flexibly adapted to different downstream task backbones. In response to the lack of open-source benchmarks, we constructed a new multi-domain KGP benchmark called KPI with two large-scale KGs and six different sub-domain tasks to evaluate our method and open-sourced it for subsequent research. We evaluated our approach based on constructed KPI benchmarks using diverse backbone models in heterogeneous downstream tasks. The experimental results show that our framework brings significant performance gains, along with its generality, efficiency, and transferability.