Accurately predicting drug-target interactions (DTIs) is pivotal for advancing drug discovery and target validation techniques. While machine learning approaches including those that are based on Graph Neural Networks (GNN) have achieved notable success in DTI prediction, many of them have difficulties in effectively integrating the diverse features of drugs, targets and their interactions. To address this limitation, we introduce a novel framework to take advantage of the power of both transductive learning and inductive learning so that features at molecular level and drug-target interaction network level can be exploited. Within this framework is a GNN-based model called Graph-in-Graph (GiG) that represents graphs of drug and target molecular structures as meta-nodes in a drug-target interaction graph, enabling a detailed exploration of their intricate relationships. To evaluate the proposed model, we have compiled a special benchmark comprising drug SMILES, protein sequences, and their interaction data, which is interesting in its own right. Our experimental results demonstrate that the GiG model significantly outperforms existing approaches across all evaluation metrics, highlighting the benefits of integrating different learning paradigms and interaction data.
The recently proposed Novel Category Discovery (NCD) adapt paradigm of transductive learning hinders its application in more real-world scenarios. In fact, few labeled data in part of new categories can well alleviate this burden, which coincides with the ease that people can label few of new category data. Therefore, this paper presents a new setting in which a trained agent is able to flexibly switch between the tasks of identifying examples of known (labelled) classes and clustering novel (completely unlabeled) classes as the number of query examples increases by leveraging knowledge learned from only a few (handful) support examples. Drawing inspiration from the discovery of novel categories using prior-based clustering algorithms, we introduce a novel framework that further relaxes its assumptions to the real-world open set level by unifying the concept of model adaptability in few-shot learning. We refer to this setting as Few-Shot Novel Category Discovery (FSNCD) and propose Semi-supervised Hierarchical Clustering (SHC) and Uncertainty-aware K-means Clustering (UKC) to examine the model's reasoning capabilities. Extensive experiments and detailed analysis on five commonly used datasets demonstrate that our methods can achieve leading performance levels across different task settings and scenarios.
Graph auto-encoder is considered a framework for unsupervised learning on graph-structured data by representing graphs in a low dimensional space. It has been proved very powerful for graph analytics. In the real world, complex relationships in various entities can be represented by heterogeneous graphs that contain more abundant semantic information than homogeneous graphs. In general, graph auto-encoders based on homogeneous graphs are not applicable to heterogeneous graphs. In addition, little work has been done to evaluate the effect of different semantics on node embedding in heterogeneous graphs for unsupervised graph representation learning. In this work, we propose a novel Heterogeneous Graph Attention Auto-Encoders (HGATE) for unsupervised representation learning on heterogeneous graph-structured data. Based on the consideration of semantic information, our architecture of HGATE reconstructs not only the edges of the heterogeneous graph but also node attributes, through stacked encoder/decoder layers. Hierarchical attention is used to learn the relevance between a node and its meta-path based neighbors, and the relevance among different meta-paths. HGATE is applicable to transductive learning as well as inductive learning. Node classification and link prediction experiments on real-world heterogeneous graph datasets demonstrate the effectiveness of HGATE for both transductive and inductive tasks.
Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over $10^5$ nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.
Message passing-based graph neural networks (GNNs) have achieved great success in many real-world applications. For a sampled mini-batch of target nodes, the message passing process is divided into two parts: message passing between nodes within the batch (MP-IB) and message passing from nodes outside the batch to those within it (MP-OB). However, MP-OB recursively relies on higher-order out-of-batch neighbors, leading to an exponentially growing computational cost with respect to the number of layers. Due to the neighbor explosion, the whole message passing stores most nodes and edges on the GPU such that many GNNs are infeasible to large-scale graphs. To address this challenge, we propose an accurate and fast mini-batch approach for large graph transductive learning, namely topological compensation (TOP), which obtains the outputs of the whole message passing solely through MP-IB, without the costly MP-OB. The major pillar of TOP is a novel concept of message invariance, which defines message-invariant transformations to convert costly MP-OB into fast MP-IB. This ensures that the modified MP-IB has the same output as the whole message passing. Experiments demonstrate that TOP is significantly faster than existing mini-batch methods by order of magnitude on vast graphs (millions of nodes and billions of edges) with limited accuracy degradation.
Transductive zero-shot learning with vision-language models leverages image-image similarities within the dataset to achieve better classification accuracy compared to the inductive setting. However, there is little work that explores the structure of the language space in this context. We propose GTA-CLIP, a novel technique that incorporates supervision from language models for joint transduction in language and vision spaces. Our approach is iterative and consists of three steps: (i) incrementally exploring the attribute space by querying language models, (ii) an attribute-augmented transductive inference procedure, and (iii) fine-tuning the language and vision encoders based on inferred labels within the dataset. Through experiments with CLIP encoders, we demonstrate that GTA-CLIP, yields an average performance improvement of 8.6% and 3.7% across 12 datasets and 3 encoders, over CLIP and transductive CLIP respectively in the zero-shot setting. We also observe similar improvements in a few-shot setting. We present ablation studies that demonstrate the value of each step and visualize how the vision and language spaces evolve over iterations driven by the transductive learning.
We delve into the challenge of semi-supervised node classification on the Contextual Stochastic Block Model (CSBM) dataset. Here, nodes from the two-cluster Stochastic Block Model (SBM) are coupled with feature vectors, which are derived from a Gaussian Mixture Model (GMM) that corresponds to their respective node labels. With only a subset of the CSBM node labels accessible for training, our primary objective becomes the accurate classification of the remaining nodes. Venturing into the transductive learning landscape, we, for the first time, pinpoint the information-theoretical threshold for the exact recovery of all test nodes in CSBM. Concurrently, we design an optimal spectral estimator inspired by Principal Component Analysis (PCA) with the training labels and essential data from both the adjacency matrix and feature vectors. We also evaluate the efficacy of graph ridge regression and Graph Convolutional Networks (GCN) on this synthetic dataset. Our findings underscore that graph ridge regression and GCN possess the ability to achieve the information threshold of exact recovery in a manner akin to the optimal estimator when using the optimal weighted self-loops. This highlights the potential role of feature learning in augmenting the proficiency of GCN, especially in the realm of semi-supervised learning.
Most graph contrastive learning (GCL) methods heavily rely on cross-view contrast, thus facing several concomitant challenges, such as the complexity of designing effective augmentations, the potential for information loss between views, and increased computational costs. To mitigate reliance on cross-view contrasts, we propose \ttt{SIGNA}, a novel single-view graph contrastive learning framework. Regarding the inconsistency between structural connection and semantic similarity of neighborhoods, we resort to soft neighborhood awareness for GCL. Specifically, we leverage dropout to obtain structurally-related yet randomly-noised embedding pairs for neighbors, which serve as potential positive samples. At each epoch, the role of partial neighbors is switched from positive to negative, leading to probabilistic neighborhood contrastive learning effect. Furthermore, we propose a normalized Jensen-Shannon divergence estimator for a better effect of contrastive learning. Surprisingly, experiments on diverse node-level tasks demonstrate that our simple single-view GCL framework consistently outperforms existing methods by margins of up to 21.74% (PPI). In particular, with soft neighborhood awareness, SIGNA can adopt MLPs instead of complicated GCNs as the encoder to generate representations in transductive learning tasks, thus speeding up its inference process by 109 times to 331 times. The source code is available at https://github.com/sunisfighting/SIGNA.
Individuals who identify as sexual and gender minorities, including lesbian, gay, bisexual, transgender, queer, and others (LGBTQ+) are more likely to experience poorer health than their heterosexual and cisgender counterparts. One primary source that drives these health disparities is minority stress (i.e., chronic and social stressors unique to LGBTQ+ communities' experiences adapting to the dominant culture). This stress is frequently expressed in LGBTQ+ users' posts on social media platforms. However, these expressions are not just straightforward manifestations of minority stress. They involve linguistic complexity (e.g., idiom or lexical diversity), rendering them challenging for many traditional natural language processing methods to detect. In this work, we designed a hybrid model using Graph Neural Networks (GNN) and Bidirectional Encoder Representations from Transformers (BERT), a pre-trained deep language model to improve the classification performance of minority stress detection. We experimented with our model on a benchmark social media dataset for minority stress detection (LGBTQ+ MiSSoM+). The dataset is comprised of 5,789 human-annotated Reddit posts from LGBTQ+ subreddits. Our approach enables the extraction of hidden linguistic nuances through pretraining on a vast amount of raw data, while also engaging in transductive learning to jointly develop representations for both labeled training data and unlabeled test data. The RoBERTa-GCN model achieved an accuracy of 0.86 and an F1 score of 0.86, surpassing the performance of other baseline models in predicting LGBTQ+ minority stress. Improved prediction of minority stress expressions on social media could lead to digital health interventions to improve the wellbeing of LGBTQ+ people-a community with high rates of stress-sensitive health problems.
Transductive tasks on graphs differ fundamentally from typical supervised machine learning tasks, as the independent and identically distributed (i.i.d.) assumption does not hold among samples. Instead, all train/test/validation samples are present during training, making them more akin to a semi-supervised task. These differences make the analysis of the models substantially different from other models. Recently, Graph Transformers have significantly improved results on these datasets by overcoming long-range dependency problems. However, the quadratic complexity of full Transformers has driven the community to explore more efficient variants, such as those with sparser attention patterns. While the attention matrix has been extensively discussed, the hidden dimension or width of the network has received less attention. In this work, we establish some theoretical bounds on how and under what conditions the hidden dimension of these networks can be compressed. Our results apply to both sparse and dense variants of Graph Transformers.
Pre-trained vision-language models (e.g., CLIP) have shown powerful zero-shot transfer capabilities. But they still struggle with domain shifts and typically require labeled data to adapt to downstream tasks, which could be costly. In this work, we aim to leverage unlabeled data that naturally spans multiple domains to enhance the transferability of vision-language models. Under this unsupervised multi-domain setting, we have identified inherent model bias within CLIP, notably in its visual and text encoders. Specifically, we observe that CLIP's visual encoder tends to prioritize encoding domain over discriminative category information, meanwhile its text encoder exhibits a preference for domain-relevant classes. To mitigate this model bias, we propose a training-free and label-free feature calibration method, Unsupervised Multi-domain Feature Calibration (UMFC). UMFC estimates image-level biases from domain-specific features and text-level biases from the direction of domain transition. These biases are subsequently subtracted from original image and text features separately, to render them domain-invariant. We evaluate our method on multiple settings including transductive learning and test-time adaptation. Extensive experiments show that our method outperforms CLIP and performs on par with the state-of-the-arts that need additional annotations or optimization. Our code is available at https://github.com/GIT-LJc/UMFC.
This paper presents a comparative study of near-duplicate image detection techniques in a real-world use case scenario, where a document management company is commissioned to manually annotate a collection of scanned photographs. Detecting duplicate and near-duplicate photographs can reduce the time spent on manual annotation by archivists. This real use case differs from laboratory settings as the deployment dataset is available in advance, allowing the use of transductive learning. We propose a transductive learning approach that leverages state-of-the-art deep learning architectures such as convolutional neural networks (CNNs) and Vision Transformers (ViTs). Our approach involves pre-training a deep neural network on a large dataset and then fine-tuning the network on the unlabeled target collection with self-supervised learning. The results show that the proposed approach outperforms the baseline methods in the task of near-duplicate image detection in the UKBench and an in-house private dataset.
The rapidly growing number and variety of Large Language Models (LLMs) present significant challenges in efficiently selecting the appropriate LLM for a given query, especially considering the trade-offs between performance and computational cost. Current LLM selection methods often struggle to generalize across new LLMs and different tasks because of their limited ability to leverage contextual interactions among tasks, queries, and LLMs, as well as their dependence on a transductive learning framework. To address these shortcomings, we introduce a novel inductive graph framework, named as GraphRouter, which fully utilizes the contextual information among tasks, queries, and LLMs to enhance the LLM selection process. GraphRouter constructs a heterogeneous graph comprising task, query, and LLM nodes, with interactions represented as edges, which efficiently captures the contextual information between the query's requirements and the LLM's capabilities. Through an innovative edge prediction mechanism, GraphRouter is able to predict attributes (the effect and cost of LLM response) of potential edges, allowing for optimized recommendations that adapt to both existing and newly introduced LLMs without requiring retraining. Comprehensive experiments across three distinct effect-cost weight scenarios have shown that GraphRouter substantially surpasses existing routers, delivering a minimum performance improvement of 12.3%. In addition, it achieves enhanced generalization across new LLMs settings and supports diverse tasks with at least a 9.5% boost in effect and a significant reduction in computational demands. This work endeavors to apply a graph-based approach for the contextual and adaptive selection of LLMs, offering insights for real-world applications. Our codes for GraphRouter will soon be released at https://github.com/ulab-uiuc/GraphRouter.
Partitioning is a known problem in computer science and is critical in chip design workflows, as advancements in this area can significantly influence design quality and efficiency. Deep Learning (DL) techniques, particularly those involving Graph Neural Networks (GNNs), have demonstrated strong performance in various node, edge, and graph prediction tasks using both inductive and transductive learning methods. A notable area of recent interest within GNNs are pooling layers and their application to graph partitioning. While these methods have yielded promising results across social, computational, and other random graphs, their effectiveness has not yet been explored in the context of VLSI hypergraph netlists. In this study, we introduce a new set of synthetic partitioning benchmarks that emulate real-world netlist characteristics and possess a known upper bound for solution cut quality. We distinguish these benchmarks with the prior work and evaluate existing state-of-the-art partitioning algorithms alongside GNN-based approaches, highlighting their respective advantages and disadvantages.
Knowledge graphs (KGs) enhance the performance of large language models (LLMs) and search engines by providing structured, interconnected data that improves reasoning and context-awareness. However, KGs only focus on text data, thereby neglecting other modalities such as speech. In this work, we introduce wav2graph, the first framework for supervised learning knowledge graph from speech data. Our pipeline are straightforward: (1) constructing a KG based on transcribed spoken utterances and a named entity database, (2) converting KG into embedding vectors, and (3) training graph neural networks (GNNs) for node classification and link prediction tasks. Through extensive experiments conducted in inductive and transductive learning contexts using state-of-the-art GNN models, we provide baseline results and error analysis for node classification and link prediction tasks on human transcripts and automatic speech recognition (ASR) transcripts, including evaluations using both encoder-based and decoder-based node embeddings, as well as monolingual and multilingual acoustic pre-trained models. All related code, data, and models are published online.
Graph node classification with few labeled nodes presents significant challenges due to limited supervision. Conventional methods often exploit the graph in a transductive learning manner. They fail to effectively utilize the abundant unlabeled data and the structural information inherent in graphs. To address these issues, we introduce a Structure-Aware Consensus Network (SACN) from three perspectives. Firstly, SACN leverages a novel structure-aware consensus learning strategy between two strongly augmented views. The proposed strategy can fully exploit the potentially useful information of the unlabeled nodes and the structural information of the entire graph. Secondly, SACN uniquely integrates the graph's structural information to achieve strong-to-strong consensus learning, improving the utilization of unlabeled data while maintaining multiview learning. Thirdly, unlike two-branch graph neural network-based methods, SACN is designed for multiview feature learning within a single-branch architecture. Furthermore, a class-aware pseudolabel selection strategy helps address class imbalance and achieve effective weak-to-strong supervision. Extensive experiments on three benchmark datasets demonstrate SACN's superior performance in node classification tasks, particularly at very low label rates, outperforming state-of-the-art methods while maintaining computational simplicity.The source code is available at https://github.com/kunzhan/SACN
Large language models (LLMs) have shown their potential in long-context understanding and mathematical reasoning. In this paper, we study the problem of using LLMs to detect tabular anomalies and show that pre-trained LLMs are zero-shot batch-level anomaly detectors. That is, without extra distribution-specific model fitting, they can discover hidden outliers in a batch of data, demonstrating their ability to identify low-density data regions. For LLMs that are not well aligned with anomaly detection and frequently output factual errors, we apply simple yet effective data-generating processes to simulate synthetic batch-level anomaly detection datasets and propose an end-to-end fine-tuning strategy to bring out the potential of LLMs in detecting real anomalies. Experiments on a large anomaly detection benchmark (ODDS) showcase i) GPT-4 has on-par performance with the state-of-the-art transductive learning-based anomaly detection methods and ii) the efficacy of our synthetic dataset and fine-tuning strategy in aligning LLMs to this task.
The need for regression models to predict circular values arises in many scientific fields. In this work we explore a family of expressive and interpretable distributions over circle-valued random functions related to Gaussian processes targeting two Euclidean dimensions conditioned on the unit circle. The probability model has connections with continuous spin models in statistical physics. Moreover, its density is very simple and has maximum-entropy, unlike previous Gaussian process-based approaches, which use wrapping or radial marginalization. For posterior inference, we introduce a new Stratonovich-like augmentation that lends itself to fast Gibbs sampling. We argue that transductive learning in these models favors a Bayesian approach to the parameters and apply our sampling scheme to the Double Metropolis-Hastings algorithm. We present experiments applying this model to the prediction of (i) wind directions and (ii) the percentage of the running gait cycle as a function of joint angles.
Recently, transductive learning methods, which leverage holdout sets during training, have gained popularity for their potential to improve speed, accuracy, and fairness in machine learning models. Despite this, the composition of the holdout set itself, particularly the balance of sensitive sub-groups, has been largely overlooked. Our experiments on CIFAR and CelebA datasets show that compositional changes in the holdout set can substantially influence fairness metrics. Imbalanced holdout sets exacerbate existing disparities, while balanced holdouts can mitigate issues introduced by imbalanced training data. These findings underline the necessity of constructing holdout sets that are both diverse and representative.
Graph neural networks (GNNs) have become instrumental in diverse real-world applications, offering powerful graph learning capabilities for tasks such as social networks and medical data analysis. Despite their successes, GNNs are vulnerable to adversarial attacks, including membership inference attacks (MIA), which threaten privacy by identifying whether a record was part of the model's training data. While existing research has explored MIA in GNNs under graph inductive learning settings, the more common and challenging graph transductive learning setting remains understudied in this context. This paper addresses this gap and proposes an effective two-stage defense, Graph Transductive Defense (GTD), tailored to graph transductive learning characteristics. The gist of our approach is a combination of a train-test alternate training schedule and flattening strategy, which successfully reduces the difference between the training and testing loss distributions. Extensive empirical results demonstrate the superior performance of our method (a decrease in attack AUROC by $9.42\%$ and an increase in utility performance by $18.08\%$ on average compared to LBP), highlighting its potential for seamless integration into various classification models with minimal overhead.