Towards generalizable Graph Contrastive Learning: An information theory perspective

Prompting techniques unlock valuable insights from pre-trained models, leading to a remarkable performance in Natural Language Processing (NLP). Inspired by NLP advancements, various graph prompt methods have emerged to transfer knowledge from pre-trained graph models to diverse downstream graph tasks. However, designing appropriate prompts for different downstream tasks remains a significant challenge due to substantial differences between pre-training graph tasks and downstream graph tasks. Moreover, existing graph prompt methods prevent transferability across different domains as they independently pre-train a model for each dataset. To address these challenges, we propose Graph Pretraining and Task-Specific Prompting (GTSP). To the best of our knowledge, GTSP is the first unified pre-training framework to handle cross-domain graph data and multiple types of graph tasks simultaneously. The key idea of our framework is to utilize similar label features between pre-training tasks and downstream tasks to seamlessly integrate the downstream task prompt into the pretrained model. We then propose a task-specific prompting architecture and design a label similarity matrix as prompt input. With GTSP, the pre-trained model can adapt to various types of downstream graph tasks, effectively avoiding the challenges of forcibly altering graph task forms. Experimental analysis conducted on benchmark datasets demonstrates the superiority of our method.

Histopathological image segmentation is a laborious and time-intensive task, often requiring analysis from experienced pathologists for accurate examinations. To reduce this burden, supervised machine-learning approaches have been adopted using large-scale annotated datasets for histopathological image analysis. However, in several scenarios, the availability of large-scale annotated data is a bottleneck while training such models. Self-supervised learning (SSL) is an alternative paradigm that provides some respite by constructing models utilizing only the unannotated data which is often abundant. The basic idea of SSL is to train a network to perform one or many pseudo or pretext tasks on unannotated data and use it subsequently as the basis for a variety of downstream tasks. It is seen that the success of SSL depends critically on the considered pretext task. While there have been many efforts in designing pretext tasks for classification problems, there have not been many attempts on SSL for histopathological image segmentation. Motivated by this, we propose an SSL approach for segmenting histopathological images via generative diffusion models. Our method is based on the observation that diffusion models effectively solve an image-to-image translation task akin to a segmentation task. Hence, we propose generative diffusion as the pretext task for histopathological image segmentation. We also utilize a multi-loss function-based fine-tuning for the downstream task. We validate our method using several metrics on two publicly available datasets along with a newly proposed head and neck (HN) cancer dataset containing Hematoxylin and Eosin (H&E) stained images along with annotations.

: Calculating the amount of information about a random function contained in another random function has important uses in communication theory. An expression for the mutual information for continuous time random processes has been given by Gelfand and Yaglom, Chiang, and Perez by generalizing Shannon's result in a natural way. Under a condition of absolute continuity of measures the continuous time expression has the same form as Shannon's result. For two Gaussian processes Gelfand and Yaglom express the mutual information in terms of a mean square estimation error. We generalize this result to diffusion processes and express the solution in a different form which is more naturally related to a corresponding filtering problem. We also use these results to calculate some information rates.

Cancer genomics is dedicated to elucidating the genes and pathways that contribute to cancer progression and development. Identifying cancer genes (CGs) associated with the initiation and progression of cancer is critical for characterization of molecular-level mechanism in cancer research. In recent years, the growing availability of high-throughput molecular data and advancements in deep learning technologies has enabled the modelling of complex interactions and topological information within genomic data. Nevertheless, because of the limited labelled data, pinpointing CGs from a multitude of potential mutations remains an exceptionally challenging task. To address this, we propose a novel deep learning framework, termed self-supervised masked graph learning (SMG), which comprises SMG reconstruction (pretext task) and task-specific fine-tuning (downstream task). In the pretext task, the nodes of multi-omic featured protein-protein interaction (PPI) networks are randomly substituted with a defined mask token. The PPI networks are then reconstructed using the graph neural network (GNN)-based autoencoder, which explores the node correlations in a self-prediction manner. In the downstream tasks, the pre-trained GNN encoder embeds the input networks into feature graphs, whereas a task-specific layer proceeds with the final prediction. To assess the performance of the proposed SMG method, benchmarking experiments are performed on three node-level tasks (identification of CGs, essential genes and healthy driver genes) and one graph-level task (identification of disease subnetwork) across eight PPI networks. Benchmarking experiments and performance comparison with existing state-of-the-art methods demonstrate the superiority of SMG on multi-omic feature engineering.

Soft-orthogonal constrained dual-stream encoder with self-supervised clustering network for brain functional connectivity data

Acquiring meaningful representations of gene expression is essential for the accurate prediction of downstream regulatory tasks, such as identifying promoters and transcription factor binding sites. However, the current dependency on supervised learning, constrained by the limited availability of labeled genomic data, impedes the ability to develop robust predictive models with broad generalization capabilities. In response, recent advancements have pivoted towards the application of self-supervised training for DNA sequence modeling, enabling the adaptation of pre-trained genomic representations to a variety of downstream tasks. Departing from the straightforward application of masked language learning techniques to DNA sequences, approaches such as MoDNA enrich genome language modeling with prior biological knowledge. In this study, we advance DNA language models by utilizing the Motif-oriented DNA (MoDNA) pre-training framework, which is established for self-supervised learning at the pre-training stage and is flexible enough for application across different downstream tasks. MoDNA distinguishes itself by efficiently learning semantic-level genomic representations from an extensive corpus of unlabeled genome data, offering a significant improvement in computational efficiency over previous approaches. The framework is pre-trained on a comprehensive human genome dataset and fine-tuned for targeted downstream tasks. Our enhanced analysis and evaluation in promoter prediction and transcription factor binding site prediction have further validated MoDNA’s exceptional capabilities, emphasizing its contribution to advancements in genomic predictive modeling.

Features based adaptive augmentation for graph contrastive learning

Unsupervised/self-supervised pre-training methods for graph representation learning have recently attracted increasing research interests, and they are shown to be able to generalize to various downstream applications. Yet, the adversarial robustness of such pre-trained graph learning models remains largely unexplored. More importantly, most existing defense techniques designed for end-to-end graph representation learning methods require pre-specified label definitions, and thus cannot be directly applied to the pre-training methods. In this paper, we propose an unsupervised defense technique to robustify pre-trained deep graph models, so that the perturbations on the input graph can be successfully identified and blocked before the model is applied to different downstream tasks. Specifically, we introduce a mutual information-based measure, graph representation vulnerability (GRV), to quantify the robustness of graph encoders on the representation space. We then formulate an optimization problem to learn the graph representation by carefully balancing the trade-off between the expressive power and the robustness (i.e., GRV) of the graph encoder. The discrete nature of graph topology and the joint space of graph data make the optimization problem intractable to solve. To handle the above difficulty and to reduce computational expense, we further relax the problem and thus provide an approximate solution. Additionally, we explore a provable connection between the robustness of the unsupervised graph encoder and that of models on downstream tasks. Extensive experiments demonstrate that even without access to labels and tasks, our model is still able to enhance robustness against adversarial attacks on three downstream tasks (node classification, link prediction, and community detection) by an average of +16.5% compared with existing methods.

Supervised deep learning methods have produced state-of-the-art results with large labeled datasets. However, accessing large labeled datasets is difficult in medical image analysis because of a shortage of medical experts, expensive annotations, and privacy constraints in the healthcare domain. Self-supervised learning is a branch of machine learning that exploits unlabeled data to encourage network weights toward a valid latent representation of the data during a so-called pretext task. The features learned by the model while solving pretext tasks are transferred to a downstream task where limited annotations are available. In this work, we propose PatchLoc, a novel pretext task whose objective is to find the location of a given patch from an image as a source of supervision. We validated the effectiveness of PatchLoc on a downstream segmentation task using three different medical datasets. PatchLoc yields substantial improvements compared to U-Net trained from scratch and other pretext task-based approaches in a low data regime.

CMNet: Classification-oriented multi-task network for hyperspectral pansharpening

Loading models pre-trained on the large-scale corpus in the general domain and fine-tuning them on specific downstream tasks is gradually becoming a paradigm in Natural Language Processing. Previous investigations prove that introducing a further pre-training phase between pre-training and fine-tuning phases to adapt the model on the domain-specific unlabeled data can bring positive effects. However, most of these further pre-training works just keep running the conventional pre-training task, e.g., masked language model, which can be regarded as the domain adaptation to bridge the data distribution gap. After observing diverse downstream tasks, we suggest that different tasks may also need a further pre-training phase with appropriate training tasks to bridge the task formulation gap. To investigate this, we carry out a study for improving multiple task-oriented dialogue downstream tasks through designing various tasks at the further pre-training phase. The experiment shows that different downstream tasks prefer different further pre-training tasks, which have intrinsic correlation and most further pre-training tasks significantly improve certain target tasks rather than all. Our investigation indicates that it is of great importance and effectiveness to design appropriate further pre-training tasks modeling specific information that benefit downstream tasks. Besides, we present multiple constructive empirical conclusions for enhancing task-oriented dialogues.

A core step of mining human mobility data is to learn accurate representations for user-generated check-in sequences. The learned representations should be able to fully describe the spatial-temporal mobility patterns of users and the high-level semantics of traveling. However, existing check-in sequence representation learning is usually implicitly achieved by end-to-end models designed for specific downstream tasks, resulting in unsatisfactory generalizable abilities and poor performance. Besides, although the sequence representation learning models that follow the contrastive learning pre-training paradigm have achieved breakthroughs in many fields like NLP, they fail to simultaneously consider the unique spatial-temporal characteristics of check-in sequences and need manual adjustments on the data augmentation strategies. So, directly applying them to check-in sequences cannot yield a meaningful pretext task. To this end, in this paper we propose a contrastive pre-training model with adversarial perturbations for check-in sequence representation learning (CACSR). Firstly, we design a novel spatial-temporal augmentation block for disturbing the spatial-temporal features of check-in sequences in the latent space to relieve the stress of designing manual data augmentation strategies. Secondly, to construct an effective contrastive pretext task, we generate “hard” positive and negative pairs for the check-in sequence by adversarial training. These two designs encourage the model to capture the high-level spatial-temporal patterns and semantics of check-in sequences while ignoring the noisy and unimportant details. We demonstrate the effectiveness and versatility of CACSR on two kinds of downstream tasks using three real-world datasets. The results show that our model outperforms both the state-of-the-art pre-training methods and the end-to-end models.

Pre-trained language models with structured semantic knowledge have demonstrated remarkable performance in a variety of downstream natural language processing tasks. The typical methods of integrating knowledge are designing different pre-training tasks and training from scratch, which requires high-end hardware, massive storage resources, and long computing times. Prompt learning is an effective approach to tuning language models for specific tasks, and it can also be used to infuse knowledge. However, most prompt learning methods accept one token as the answer, instead of multiple tokens. To tackle this problem, we propose the long-answer prompt learning method (KLAPrompt), with three different long-answer strategies, to incorporate semantic knowledge into pre-trained language models, and we compare the performance of these three strategies through experiments. We also explore the effectiveness of the KLAPrompt method in the medical field. Additionally, we generate a word sense prediction dataset (WSP) based on the Xinhua Dictionary and a disease and category prediction dataset (DCP) based on MedicalKG. Experimental results show that discrete answers with the answer space partitioning strategy achieve the best results, and introducing structured semantic information can consistently improve language modeling and downstream tasks.

Supervised learning technologies have been used in medical-data classification to improve diagnosis efficiency and reduce human diagnosis errors. A large amount of manually annotated data are required for the fully supervised learning process. However, annotating data information will consume a large amount of manpower and resources. Self-supervised learning has great advantages in solving this problem. Self-supervised learning mainly uses pretext tasks to mine its own supervised information from large-scale unsupervised data. And this constructed supervised information is used to train the network to learn valuable representations for downstream tasks. This study designs a general and efficient model for the diagnosis and classification of medical sensor data based on contrastive predictive coding (CPC) in self-supervised learning, called TCC, which consists of two steps. The first step is to design a pretext task based on the idea of CPC, which aims to extract effective features between different categories using its encoder. The second step designs a downstream classification task with lower time and space complexity to perform a supervised type of training using the features extracted by the encoder of the pretext task. Finally, to demonstrate the performance of the proposed framework in this paper, we compare the proposed framework with recent state-of-the-art works. Experiments comparing the proposed framework with supervised learning are also set up under the condition of different proportions of labeled data.

Unsupervised multi-view graph representation learning with dual weight-net