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.

Self-Explainable Temporal Graph Networks based on Graph Information Bottleneck

Temporal Graph Neural Networks (TGNN) have the ability to capture both the graph topology and dynamic dependencies of interactions within a graph over time. There has been a growing need to explain the predictions of TGNN models due to the difficulty in identifying how past events influence their predictions. Since the explanation model for a static graph cannot be readily applied to temporal graphs due to its inability to capture temporal dependencies, recent studies proposed explanation models for temporal graphs. However, existing explanation models for temporal graphs rely on post-hoc explanations, requiring separate models for prediction and explanation, which is limited in two aspects: efficiency and accuracy of explanation. In this work, we propose a novel built-in explanation framework for temporal graphs, called Self-Explainable Temporal Graph Networks based on Graph Information Bottleneck (TGIB). TGIB provides explanations for event occurrences by introducing stochasticity in each temporal event based on the Information Bottleneck theory. Experimental results demonstrate the superiority of TGIB in terms of both the link prediction performance and explainability compared to state-of-the-art methods. This is the first work that simultaneously performs prediction and explanation for temporal graphs in an end-to-end manner.

Continual Traffic Forecasting via Mixture of Experts

The real-world traffic networks undergo expansion through the installation of new sensors, implying that the traffic patterns continually evolve over time. Incrementally training a model on the newly added sensors would make the model forget the past knowledge, i.e., catastrophic forgetting, while retraining the model on the entire network to capture these changes is highly inefficient. To address these challenges, we propose a novel Traffic Forecasting Mixture of Experts (TFMoE) for traffic forecasting under evolving networks. The main idea is to segment the traffic flow into multiple homogeneous groups, and assign an expert model responsible for a specific group. This allows each expert model to concentrate on learning and adapting to a specific set of patterns, while minimizing interference between the experts during training, thereby preventing the dilution or replacement of prior knowledge, which is a major cause of catastrophic forgetting. Through extensive experiments on a real-world long-term streaming network dataset, PEMSD3-Stream, we demonstrate the effectiveness and efficiency of TFMoE. Our results showcase superior performance and resilience in the face of catastrophic forgetting, underscoring the effectiveness of our approach in dealing with continual learning for traffic flow forecasting in long-term streaming networks.