Biomedical Knowledge Graph: A Survey of Domains, Tasks, and Real-World Applications

Biomedical knowledge graphs (BKGs) have emerged as powerful tools for organizing and leveraging the vast and complex data found across the biomedical field. Yet, current reviews of BKGs often limit their scope to specific domains or methods, overlooking the broader landscape and the rapid technological progress reshaping it. In this survey, we address this gap by offering a systematic review of BKGs from three core perspectives: domains, tasks, and applications. We begin by examining how BKGs are constructed from diverse data sources, including molecular interactions, pharmacological datasets, and clinical records. Next, we discuss the essential tasks enabled by BKGs, focusing on knowledge management, retrieval, reasoning, and interpretation. Finally, we highlight real-world applications in precision medicine, drug discovery, and scientific research, illustrating the translational impact of BKGs across multiple sectors. By synthesizing these perspectives into a unified framework, this survey not only clarifies the current state of BKG research but also establishes a foundation for future exploration, enabling both innovative methodological advances and practical implementations.

Molecule-dynamic-based Aging Clock and Aging Roadmap Forecast with Sundial

Addressing the unavoidable bias inherent in supervised aging clocks, we introduce Sundial, a novel framework that models molecular dynamics through a diffusion field, capturing both the population-level aging process and the individual-level relative aging order. Sundial enables unbiasedestimation of biological age and the forecast of aging roadmap. Fasteraging individuals from Sundial exhibit a higher disease risk compared to those identified from supervised aging clocks. This framework opens new avenues for exploring key topics, including age- and sex-specific aging dynamics and faster yet healthy aging paths.

FOCUS: Knowledge-enhanced Adaptive Visual Compression for Few-shot Whole Slide Image Classification

Few-shot learning presents a critical solution for cancer diagnosis in computational pathology (CPath), addressing fundamental limitations in data availability, particularly the scarcity of expert annotations and patient privacy constraints. A key challenge in this paradigm stems from the inherent disparity between the limited training set of whole slide images (WSIs) and the enormous number of contained patches, where a significant portion of these patches lacks diagnostically relevant information, potentially diluting the model's ability to learn and focus on critical diagnostic features. While recent works attempt to address this by incorporating additional knowledge, several crucial gaps hinder further progress: (1) despite the emergence of powerful pathology foundation models (FMs), their potential remains largely untapped, with most approaches limiting their use to basic feature extraction; (2) current language guidance mechanisms attempt to align text prompts with vast numbers of WSI patches all at once, struggling to leverage rich pathological semantic information. To this end, we introduce the knowledge-enhanced adaptive visual compression framework, dubbed FOCUS, which uniquely combines pathology FMs with language prior knowledge to enable a focused analysis of diagnostically relevant regions by prioritizing discriminative WSI patches. Our approach implements a progressive three-stage compression strategy: we first leverage FMs for global visual redundancy elimination, and integrate compressed features with language prompts for semantic relevance assessment, then perform neighbor-aware visual token filtering while preserving spatial coherence. Extensive experiments on pathological datasets spanning breast, lung, and ovarian cancers demonstrate its superior performance in few-shot pathology diagnosis. Code will be made available at https://github.com/dddavid4real/FOCUS.

Automated Movement Detection with Dirichlet Process Mixture Models and Electromyography

Numerous sleep disorders are characterised by movement during sleep, these include rapid-eye movement sleep behaviour disorder (RBD) and periodic limb movement disorder. The process of diagnosing movement related sleep disorders requires laborious and time-consuming visual analysis of sleep recordings. This process involves sleep clinicians visually inspecting electromyogram (EMG) signals to identify abnormal movements. The distribution of characteristics that represent movement can be diverse and varied, ranging from brief moments of tensing to violent outbursts. This study proposes a framework for automated limb-movement detection by fusing data from two EMG sensors (from the left and right limb) through a Dirichlet process mixture model. Several features are extracted from 10 second mini-epochs, where each mini-epoch has been classified as 'leg-movement' or 'no leg-movement' based on annotations of movement from sleep clinicians. The distributions of the features from each category can be estimated accurately using Gaussian mixture models with the Dirichlet process as a prior. The available dataset includes 36 participants that have all been diagnosed with RBD. The performance of this framework was evaluated by a 10-fold cross validation scheme (participant independent). The study was compared to a random forest model and outperformed it with a mean accuracy, sensitivity, and specificity of 94\%, 48\%, and 95\%, respectively. These results demonstrate the ability of this framework to automate the detection of limb movement for the potential application of assisting clinical diagnosis and decision-making.

More Information Supervised Probabilistic Deep Face Embedding Learning

Researches using margin based comparison loss demonstrate the effectiveness of penalizing the distance between face feature and their corresponding class centers. Despite their popularity and excellent performance, they do not explicitly encourage the generic embedding learning for an open set recognition problem. In this paper, we analyse margin based softmax loss in probability view. With this perspective, we propose two general principles: 1) monotonic decreasing and 2) margin probability penalty, for designing new margin loss functions. Unlike methods optimized with single comparison metric, we provide a new perspective to treat open set face recognition as a problem of information transmission. And the generalization capability for face embedding is gained with more clean information. An auto-encoder architecture called Linear-Auto-TS-Encoder(LATSE) is proposed to corroborate this finding. Extensive experiments on several benchmarks demonstrate that LATSE help face embedding to gain more generalization capability and it boosted the single model performance with open training dataset to more than $99\%$ on MegaFace test.

Deep Frequent Spatial Temporal Learning for Face Anti-Spoofing

Face anti-spoofing is crucial for the security of face recognition system, by avoiding invaded with presentation attack. Previous works have shown the effectiveness of using depth and temporal supervision for this task. However, depth supervision is often considered only in a single frame, and temporal supervision is explored by utilizing certain signals which is not robust to the change of scenes. In this work, motivated by two stream ConvNets, we propose a novel two stream FreqSaptialTemporalNet for face anti-spoofing which simultaneously takes advantage of frequent, spatial and temporal information. Compared with existing methods which mine spoofing cues in multi-frame RGB image, we make multi-frame spectrum image as one input stream for the discriminative deep neural network, encouraging the primary difference between live and fake video to be automatically unearthed. Extensive experiments show promising improvement results using the proposed architecture. Meanwhile, we proposed a concise method to obtain a large amount of spoofing training data by utilizing a frequent augmentation pipeline, which contributes detail visualization between live and fake images as well as data insufficiency issue when training large networks.

Video Imagination from a Single Image with Transformation Generation

In this work, we focus on a challenging task: synthesizing multiple imaginary videos given a single image. Major problems come from high dimensionality of pixel space and the ambiguity of potential motions. To overcome those problems, we propose a new framework that produce imaginary videos by transformation generation. The generated transformations are applied to the original image in a novel volumetric merge network to reconstruct frames in imaginary video. Through sampling different latent variables, our method can output different imaginary video samples. The framework is trained in an adversarial way with unsupervised learning. For evaluation, we propose a new assessment metric $RIQA$. In experiments, we test on 3 datasets varying from synthetic data to natural scene. Our framework achieves promising performance in image quality assessment. The visual inspection indicates that it can successfully generate diverse five-frame videos in acceptable perceptual quality.

Beyond Monte Carlo Tree Search: Playing Go with Deep Alternative Neural Network and Long-Term Evaluation

Monte Carlo tree search (MCTS) is extremely popular in computer Go which determines each action by enormous simulations in a broad and deep search tree. However, human experts select most actions by pattern analysis and careful evaluation rather than brute search of millions of future nteractions. In this paper, we propose a computer Go system that follows experts way of thinking and playing. Our system consists of two parts. The first part is a novel deep alternative neural network (DANN) used to generate candidates of next move. Compared with existing deep convolutional neural network (DCNN), DANN inserts recurrent layer after each convolutional layer and stacks them in an alternative manner. We show such setting can preserve more contexts of local features and its evolutions which are beneficial for move prediction. The second part is a long-term evaluation (LTE) module used to provide a reliable evaluation of candidates rather than a single probability from move predictor. This is consistent with human experts nature of playing since they can foresee tens of steps to give an accurate estimation of candidates. In our system, for each candidate, LTE calculates a cumulative reward after several future interactions when local variations are settled. Combining criteria from the two parts, our system determines the optimal choice of next move. For more comprehensive experiments, we introduce a new professional Go dataset (PGD), consisting of 253233 professional records. Experiments on GoGoD and PGD datasets show the DANN can substantially improve performance of move prediction over pure DCNN. When combining LTE, our system outperforms most relevant approaches and open engines based on MCTS.

Long-Term Video Interpolation with Bidirectional Predictive Network

This paper considers the challenging task of long-term video interpolation. Unlike most existing methods that only generate few intermediate frames between existing adjacent ones, we attempt to speculate or imagine the procedure of an episode and further generate multiple frames between two non-consecutive frames in videos. In this paper, we present a novel deep architecture called bidirectional predictive network (BiPN) that predicts intermediate frames from two opposite directions. The bidirectional architecture allows the model to learn scene transformation with time as well as generate longer video sequences. Besides, our model can be extended to predict multiple possible procedures by sampling different noise vectors. A joint loss composed of clues in image and feature spaces and adversarial loss is designed to train our model. We demonstrate the advantages of BiPN on two benchmarks Moving 2D Shapes and UCF101 and report competitive results to recent approaches.