Learning to Describe for Predicting Zero-shot Drug-Drug Interactions

Adverse drug-drug interactions~(DDIs) can compromise the effectiveness of concurrent drug administration, posing a significant challenge in healthcare. As the development of new drugs continues, the potential for unknown adverse effects resulting from DDIs becomes a growing concern. Traditional computational methods for DDI prediction may fail to capture interactions for new drugs due to the lack of knowledge. In this paper, we introduce a new problem setup as zero-shot DDI prediction that deals with the case of new drugs. Leveraging textual information from online databases like DrugBank and PubChem, we propose an innovative approach TextDDI with a language model-based DDI predictor and a reinforcement learning~(RL)-based information selector, enabling the selection of concise and pertinent text for accurate DDI prediction on new drugs. Empirical results show the benefits of the proposed approach on several settings including zero-shot and few-shot DDI prediction, and the selected texts are semantically relevant. Our code and data are available at \url{https://github.com/zhufq00/DDIs-Prediction}.

An AI-enabled Agent-Based Model and Its Application in Measles Outbreak Simulation for New Zealand

Agent Based Models (ABMs) have emerged as a powerful tool for investigating complex social interactions, particularly in the context of public health and infectious disease investigation. In an effort to enhance the conventional ABM, enabling automated model calibration and reducing the computational resources needed for scaling up the model, we have developed a tensorized and differentiable agent-based model by coupling Graph Neural Network (GNN) and Long Short-Term Memory (LSTM) network. The model was employed to investigate the 2019 measles outbreak occurred in New Zealand, demonstrating a promising ability to accurately simulate the outbreak dynamics, particularly during the peak period of repeated cases. This paper shows that by leveraging the latest Artificial Intelligence (AI) technology and the capabilities of traditional ABMs, we gain deeper insights into the dynamics of infectious disease outbreaks. This, in turn, helps us make more informed decision when developing effective strategies that strike a balance between managing outbreaks and minimizing disruptions to everyday life.

EntailE: Introducing Textual Entailment in Commonsense Knowledge Graph Completion

Commonsense knowledge graph completion is a new challenge for commonsense knowledge graph construction and application. In contrast to factual knowledge graphs such as Freebase and YAGO, commonsense knowledge graphs (CSKGs; e.g., ConceptNet) utilize free-form text to represent named entities, short phrases, and events as their nodes. Such a loose structure results in large and sparse CSKGs, which makes the semantic understanding of these nodes more critical for learning rich commonsense knowledge graph embedding. While current methods leverage semantic similarities to increase the graph density, the semantic plausibility of the nodes and their relations are under-explored. Previous works adopt conceptual abstraction to improve the consistency of modeling (event) plausibility, but they are not scalable enough and still suffer from data sparsity. In this paper, we propose to adopt textual entailment to find implicit entailment relations between CSKG nodes, to effectively densify the subgraph connecting nodes within the same conceptual class, which indicates a similar level of plausibility. Each node in CSKG finds its top entailed nodes using a finetuned transformer over natural language inference (NLI) tasks, which sufficiently capture textual entailment signals. The entailment relation between these nodes are further utilized to: 1) build new connections between source triplets and entailed nodes to densify the sparse CSKGs; 2) enrich the generalization ability of node representations by comparing the node embeddings with a contrastive loss. Experiments on two standard CSKGs demonstrate that our proposed framework EntailE can improve the performance of CSKG completion tasks under both transductive and inductive settings.

Graph-Skeleton: ~1% Nodes are Sufficient to Represent Billion-Scale Graph

Due to the ubiquity of graph data on the web, web graph mining has become a hot research spot. Nonetheless, the prevalence of large-scale web graphs in real applications poses significant challenges to storage, computational capacity and graph model design. Despite numerous studies to enhance the scalability of graph models, a noticeable gap remains between academic research and practical web graph mining applications. One major cause is that in most industrial scenarios, only a small part of nodes in a web graph are actually required to be analyzed, where we term these nodes as target nodes, while others as background nodes. In this paper, we argue that properly fetching and condensing the background nodes from massive web graph data might be a more economical shortcut to tackle the obstacles fundamentally. To this end, we make the first attempt to study the problem of massive background nodes compression for target nodes classification. Through extensive experiments, we reveal two critical roles played by the background nodes in target node classification: enhancing structural connectivity between target nodes, and feature correlation with target nodes. Followingthis, we propose a novel Graph-Skeleton1 model, which properly fetches the background nodes, and further condenses the semantic and topological information of background nodes within similar target-background local structures. Extensive experiments on various web graph datasets demonstrate the effectiveness and efficiency of the proposed method. In particular, for MAG240M dataset with 0.24 billion nodes, our generated skeleton graph achieves highly comparable performance while only containing 1.8% nodes of the original graph.

One Graph Model for Cross-domain Dynamic Link Prediction

This work proposes DyExpert, a dynamic graph model for cross-domain link prediction. It can explicitly model historical evolving processes to learn the evolution pattern of a specific downstream graph and subsequently make pattern-specific link predictions. DyExpert adopts a decode-only transformer and is capable of efficiently parallel training and inference by \textit{conditioned link generation} that integrates both evolution modeling and link prediction. DyExpert is trained by extensive dynamic graphs across diverse domains, comprising 6M dynamic edges. Extensive experiments on eight untrained graphs demonstrate that DyExpert achieves state-of-the-art performance in cross-domain link prediction. Compared to the advanced baseline under the same setting, DyExpert achieves an average of 11.40% improvement Average Precision across eight graphs. More impressive, it surpasses the fully supervised performance of 8 advanced baselines on 6 untrained graphs.

Prototypical Contrastive Learning through Alignment and Uniformity for Recommendation

Graph Collaborative Filtering (GCF), one of the most widely adopted recommendation system methods, effectively captures intricate relationships between user and item interactions. Graph Contrastive Learning (GCL) based GCF has gained significant attention as it leverages self-supervised techniques to extract valuable signals from real-world scenarios. However, many methods usually learn the instances of discrimination tasks that involve the construction of contrastive pairs through random sampling. GCL approaches suffer from sampling bias issues, where the negatives might have a semantic structure similar to that of the positives, thus leading to a loss of effective feature representation. To address these problems, we present the \underline{Proto}typical contrastive learning through \underline{A}lignment and \underline{U}niformity for recommendation, which is called \textbf{ProtoAU}. Specifically, we first propose prototypes (cluster centroids) as a latent space to ensure consistency across different augmentations from the origin graph, aiming to eliminate the need for random sampling of contrastive pairs. Furthermore, the absence of explicit negatives means that directly optimizing the consistency loss between instance and prototype could easily result in dimensional collapse issues. Therefore, we propose aligning and maintaining uniformity in the prototypes of users and items as optimization objectives to prevent falling into trivial solutions. Finally, we conduct extensive experiments on four datasets and evaluate their performance on the task of link prediction. Experimental results demonstrate that the proposed ProtoAU outperforms other representative methods. The source codes of our proposed ProtoAU are available at \url{https://github.com/oceanlvr/ProtoAU}.

On Leveraging Large Language Models for Enhancing Entity Resolution

Entity resolution, the task of identifying and consolidating records that pertain to the same real-world entity, plays a pivotal role in various sectors such as e-commerce, healthcare, and law enforcement. The emergence of Large Language Models (LLMs) like GPT-4 has introduced a new dimension to this task, leveraging their advanced linguistic capabilities. This paper explores the potential of LLMs in the entity resolution process, shedding light on both their advantages and the computational complexities associated with large-scale matching. We introduce strategies for the efficient utilization of LLMs, including the selection of an optimal set of matching questions, namely MQsSP, which is proved to be a NP-hard problem. Our approach optimally chooses the most effective matching questions while keep consumption limited to your budget . Additionally, we propose a method to adjust the distribution of possible partitions after receiving responses from LLMs, with the goal of reducing the uncertainty of entity resolution. We evaluate the effectiveness of our approach using entropy as a metric, and our experimental results demonstrate the efficiency and effectiveness of our proposed methods, offering promising prospects for real-world applications.

Single-Cell RNA-seq Synthesis with Latent Diffusion Model

The single-cell RNA sequencing (scRNA-seq) technology enables researchers to study complex biological systems and diseases with high resolution. The central challenge is synthesizing enough scRNA-seq samples; insufficient samples can impede downstream analysis and reproducibility. While various methods have been attempted in past research, the resulting scRNA-seq samples were often of poor quality or limited in terms of useful specific cell subpopulations. To address these issues, we propose a novel method called Single-Cell Latent Diffusion (SCLD) based on the Diffusion Model. This method is capable of synthesizing large-scale, high-quality scRNA-seq samples, including both 'holistic' or targeted specific cellular subpopulations within a unified framework. A pre-guidance mechanism is designed for synthesizing specific cellular subpopulations, while a post-guidance mechanism aims to enhance the quality of scRNA-seq samples. The SCLD can synthesize large-scale and high-quality scRNA-seq samples for various downstream tasks. Our experimental results demonstrate state-of-the-art performance in cell classification and data distribution distances when evaluated on two scRNA-seq benchmarks. Additionally, visualization experiments show the SCLD's capability in synthesizing specific cellular subpopulations.

Fine-tuning Graph Neural Networks by Preserving Graph Generative Patterns

Recently, the paradigm of pre-training and fine-tuning graph neural networks has been intensively studied and applied in a wide range of graph mining tasks. Its success is generally attributed to the structural consistency between pre-training and downstream datasets, which, however, does not hold in many real-world scenarios. Existing works have shown that the structural divergence between pre-training and downstream graphs significantly limits the transferability when using the vanilla fine-tuning strategy. This divergence leads to model overfitting on pre-training graphs and causes difficulties in capturing the structural properties of the downstream graphs. In this paper, we identify the fundamental cause of structural divergence as the discrepancy of generative patterns between the pre-training and downstream graphs. Furthermore, we propose G-Tuning to preserve the generative patterns of downstream graphs. Given a downstream graph G, the core idea is to tune the pre-trained GNN so that it can reconstruct the generative patterns of G, the graphon W. However, the exact reconstruction of a graphon is known to be computationally expensive. To overcome this challenge, we provide a theoretical analysis that establishes the existence of a set of alternative graphons called graphon bases for any given graphon. By utilizing a linear combination of these graphon bases, we can efficiently approximate W. This theoretical finding forms the basis of our proposed model, as it enables effective learning of the graphon bases and their associated coefficients. Compared with existing algorithms, G-Tuning demonstrates an average improvement of 0.5% and 2.6% on in-domain and out-of-domain transfer learning experiments, respectively.

Compositional Generalization for Multi-label Text Classification: A Data-Augmentation Approach

Despite significant advancements in multi-label text classification, the ability of existing models to generalize to novel and seldom-encountered complex concepts, which are compositions of elementary ones, remains underexplored. This research addresses this gap. By creating unique data splits across three benchmarks, we assess the compositional generalization ability of existing multi-label text classification models. Our results show that these models often fail to generalize to compositional concepts encountered infrequently during training, leading to inferior performance on tests with these new combinations. To address this, we introduce a data augmentation method that leverages two innovative text generation models designed to enhance the classification models' capacity for compositional generalization. Our experiments show that this data augmentation approach significantly improves the compositional generalization capabilities of classification models on our benchmarks, with both generation models surpassing other text generation baselines.