SMG: self-supervised masked graph learning for cancer gene identification.

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.

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.

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.

Self-supervised video representation learning leaves out heavy manual annotation by automatically excavating supervisory signals. Although contrastive learning based approaches exhibit superior performances, pretext task based approaches still deserve further study. This is because the pretext tasks exploit the nature of data and encourage feature extractors to learn spatiotemporal logic by discovering dependencies among video clips or cubes, without manual engineering on data augmentations or manual construction of contrastive pairs. To utilize chronological property more effectively and efficiently, this work proposes a novel pretext task, named serial restoration of shuffled clips (SRSC), disentangled by an elaborately designed task network composed of an order-aware encoder and a serial restoration decoder. In contrast to other order based pretext tasks that formulate clip order recognition as a one-step classification problem, the proposed SRSC task restores shuffled clips into the right order in multiple steps. Owing to the excellent elasticity of SRSC, a novel taxonomy of curriculum learning is further proposed to equip SRSC with different pre-training strategies. According to the factors that affect the complexity of solving the SRSC task, the proposed curriculum learning strategies can be categorized into task based, model based and data based. Extensive experiments are conducted on the subdivided strategies to explore their effectiveness and noteworthy laws. Compared with existing approaches, this work demonstrates that the proposed approach achieves state-of-the-art performances in pretext task based self-supervised video representation learning and a majority of the proposed strategies further boost the performance of downstream tasks. For the first time, the features pre-trained by the pretext tasks are applied to video captioning by feature-level early fusion, and enhance the input of existing approaches as a lightweight plugin.

Attribute graphs are a crucial data structure for graph communities. However, the presence of redundancy and noise in the attribute graph can impair the aggregation effect of integrating two different heterogeneous distributions of attribute and structural features, resulting in inconsistent and distorted data that ultimately compromises the accuracy and reliability of attribute graph learning. For instance, redundant or irrelevant attributes can result in overfitting, while noisy attributes can lead to underfitting. Similarly, redundant or noisy structural features can affect the accuracy of graph representations, making it challenging to distinguish between different nodes or communities. To address these issues, we propose the embedded fusion graph auto-encoder framework for self-supervised learning (SSL), which leverages multitask learning to fuse node features across different tasks to reduce redundancy. The embedding fusion graph auto-encoder (EFGAE) framework comprises two phases: pretraining (PT) and downstream task learning (DTL). During the PT phase, EFGAE uses a graph auto-encoder (GAE) based on adversarial contrastive learning to learn structural and attribute embeddings separately and then fuses these embeddings to obtain a representation of the entire graph. During the DTL phase, we introduce an adaptive graph convolutional network (AGCN), which is applied to graph neural network (GNN) classifiers to enhance recognition for downstream tasks. The experimental results demonstrate that our approach outperforms state-of-the-art (SOTA) techniques in terms of accuracy, generalization ability, and robustness.

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

Supervised learning methods have shown effectiveness in estimating spatial acoustic parameters such as time difference of arrival, direct-to-reverberant ratio and reverberation time. However, they still suffer from the simulation-to-reality generalization problem due to the mismatch between simulated and real-world acoustic characteristics and the deficiency of annotated real-world data. To this end, this work proposes a selfsupervised method that takes full advantage of unlabeled data for spatial acoustic parameter estimation. First, a new pretext task, i.e. cross-channel signal reconstruction (CCSR), is designed to learn a universal spatial acoustic representation from unlabeled multi-channel microphone signals. We mask partial signals of one channel and ask the model to reconstruct them, which makes it possible to learn spatial acoustic information from unmasked signals and extract source information from the other microphone channel. An encoder-decoder structure is used to disentangle the two kinds of information. By fine-tuning the pre-trained spatial encoder with a small annotated dataset, this encoder can be used to estimate spatial acoustic parameters. Second, a novel multi-channel audio Conformer (MC-Conformer) is adopted as the encoder model architecture, which is suitable for both the pretext and downstream tasks. It is carefully designed to be able to capture the local and global characteristics of spatial acoustics exhibited in the time-frequency domain. Experimental results of five acoustic parameter estimation tasks on both simulated and real-world data show the effectiveness of the proposed method. To the best of our knowledge, this is the first self-supervised learning method in the field of spatial acoustic representation learning and multi-channel audio signal processing. 1

Graph Neural Networks (GNNs) have achieved remarkable success by extending traditional convolution to learning on non-Euclidean data. The key to the GNNs is adopting the neural message-passing paradigm with two stages: aggregation and update. The current design of GNNs considers the topology information in the aggregation stage. However, in the updating stage, all nodes share the same updating function. The identical updating function treats each node embedding as i.i.d. random variables and thus ignores the implicit relationships between neighborhoods, which limits the capacity of the GNNs. The updating function is usually implemented with a linear transformation followed by a non-linear activation function. To make the updating function topology-aware, we inject the topological information into the non-linear activation function and propose Graph-adaptive Rectified Linear Unit (GReLU), which is a new parametric activation function incorporating the neighborhood information in a novel and efficient way. The parameters of GReLU are obtained from a hyperfunction based on both node features and the corresponding adjacent matrix. To reduce the risk of overfitting and the computational cost, we decompose the hyperfunction as two independent components for nodes and features respectively. We conduct comprehensive experiments to show that our plug-and-play GReLU method is efficient and effective given different GNN backbones and various downstream tasks.

Traditional approaches for learning representations from somatic mutation data often rely on the distribution of motif counts, which have limitations, including the use of small sequence contexts and the exclusion of critical information, such as mutation location and interactions among mutations. Recent efforts have leveraged advances in natural language processing (NLP) to improve representation learning from somatic mutations by incorporating larger sequence contexts into shallow networks. More recently, studies have demonstrated the feasibility of leveraging attention mechanisms to learn meaningful representations. However, these methods primarily use supervised or weakly supervised learning paradigms, which are inherently task-specific. The development of general-purpose representations, by harnessing the vast amount of somatic mutation data through self-supervised techniques, remains underexplored. Such representations could drive progress in applications including tumor subtype classification, biomarker discovery, patient stratification, drug response prediction, and pathway enrichment analysis. This study aims to develop a deep, unsupervised learning framework that leverages abundant somatic mutation data to generate robust, general-purpose representations. By adapting recent advances in self-supervised learning, the proposed approach seeks to establish a foundation model capable of capturing meaningful patterns in mutation data for diverse downstream tasks. The framework employs novel tokenization and embedding strategies to encode mutation sequences and utilizes transformer-based architectures to model contextual dependencies. The process of inputting mutation data into a transformer architecture, particularly the tokenization step, is critical for this problem, and we explore various tokenization strategies. Benchmarking these representations will include evaluating their utility across tumor subtype classification, biomarker discovery, patient stratification, drug response prediction, identification of mutational signatures. Although the model is under development, experiments from prior work—limited to mutation identifiers without leveraging sequence motifs, mutation location, or other contextual information—have demonstrated the feasibility of encoding mutational data into meaningful representations using transformer-based architectures and self-supervised learning. Building on these findings, this framework will benchmark its performance on multiple downstream tasks, including tumor subtype classification and patient stratification. Citation Format: Marzieh Haghighi, Gustavo Alonso Arango Argoty, Etai Jacob. Self-supervised representation learning of somatic mutational data [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 5059.

Accurately predicting essential genes using computational methods can greatly reduce the effort in finding them via wet experiments at both time and resource scales, and further accelerate the process of drug discovery. Several computational methods have been proposed for predicting essential genes in model organisms by integrating multiple biological data sources either via centrality measures or machine learning based methods. However, the methods aiming to predict human essential genes are still limited and the performance still need improve. In addition, most of the machine learning based essential gene prediction methods are lack of skills to handle the imbalanced learning issue inherent in the essential gene prediction problem, which might be one factor affecting their performance. We propose a deep learning based method, DeepHE, to predict human essential genes by integrating features derived from sequence data and protein-protein interaction (PPI) network. A deep learning based network embedding method is utilized to automatically learn features from PPI network. In addition, 89 sequence features were derived from DNA sequence and protein sequence for each gene. These two types of features are integrated to train a multilayer neural network. A cost-sensitive technique is used to address the imbalanced learning problem when training the deep neural network. The experimental results for predicting human essential genes show that our proposed method, DeepHE, can accurately predict human gene essentiality with an average performance of AUC higher than 94%, the area under precision-recall curve (AP) higher than 90%, and the accuracy higher than 90%. We also compare DeepHE with several widely used traditional machine learning models (SVM, Naïve Bayes, Random Forest, and Adaboost) using the same features and utilizing the same cost-sensitive technique to against the imbalanced learning issue. The experimental results show that DeepHE significantly outperforms the compared machine learning models. We have demonstrated that human essential genes can be accurately predicted by designing effective machine learning algorithm and integrating representative features captured from available biological data. The proposed deep learning framework is effective for such task.

DrasCLR: A self-supervised framework of learning disease-related and anatomy-specific representation for 3D lung CT images

Towards generalizable Graph Contrastive Learning: An information theory perspective

Deep models trained in supervised mode have achieved remarkable success on a variety of tasks. When labeled samples are limited, self-supervised learning (SSL) is emerging as a new paradigm for making use of large amounts of unlabeled samples. SSL has achieved promising performance on natural language and image learning tasks. Recently, there is a trend to extend such success to graph data using graph neural networks (GNNs). In this survey, we provide a unified review of different ways of training GNNs using SSL. Specifically, we categorize SSL methods into contrastive and predictive models. In either category, we provide a unified framework for methods as well as how these methods differ in each component under the framework. Our unified treatment of SSL methods for GNNs sheds light on the similarities and differences of various methods, setting the stage for developing new methods and algorithms. We also summarize different SSL settings and the corresponding datasets used in each setting. To facilitate methodological development and empirical comparison, we develop a standardized testbed for SSL in GNNs, including implementations of common baseline methods, datasets, and evaluation metrics.

Backgrounds:HER-2 positive breast cancer is a subtype of breast cancer with poor clinical outcome. The aim of this study was to identify differentially expressed genes (DEGs) for HER-2 positive breast cancer and elucidate the potential interactions among them.Material and methods:Three gene expression profiles (GSE29431, GSE45827, and GSE65194) were derived from the Gene Expression Omnibus (GEO) database. GEO2R tool was applied to obtain DEGs between HER-2 positive breast cancer and normal breast tissues. Gene ontology (GO) annotation analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis was performed by the Database for Annotation, Visualization and Integrated Discovery (David) online tool. Protein-protein interaction (PPI) network, hub gene identification and module analysis was conducted by Cytoscape software. Online Kaplan–Meier plotter survival analysis tool was also used to investigate the prognostic values of hub genes in HER-2 positive breast cancer patients.Results:A total of 54 upregulated DEGs and 269 downregulated DEGs were identified. Among them, 10 hub genes including CCNB1, RAC1, TOP2A, KIF20A, RRM2, ASPM, NUSAP1, BIRC5, BUB1B, and CEP55 demonstrated by connectivity degree in the PPI network were screened out. In Kaplan–Meier plotter survival analysis, the overexpression of RAC1 and RRM2 were shown to be associated with an unfavorable prognosis in HER-2 positive breast cancer patients.Conclusions:This present study identified a number of potential target genes and pathways which might impact the oncogenesis and progression of HER-2 positive breast cancer. These findings could provide new insights into the detection of novel diagnostic and therapeutic biomarkers for this disease.

The identification of tumor driver genes facilitates accurate cancer diagnosis and treatment, playing a key role in precision oncology, along with gene signaling, regulation, and their interaction with protein complexes. To tackle the challenge of distinguishing driver genes from a large number of genomic data, we construct a feature extraction framework for discovering pan-cancer driver genes based on multi-omics data (mutations, gene expression, copy number variants, and DNA methylation) combined with protein-protein interaction (PPI) networks. Using a network propagation algorithm, we mine functional information among nodes in the PPI network, focusing on genes with weak node information to represent specific cancer information. From these functional features, we extract distribution features of pan-cancer data, pan-cancer TOPSIS features of functional features using the ideal solution method, and SetExpan features of pan-cancer data from the gene functional features, a method to rank pan-cancer data based on the average inverse rank. These features represent the common message of pan-cancer. Finally, we use the lightGBM classification algorithm for gene prediction. Experimental results show that our method outperforms existing methods in terms of the area under the check precision-recall curve (AUPRC) and demonstrates better performance across different PPI networks. This indicates our framework's effectiveness in predicting potential cancer genes, offering valuable insights for the diagnosis and treatment of tumors.