Deep neural networks (DNNs) have been found vulnerable to backdoor attacks, raising security concerns about their deployment in mission-critical applications. There are various approaches to detect backdoor attacks, however they all make certain assumptions about the target attack to be detected and require equal and huge numbers of clean and backdoor samples for training, which renders these detection methods quite limiting in real-world circumstances. This study proposes a novel one-class classification framework called One-class Graph Embedding Classification (OCGEC) that uses GNNs for model-level backdoor detection with only a little amount of clean data. First, we train thousands of tiny models as raw datasets from a small number of clean datasets. Following that, we design a ingenious model-to-graph method for converting the model's structural details and weight features into graph data. We then pre-train a generative self-supervised graph autoencoder (GAE) to better learn the features of benign models in order to detect backdoor models without knowing the attack strategy. After that, we dynamically combine the GAE and one-class classifier optimization goals to form classification boundaries that distinguish backdoor models from benign models. Our OCGEC combines the powerful representation capabilities of graph neural networks with the utility of one-class classification techniques in the field of anomaly detection. In comparison to other baselines, it achieves AUC scores of more than 98% on a number of tasks, which far exceeds existing methods for detection even when they rely on a huge number of positive and negative samples. Our pioneering application of graphic scenarios for generic backdoor detection can provide new insights that can be used to improve other backdoor defense tasks. Code is available at https://github.com/jhy549/OCGEC.
Binary similarity involves determining whether two binary programs exhibit similar functionality, often originating from the same source code. In this work, we propose VexIR2Vec, an approach for binary similarity using VEX-IR, an architecture-neutral Intermediate Representation (IR). We extract the embeddings from sequences of basic blocks, termed peepholes, derived by random walks on the control-flow graph. The peepholes are normalized using transformations inspired by compiler optimizations. The VEX-IR Normalization Engine mitigates, with these transformations, the architectural and compiler-induced variations in binaries while exposing semantic similarities. We then learn the vocabulary of representations at the entity level of the IR using the knowledge graph embedding techniques in an unsupervised manner. This vocabulary is used to derive function embeddings for similarity assessment using VexNet, a feed-forward Siamese network designed to position similar functions closely and separate dissimilar ones in an n-dimensional space. This approach is amenable for both diffing and searching tasks, ensuring robustness against Out-Of-Vocabulary (OOV) issues. We evaluate VexIR2Vec on a dataset comprising 2.7M functions and 15.5K binaries from 7 projects compiled across 12 compilers targeting x86 and ARM architectures. In diffing experiments, VexIR2Vec outperforms the nearest baselines by $40\%$, $18\%$, $21\%$, and $60\%$ in cross-optimization, cross-compilation, cross-architecture, and obfuscation settings, respectively. In the searching experiment, VexIR2Vec achieves a mean average precision of $0.76$, outperforming the nearest baseline by $46\%$. Our framework is highly scalable and is built as a lightweight, multi-threaded, parallel library using only open-source tools. VexIR2Vec is $3.1$-$3.5 \times$ faster than the closest baselines and orders-of-magnitude faster than other tools.
The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional alignment-based methods are dedicated to precise comparisons between pairs, exhibiting high accuracy. However, their sluggish processing speed is no longer adequate for managing the current massive volume of data. In response to this challenge, we propose a novel deep-learning approach FoldExplorer. It harnesses the powerful capabilities of graph attention neural networks and protein large language models for protein structures and sequences data processing to generate embeddings for protein structures. The structural embeddings can be used for fast and accurate protein search. The embeddings also provide insights into the protein space. FoldExplorer demonstrates a substantial performance improvement of 5% to 8% over the current state-of-the-art algorithm on the benchmark datasets. Meanwhile, FoldExplorer does not compromise on search speed and excels particularly in searching on a large-scale dataset.
Embedding graphs in continous spaces is a key factor in designing and developing algorithms for automatic information extraction to be applied in diverse tasks (e.g., learning, inferring, predicting). The reliability of graph embeddings directly depends on how much the geometry of the continuous space matches the graph structure. Manifolds are mathematical structure that can enable to incorporate in their topological spaces the graph characteristics, and in particular nodes distances. State-of-the-art of manifold-based graph embedding algorithms take advantage of the assumption that the projection on a tangential space of each point in the manifold (corresponding to a node in the graph) would locally resemble a Euclidean space. Although this condition helps in achieving efficient analytical solutions to the embedding problem, it does not represent an adequate set-up to work with modern real life graphs, that are characterized by weighted connections across nodes often computed over sparse datasets with missing records. In this work, we introduce a new class of manifold, named soft manifold, that can solve this situation. In particular, soft manifolds are mathematical structures with spherical symmetry where the tangent spaces to each point are hypocycloids whose shape is defined according to the velocity of information propagation across the data points. Using soft manifolds for graph embedding, we can provide continuous spaces to pursue any task in data analysis over complex datasets. Experimental results on reconstruction tasks on synthetic and real datasets show how the proposed approach enable more accurate and reliable characterization of graphs in continuous spaces with respect to the state-of-the-art.
Knowledge graph embedding (KGE) models represent the entities and relations of a knowledge graph (KG) using dense continuous representations called embeddings. KGE methods have recently gained traction for tasks such as knowledge graph completion and reasoning as well as to provide suitable entity representations for downstream learning tasks. While a large part of the available literature focuses on small KGs, a number of frameworks that are able to train KGE models for large-scale KGs by parallelization across multiple GPUs or machines have recently been proposed. So far, the benefits and drawbacks of the various parallelization techniques have not been studied comprehensively. In this paper, we report on an experimental study in which we presented, re-implemented in a common computational framework, investigated, and improved the available techniques. We found that the evaluation methodologies used in prior work are often not comparable and can be misleading, and that most of currently implemented training methods tend to have a negative impact on embedding quality. We propose a simple but effective variation of the stratification technique used by PyTorch BigGraph for mitigation. Moreover, basic random partitioning can be an effective or even the best-performing choice when combined with suitable sampling techniques. Ultimately, we found that efficient and effective parallel training of large-scale KGE models is indeed achievable but requires a careful choice of techniques.
The paper presents a novel two-stream network architecture for enhancing scene understanding in computer vision. This architecture utilizes a graph feature stream and an image feature stream, aiming to merge the strengths of both modalities for improved performance in image classification and scene graph generation tasks. The graph feature stream network comprises a segmentation structure, scene graph generation, and a graph representation module. The segmentation structure employs the UPSNet architecture with a backbone that can be a residual network, Vit, or Swin Transformer. The scene graph generation component focuses on extracting object labels and neighborhood relationships from the semantic map to create a scene graph. Graph Convolutional Networks (GCN), GraphSAGE, and Graph Attention Networks (GAT) are employed for graph representation, with an emphasis on capturing node features and their interconnections. The image feature stream network, on the other hand, focuses on image classification through the use of Vision Transformer and Swin Transformer models. The two streams are fused using various data fusion methods. This fusion is designed to leverage the complementary strengths of graph-based and image-based features.Experiments conducted on the ADE20K dataset demonstrate the effectiveness of the proposed two-stream network in improving image classification accuracy compared to conventional methods. This research provides a significant contribution to the field of computer vision, particularly in the areas of scene understanding and image classification, by effectively combining graph-based and image-based approaches.
The strength of a supply chain is an important measure of a country's or region's technical advancement and overall competitiveness. Establishing supply chain risk assessment models for effective management and mitigation of potential risks has become increasingly crucial. As the number of businesses grows, the important relationships become more complicated and difficult to measure. This emphasizes the need of extracting relevant information from graph data. Previously, academics mostly employed knowledge inference to increase the visibility of links between nodes in the supply chain. However, they have not solved the data hunger problem of single node feature characteristics. We propose a hierarchical knowledge transferable graph neural network-based (HKTGNN) supply chain risk assessment model to address these issues. Our approach is based on current graph embedding methods for assessing corporate investment risk assessment. We embed the supply chain network corresponding to individual goods in the supply chain using the graph embedding module, resulting in a directed homogeneous graph with just product nodes. This reduces the complicated supply chain network into a basic product network. It addresses difficulties using the domain difference knowledge transferable module based on centrality, which is presented by the premise that supply chain feature characteristics may be biased in the actual world. Meanwhile, the feature complement and message passing will alleviate the data hunger problem, which is driven by domain differences. Our model outperforms in experiments on a real-world supply chain dataset. We will give an equation to prove that our comparative experiment is both effective and fair.
Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway simulations of such reactions. Here we present ViDa, a new approach for visualizing DNA reaction folding trajectories over the energy landscape of secondary structures. We integrate a deep graph embedding model with common dimensionality reduction approaches, to map high-dimensional data onto 2D Euclidean space. We assess ViDa on two well-studied and contrasting DNA hybridization reactions. Our preliminary results suggest that ViDa's visualization successfully separates trajectories with different folding mechanisms, thereby providing useful insight to users, and is a big improvement over the current state-of-the-art in DNA kinetics visualization.
We introduce the Pointer Q-Network (PQN), a hybrid neural architecture that integrates model-free Q-value policy approximation with Pointer Networks (Ptr-Nets) to enhance the optimality of attention-based sequence generation, focusing on long-term outcomes. This integration proves particularly effective in solving combinatorial optimization (CO) tasks, especially the Travelling Salesman Problem (TSP), which is the focus of our study. We address this challenge by defining a Markov Decision Process (MDP) compatible with PQN, which involves iterative graph embedding, encoding and decoding by an LSTM-based recurrent neural network. This process generates a context vector and computes raw attention scores, which are dynamically adjusted by Q-values calculated for all available state-action pairs before applying softmax. The resulting attention vector is utilized as an action distribution, with actions selected hinged to exploration-exploitation dynamic adaptibility of PQN. Our empirical results demonstrate the efficacy of this approach, also testing the model in unstable environments.
Recently, nonnegative matrix factorization (NMF) has been widely adopted for community detection, because of its better interpretability. However, the existing NMF-based methods have the following three problems: 1) they directly transform the original network into community membership space, so it is difficult for them to capture the hierarchical information; 2) they often only pay attention to the topology of the network and ignore its node attributes; 3) it is hard for them to learn the global structure information necessary for community detection. Therefore, we propose a new community detection algorithm, named Contrastive Deep Nonnegative Matrix Factorization (CDNMF). Firstly, we deepen NMF to strengthen its capacity for information extraction. Subsequently, inspired by contrastive learning, our algorithm creatively constructs network topology and node attributes as two contrasting views. Furthermore, we utilize a debiased negative sampling layer and learn node similarity at the community level, thereby enhancing the suitability of our model for community detection. We conduct experiments on three public real graph datasets and the proposed model has achieved better results than state-of-the-art methods. Code available at https://github.com/6lyc/CDNMF.git.
Knowledge Graphs are a widely used method to represent relations between entities in various AI applications, and Graph Embedding has rapidly become a standard technique to represent Knowledge Graphs in such a way as to facilitate inferences and decisions. As this representation is obtained from behavioural data, and is not in a form readable by humans, there is a concern that it might incorporate unintended information that could lead to biases. We propose EXTRACT: a suite of Explainable and Transparent methods to ConTrol bias in knowledge graph embeddings, so as to assess and decrease the implicit presence of protected information. Our method uses Canonical Correlation Analysis (CCA) to investigate the presence, extent and origins of information leaks during training, then decomposes embeddings into a sum of their private attributes by solving a linear system. Our experiments, performed on the MovieLens1M dataset, show that a range of personal attributes can be inferred from a user's viewing behaviour and preferences, including gender, age, and occupation. Further experiments, performed on the KG20C citation dataset, show that the information about the conference in which a paper was published can be inferred from the citation network of that article. We propose four transparent methods to maintain the capability of the embedding to make the intended predictions without retaining unwanted information. A trade-off between these two goals is observed.
In the era of the Internet of Things (IoT), the retrieval of relevant medical information has become essential for efficient clinical decision-making. This paper introduces MedFusionRank, a novel approach to zero-shot medical information retrieval (MIR) that combines the strengths of pre-trained language models and statistical methods while addressing their limitations. The proposed approach leverages a pre-trained BERT-style model to extract compact yet informative keywords. These keywords are then enriched with domain knowledge by linking them to conceptual entities within a medical knowledge graph. Experimental evaluations on medical datasets demonstrate MedFusion Rank's superior performance over existing methods, with promising results with a variety of evaluation metrics. MedFusionRank demonstrates efficacy in retrieving relevant information, even from short or single-term queries.
Conspiracy theories, as a type of misinformation, are narratives that explains an event or situation in an irrational or malicious manner. While most previous work examined conspiracy theory in social media short texts, limited attention was put on such misinformation in long news documents. In this paper, we aim to identify whether a news article contains conspiracy theories. We observe that a conspiracy story can be made up by mixing uncorrelated events together, or by presenting an unusual distribution of relations between events. Achieving a contextualized understanding of events in a story is essential for detecting conspiracy theories. Thus, we propose to incorporate an event relation graph for each article, in which events are nodes, and four common types of event relations, coreference, temporal, causal, and subevent relations, are considered as edges. Then, we integrate the event relation graph into conspiracy theory identification in two ways: an event-aware language model is developed to augment the basic language model with the knowledge of events and event relations via soft labels; further, a heterogeneous graph attention network is designed to derive a graph embedding based on hard labels. Experiments on a large benchmark dataset show that our approach based on event relation graph improves both precision and recall of conspiracy theory identification, and generalizes well for new unseen media sources.
Learning good self-supervised graph representations that are beneficial to downstream tasks is challenging. Among a variety of methods, contrastive learning enjoys competitive performance. The embeddings of contrastive learning are arranged on a hypersphere that enables the Cosine distance measurement in the Euclidean space. However, the underlying structure of many domains such as graphs exhibits highly non-Euclidean latent geometry. To this end, we propose a novel contrastive learning framework to learn high-quality graph embedding. Specifically, we design the alignment metric that effectively captures the hierarchical data-invariant information, as well as we propose a substitute of uniformity metric to prevent the so-called dimensional collapse. We show that in the hyperbolic space one has to address the leaf- and height-level uniformity which are related to properties of trees, whereas in the ambient space of the hyperbolic manifold, these notions translate into imposing an isotropic ring density towards boundaries of Poincar\'e ball. This ring density can be easily imposed by promoting the isotropic feature distribution on the tangent space of manifold. In the experiments, we demonstrate the efficacy of our proposed method across different hyperbolic graph embedding techniques in both supervised and self-supervised learning settings.
Graph embedding methods such as Graph Neural Networks (GNNs) and Graph Transformers have contributed to the development of graph reasoning algorithms for various tasks on knowledge graphs. However, the lack of interpretability and explainability of graph embedding methods has limited their applicability in scenarios requiring explicit reasoning. In this paper, we introduce the Graph Agent (GA), an intelligent agent methodology of leveraging large language models (LLMs), inductive-deductive reasoning modules, and long-term memory for knowledge graph reasoning tasks. GA integrates aspects of symbolic reasoning and existing graph embedding methods to provide an innovative approach for complex graph reasoning tasks. By converting graph structures into textual data, GA enables LLMs to process, reason, and provide predictions alongside human-interpretable explanations. The effectiveness of the GA was evaluated on node classification and link prediction tasks. Results showed that GA reached state-of-the-art performance, demonstrating accuracy of 90.65%, 95.48%, and 89.32% on Cora, PubMed, and PrimeKG datasets, respectively. Compared to existing GNN and transformer models, GA offered advantages of explicit reasoning ability, free-of-training, easy adaption to various graph reasoning tasks
The construction of large open knowledge bases (OKBs) is integral to many applications in the field of mobile computing. Noun phrases and relational phrases in OKBs often suffer from redundancy and ambiguity, which calls for the investigation on OKB canonicalization. However, in order to meet the requirements of some privacy protection regulations and to ensure the timeliness of the data, the canonicalized OKB often needs to remove some sensitive information or outdated data. The machine unlearning in OKB canonicalization is an excellent solution to the above problem. Current solutions address OKB canonicalization by devising advanced clustering algorithms and using knowledge graph embedding (KGE) to further facilitate the canonicalization process. Effective schemes are urgently needed to fully synergise machine unlearning with clustering and KGE learning. To this end, we put forward a multi-task unlearning framework, namely MulCanon, to tackle machine unlearning problem in OKB canonicalization. Specifically, the noise characteristics in the diffusion model are utilized to achieve the effect of machine unlearning for data in OKB. MulCanon unifies the learning objectives of diffusion model, KGE and clustering algorithms, and adopts a two-step multi-task learning paradigm for training. A thorough experimental study on popular OKB canonicalization datasets validates that MulCanon achieves advanced machine unlearning effects.
Computer vision often treats human perception as homogeneous: an implicit assumption that visual stimuli are perceived similarly by everyone. This assumption is reflected in the way researchers collect datasets and train vision models. By contrast, literature in cross-cultural psychology and linguistics has provided evidence that people from different cultural backgrounds observe vastly different concepts even when viewing the same visual stimuli. In this paper, we study how these differences manifest themselves in vision-language datasets and models, using language as a proxy for culture. By comparing textual descriptions generated across 7 languages for the same images, we find significant differences in the semantic content and linguistic expression. When datasets are multilingual as opposed to monolingual, descriptions have higher semantic coverage on average, where coverage is measured using scene graphs, model embeddings, and linguistic taxonomies. For example, multilingual descriptions have on average 29.9% more objects, 24.5% more relations, and 46.0% more attributes than a set of monolingual captions. When prompted to describe images in different languages, popular models (e.g. LLaVA) inherit this bias and describe different parts of the image. Moreover, finetuning models on captions from one language performs best on corresponding test data from that language, while finetuning on multilingual data performs consistently well across all test data compositions. Our work points towards the need to account for and embrace the diversity of human perception in the computer vision community.
Current item-item collaborative filtering algorithms based on artificial neural network, such as Item2vec, have become ubiquitous and are widely applied in the modern recommender system. However, these approaches do not apply to the large-scale item-based recommendation system because of their extremely long training time. To overcome the shortcoming that current algorithms have high training time costs and poor stability when dealing with large-scale data sets, the item graph embedding algorithm Item-Graph2vec is described here. This algorithm transforms the users' shopping list into a item co-occurrence graph, obtains item sequences through randomly travelling on this co-occurrence graph and finally trains item vectors through sequence samples. We posit that because of the stable size of item, the size and density of the item co-occurrence graph change slightly with the increase in the training corpus. Therefore, Item-Graph2vec has a stable runtime on the large scale data set, and its performance advantage becomes more and more obvious with the growth of the training corpus. Extensive experiments conducted on real-world data sets demonstrate that Item-Graph2vec outperforms Item2vec by 3 times in terms of efficiency on douban data set, while the error generated by the random walk sampling is small.
A variety of knowledge graph embedding approaches have been developed. Most of them obtain embeddings by learning the structure of the knowledge graph within a link prediction setting. As a result, the embeddings reflect only the structure of a single knowledge graph, and embeddings for different knowledge graphs are not aligned, e.g., they cannot be used to find similar entities across knowledge graphs via nearest neighbor search. However, knowledge graph embedding applications such as entity disambiguation require a more global representation, i.e., a representation that is valid across multiple sources. We propose to learn universal knowledge graph embeddings from large-scale interlinked knowledge sources. To this end, we fuse large knowledge graphs based on the owl:sameAs relation such that every entity is represented by a unique identity. We instantiate our idea by computing universal embeddings based on DBpedia and Wikidata yielding embeddings for about 180 million entities, 15 thousand relations, and 1.2 billion triples. We believe our computed embeddings will support the emerging field of graph foundation models. Moreover, we develop a convenient API to provide embeddings as a service. Experiments on link prediction suggest that universal knowledge graph embeddings encode better semantics compared to embeddings computed on a single knowledge graph. For reproducibility purposes, we provide our source code and datasets open access.
Graph data structures are widely used to store relational information between several entities. With data being generated worldwide on a large scale, we see a significant growth in the generation of knowledge graphs. Thing in the future is Orange's take on a knowledge graph in the domain of the Web Of Things (WoT), where the main objective of the platform is to provide a digital representation of the physical world and enable cross-domain applications to be built upon this massive and highly connected graph of things. In this context, as the knowledge graph grows in size, it is prone to have noisy and messy data. In this paper, we explore state-of-the-art knowledge graph embedding (KGE) methods to learn numerical representations of the graph entities and, subsequently, explore downstream tasks like link prediction, node classification, and triple classification. We also investigate Graph neural networks (GNN) alongside KGEs and compare their performance on the same downstream tasks. Our evaluation highlights the encouraging performance of both KGE and GNN-based methods on node classification, and the superiority of GNN approaches in the link prediction task. Overall, we show that state-of-the-art approaches are relevant in a WoT context, and this preliminary work provides insights to implement and evaluate them in this context.