On Measuring Unnoticeability of Graph Adversarial Attacks: Observations, New Measure, and Applications

Adversarial attacks are allegedly unnoticeable. Prior studies have designed attack noticeability measures on graphs, primarily using statistical tests to compare the topology of original and (possibly) attacked graphs. However, we observe two critical limitations in the existing measures. First, because the measures rely on simple rules, attackers can readily enhance their attacks to bypass them, reducing their attack "noticeability" and, yet, maintaining their attack performance. Second, because the measures naively leverage global statistics, such as degree distributions, they may entirely overlook attacks until severe perturbations occur, letting the attacks be almost "totally unnoticeable." To address the limitations, we introduce HideNSeek, a learnable measure for graph attack noticeability. First, to mitigate the bypass problem, HideNSeek learns to distinguish the original and (potential) attack edges using a learnable edge scorer (LEO), which scores each edge on its likelihood of being an attack. Second, to mitigate the overlooking problem, HideNSeek conducts imbalance-aware aggregation of all the edge scores to obtain the final noticeability score. Using six real-world graphs, we empirically demonstrate that HideNSeek effectively alleviates the observed limitations, and LEO (i.e., our learnable edge scorer) outperforms eleven competitors in distinguishing attack edges under five different attack methods. For an additional application, we show that LEO boost the performance of robust GNNs by removing attack-like edges.

RA-SGG: Retrieval-Augmented Scene Graph Generation Framework via Multi-Prototype Learning

Scene Graph Generation (SGG) research has suffered from two fundamental challenges: the long-tailed predicate distribution and semantic ambiguity between predicates. These challenges lead to a bias towards head predicates in SGG models, favoring dominant general predicates while overlooking fine-grained predicates. In this paper, we address the challenges of SGG by framing it as multi-label classification problem with partial annotation, where relevant labels of fine-grained predicates are missing. Under the new frame, we propose Retrieval-Augmented Scene Graph Generation (RA-SGG), which identifies potential instances to be multi-labeled and enriches the single-label with multi-labels that are semantically similar to the original label by retrieving relevant samples from our established memory bank. Based on augmented relations (i.e., discovered multi-labels), we apply multi-prototype learning to train our SGG model. Several comprehensive experiments have demonstrated that RA-SGG outperforms state-of-the-art baselines by up to 3.6% on VG and 5.9% on GQA, particularly in terms of F@K, showing that RA-SGG effectively alleviates the issue of biased prediction caused by the long-tailed distribution and semantic ambiguity of predicates.

3D Interaction Geometric Pre-training for Molecular Relational Learning

Molecular Relational Learning (MRL) is a rapidly growing field that focuses on understanding the interaction dynamics between molecules, which is crucial for applications ranging from catalyst engineering to drug discovery. Despite recent progress, earlier MRL approaches are limited to using only the 2D topological structure of molecules, as obtaining the 3D interaction geometry remains prohibitively expensive. This paper introduces a novel 3D geometric pre-training strategy for MRL (3DMRL) that incorporates a 3D virtual interaction environment, overcoming the limitations of costly traditional quantum mechanical calculation methods. With the constructed 3D virtual interaction environment, 3DMRL trains 2D MRL model to learn the overall 3D geometric information of molecular interaction through contrastive learning. Moreover, fine-grained interaction between molecules is learned through force prediction loss, which is crucial in understanding the wide range of molecular interaction processes. Extensive experiments on various tasks using real-world datasets, including out-of-distribution and extrapolation scenarios, demonstrate the effectiveness of 3DMRL, showing up to a 24.93\% improvement in performance across 40 tasks.

Revisiting Fake News Detection: Towards Temporality-aware Evaluation by Leveraging Engagement Earliness

Social graph-based fake news detection aims to identify news articles containing false information by utilizing social contexts, e.g., user information, tweets and comments. However, conventional methods are evaluated under less realistic scenarios, where the model has access to future knowledge on article-related and context-related data during training. In this work, we newly formalize a more realistic evaluation scheme that mimics real-world scenarios, where the data is temporality-aware and the detection model can only be trained on data collected up to a certain point in time. We show that the discriminative capabilities of conventional methods decrease sharply under this new setting, and further propose DAWN, a method more applicable to such scenarios. Our empirical findings indicate that later engagements (e.g., consuming or reposting news) contribute more to noisy edges that link real news-fake news pairs in the social graph. Motivated by this, we utilize feature representations of engagement earliness to guide an edge weight estimator to suppress the weights of such noisy edges, thereby enhancing the detection performance of DAWN. Through extensive experiments, we demonstrate that DAWN outperforms existing fake news detection methods under real-world environments. The source code is available at https://github.com/LeeJunmo/DAWN.

Retrieval-Retro: Retrieval-based Inorganic Retrosynthesis with Expert Knowledge

While inorganic retrosynthesis planning is essential in the field of chemical science, the application of machine learning in this area has been notably less explored compared to organic retrosynthesis planning. In this paper, we propose Retrieval-Retro for inorganic retrosynthesis planning, which implicitly extracts the precursor information of reference materials that are retrieved from the knowledge base regarding domain expertise in the field. Specifically, instead of directly employing the precursor information of reference materials, we propose implicitly extracting it with various attention layers, which enables the model to learn novel synthesis recipes more effectively. Moreover, during retrieval, we consider the thermodynamic relationship between target material and precursors, which is essential domain expertise in identifying the most probable precursor set among various options. Extensive experiments demonstrate the superiority of Retrieval-Retro in retrosynthesis planning, especially in discovering novel synthesis recipes, which is crucial for materials discovery. The source code for Retrieval-Retro is available at https://github.com/HeewoongNoh/Retrieval-Retro.

Diversify-verify-adapt: Efficient and Robust Retrieval-Augmented Ambiguous Question Answering

The retrieval augmented generation (RAG) framework addresses an ambiguity in user queries in QA systems by retrieving passages that cover all plausible interpretations and generating comprehensive responses based on the passages. However, our preliminary studies reveal that a single retrieval process often suffers from low quality results, as the retrieved passages frequently fail to capture all plausible interpretations. Although the iterative RAG approach has been proposed to address this problem, it comes at the cost of significantly reduced efficiency. To address these issues, we propose the diversify-verify-adapt (DIVA) framework. DIVA first diversifies the retrieved passages to encompass diverse interpretations. Subsequently, DIVA verifies the quality of the passages and adapts the most suitable approach tailored to their quality. This approach improves the QA systems accuracy and robustness by handling low quality retrieval issue in ambiguous questions, while enhancing efficiency.

Debiased Graph Poisoning Attack via Contrastive Surrogate Objective

Graph neural networks (GNN) are vulnerable to adversarial attacks, which aim to degrade the performance of GNNs through imperceptible changes on the graph. However, we find that in fact the prevalent meta-gradient-based attacks, which utilizes the gradient of the loss w.r.t the adjacency matrix, are biased towards training nodes. That is, their meta-gradient is determined by a training procedure of the surrogate model, which is solely trained on the training nodes. This bias manifests as an uneven perturbation, connecting two nodes when at least one of them is a labeled node, i.e., training node, while it is unlikely to connect two unlabeled nodes. However, these biased attack approaches are sub-optimal as they do not consider flipping edges between two unlabeled nodes at all. This means that they miss the potential attacked edges between unlabeled nodes that significantly alter the representation of a node. In this paper, we investigate the meta-gradients to uncover the root cause of the uneven perturbations of existing attacks. Based on our analysis, we propose a Meta-gradient-based attack method using contrastive surrogate objective (Metacon), which alleviates the bias in meta-gradient using a new surrogate loss. We conduct extensive experiments to show that Metacon outperforms existing meta gradient-based attack methods through benchmark datasets, while showing that alleviating the bias towards training nodes is effective in attacking the graph structure.

Mew: Multiplexed Immunofluorescence Image Analysis through an Efficient Multiplex Network

Recent advancements in graph-based approaches for multiplexed immunofluorescence (mIF) images have significantly propelled the field forward, offering deeper insights into patient-level phenotyping. However, current graph-based methodologies encounter two primary challenges: (1) Cellular Heterogeneity, where existing approaches fail to adequately address the inductive biases inherent in graphs, particularly the homophily characteristic observed in cellular connectivity and; (2) Scalability, where handling cellular graphs from high-dimensional images faces difficulties in managing a high number of cells. To overcome these limitations, we introduce Mew, a novel framework designed to efficiently process mIF images through the lens of multiplex network. Mew innovatively constructs a multiplex network comprising two distinct layers: a Voronoi network for geometric information and a Cell-type network for capturing cell-wise homogeneity. This framework equips a scalable and efficient Graph Neural Network (GNN), capable of processing the entire graph during training. Furthermore, Mew integrates an interpretable attention module that autonomously identifies relevant layers for image classification. Extensive experiments on a real-world patient dataset from various institutions highlight Mew's remarkable efficacy and efficiency, marking a significant advancement in mIF image analysis. The source code of Mew can be found here: \url{https://github.com/UNITES-Lab/Mew}

Semantic Diversity-aware Prototype-based Learning for Unbiased Scene Graph Generation

The scene graph generation (SGG) task involves detecting objects within an image and predicting predicates that represent the relationships between the objects. However, in SGG benchmark datasets, each subject-object pair is annotated with a single predicate even though a single predicate may exhibit diverse semantics (i.e., semantic diversity), existing SGG models are trained to predict the one and only predicate for each pair. This in turn results in the SGG models to overlook the semantic diversity that may exist in a predicate, thus leading to biased predictions. In this paper, we propose a novel model-agnostic Semantic Diversity-aware Prototype-based Learning (DPL) framework that enables unbiased predictions based on the understanding of the semantic diversity of predicates. Specifically, DPL learns the regions in the semantic space covered by each predicate to distinguish among the various different semantics that a single predicate can represent. Extensive experiments demonstrate that our proposed model-agnostic DPL framework brings significant performance improvement on existing SGG models, and also effectively understands the semantic diversity of predicates.

Molecule Language Model with Augmented Pairs and Expertise Transfer

Understanding the molecules and their textual descriptions via molecule language models (MoLM) recently got a surge of interest among researchers. However, unique challenges exist in the field of MoLM due to 1) a limited amount of molecule-text paired data and 2) missing expertise that occurred due to the specialized areas of focus among the experts. To this end, we propose AMOLE, which 1) augments molecule-text pairs with structural similarity preserving loss, and 2) transfers the expertise between the molecules. Extensive experiments on various downstream tasks demonstrate the superiority of AMOLE in comprehending molecules and their descriptions, highlighting its potential for application in real-world drug discovery.