Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI networks, more faithfully depiction of complex protein interaction patterns for cancer genes within the graph structure remains largely unexplored. This study takes a pioneering step toward bridging biological anomalies in protein interactions caused by cancer genes to statistical graph anomaly. We find a unique graph anomaly exhibited by cancer genes, namely weight heterogeneity, which manifests as significantly higher variance in edge weights of cancer gene nodes within the graph. Additionally, from the spectral perspective, we demonstrate that the weight heterogeneity could lead to the "flattening out" of spectral energy, with a concentration towards the extremes of the spectrum. Building on these insights, we propose the HIerarchical-Perspective Graph Neural Network (HIPGNN) that not only determines spectral energy distribution variations on the spectral perspective, but also perceives detailed protein interaction context on the spatial perspective. Extensive experiments are conducted on two reprocessed datasets STRINGdb and CPDB, and the experimental results demonstrate the superiority of HIPGNN.

Characterizing the binding interactions between major histocompatibility complex (MHC) class II molecules and peptides is crucial for studying the immune system, offering potential applications for neoantigen design, vaccine development, and personalized immunotherapy. Motivated by this profound meaning, we developed a model that integrates large language models (LLMs) and deep hypergraph learning for predicting MHC class II-peptide binding reactivity, affinity, and residue contact profiling. pMHChat takes MHC pseudo-sequences and peptide sequences as inputs and processes them through four stages: LLMs fine-tune stage, feature encoding and map fusion stage, task-specific prediction stage, and downstream analysis stage. pMHChat distinguishes itself in capturing contextually relevant and high-order spatial interactions of the peptide-MHC (pMHC) complex. Specifically, in a five-fold cross-validation experiment, pMHChat achieves superior performance, with a mean area under the receiver operating characteristic curve of 0.8744 and an area under the precision-recall curve of 0.8390 in the binding reactivity task, as well as a mean Pearson correlation coefficient of 0.7311 in the binding affinity prediction task. Furthermore, pMHChat also demonstrates the best performance in both the leave-one-molecule-out setting and independent evaluation. Notably, pMHChat can provide residue contact profiling, showing its potential application in recognizing critical binding patterns of the pMHC complex. Our findings highlight pMHChat's capacity to advance both predictive accuracy and detailed insights into the MHC-peptide binding process. We anticipate that pMHChat will serve as a powerful tool for elucidating MHC-peptide interactions, with promising applications in immunological research and therapeutic development.

Antimicrobial peptides (AMPs) are short peptides that play critical roles in diverse biological processes and exhibit functional activities against target organisms. While numerous methods have demonstrated the effectiveness of deep neural networks for AMP identification using sequence features; nevertheless, higher-level peptide characteristics-such as 3D structure and geometric surface features-have not been comprehensively explored. To address this gap, we introduce the SSFGM-Model (Sequence, Structure, Surface, Graph, and Geometric-based Model), a novel framework that integrates multiple feature types to enhance AMP identification. The model represents each peptide sequence as a graph, where nodes are characterized by amino acid features derived from ProteinBERT, ESM-2, and One-hot embeddings. Graph convolutional networks and an attention mechanism are employed to capture high-order structural and sequential relationships. Additionally, surface geometry and physicochemical properties are processed using a geometric neural network. Finally, a feature fusion strategy combines the outputs from these subnetworks to enable robust AMP identification. Extensive benchmarking experiments demonstrate that the SSFGM-Model outperforms current state-of-the-art methods. An ablation study further confirms the critical role of sequence, structural, and surface features in AMP identification. The key contribution of this work is the innovative integration of multiple levels of peptide characteristics and the combination of geometric and graph neural networks. This approach provides a more comprehensive understanding of the sequence-structure-function relationship of peptides, paving the way for more accurate AMP prediction. The SSFGM-Model has a significant potential for applications in the discovery and design of novel AMP-based therapeutics. The source code is publicly available at https://github.com/ggcameronnogg/SSFGM-Model.

High-throughput sequencing methods have brought about a huge change in omics-based biomedical study. Integrating various omics data is possibly useful for identifying some correlations across data modalities, thus improving our understanding of the underlying biological mechanisms and complexity. Nevertheless, most existing graph-based feature extraction methods overlook the complementary information and correlations across modalities. Moreover, these methods tend to treat the features of each omics modality equally, which contradicts current biological principles. To solve these challenges, we introduce a novel approach for integrating multi-omics data termed Multi-Omics hypeRgraph integration nEtwork (MORE). MORE initially constructs a comprehensive hyperedge group by extensively investigating the informative correlations within and across modalities. Subsequently, the multi-omics hypergraph encoding module is employed to learn the enriched omics-specific information. Afterward, the multi-omics self-attention mechanism is then utilized to adaptatively aggregate valuable correlations across modalities for representation learning and making the final prediction. We assess MORE's performance on datasets characterized by message RNA (mRNA) expression, Deoxyribonucleic Acid (DNA) methylation, and microRNA (miRNA) expression for Alzheimer's disease, invasive breast carcinoma, and glioblastoma. The results from three classification tasks highlight the competitive advantage of MORE in contrast with current state-of-the-art (SOTA) methods. Moreover, the results also show that MORE has the capability to identify a greater variety of disease-related biomarkers compared to existing methods, highlighting its advantages in biomedical data mining and interpretation. Overall, MORE can be investigated as a valuable tool for facilitating multi-omics analysis and novel biomarker discovery. Our code and data can be publicly accessed at https://github.com/Wangyuhanxx/MORE.

Histo-genomic multi-modal methods have emerged as a powerful paradigm, demonstrating significant potential for cancer prognosis. However, genome sequencing, unlike histopathology imaging, is still not widely accessible in underdeveloped regions, limiting the application of these multi-modal approaches in clinical settings. To address this, we propose a novel Genome-informed Hyper-Attention Network, termed G-HANet, which is capable of effectively learning the histo-genomic associations during training to elevate uni-modal whole slide image (WSI)-based inference for the first time. Compared with the potential knowledge distillation strategy for this setting (i.e., distilling a multi-modal network to a uni-modal network), our end-to-end model is superior in training efficiency and learning cross-modal interactions. Specifically, the network comprises cross-modal associating branch (CAB) and hyper-attention survival branch (HSB). Through the genomic data reconstruction from WSIs, CAB effectively distills the associations between functional genotypes and morphological phenotypes and offers insights into the gene expression profiles in the feature space. Subsequently, HSB leverages the distilled histo-genomic associations as well as the generated morphology-based weights to achieve the hyper-attention modeling of the patients from both histopathology and genomic perspectives to improve cancer prognosis. Extensive experiments are conducted on five TCGA benchmarking datasets and the results demonstrate that G-HANet significantly outperforms the state-of-the-art WSI-based methods and achieves competitive performance with genome-based and multi-modal methods. G-HANet is expected to be explored as a useful tool by the research community to address the current bottleneck of insufficient histo-genomic data pairing in the context of cancer prognosis and precision oncology. The code is available at https://github.com/ZacharyWang-007/G-HANet.

Accurate prediction of transcription factor binding sites (TFBSs) is essential for understanding gene regulation mechanisms and the etiology of diseases. Despite numerous advances in deep learning for predicting TFBSs, their performance can still be enhanced. In this study, we propose MLSNet, a novel deep learning architecture designed specifically to predict TFBSs. MLSNet innovatively integrates multisize convolutional fusion with long short-term memory (LSTM) networks to effectively capture DNA-sparse higher-order sequence features. Further, MLSNet incorporates super token attention and Bi-LSTM to systematically extract and integrate higher-order DNA shape features. Experimental results on 165 ChIP-seq (chromatin immunoprecipitation followed by sequencing) datasets indicate that MLSNet consistently outperforms several state-of-the-art algorithms in the prediction of TFBSs. Specifically, MLSNet reports average metrics: 0.8306 for ACC, 0.8992 for AUROC, and 0.9035 for AUPRC, surpassing the second-best methods by 1.82%, 1.68%, and 1.54%, respectively. This research delineates the effectiveness of combining multi-size convolutional layers with LSTM and DNA shape-based features in enhancing predictive accuracy. Moreover, this study comprehensively assesses the variability in model performance across different cell lines and transcription factors. The source code of MLSNet is available at https://github.com/minghaidea/MLSNet.

Histopathology image-based survival prediction aims to provide a precise assessment of cancer prognosis and can inform personalized treatment decision-making in order to improve patient outcomes. However, existing methods cannot automatically model the complex correlations between numerous morphologically diverse patches in each whole slide image (WSI), thereby preventing them from achieving a more profound understanding and inference of the patient status. To address this, here we propose a novel deep learning framework, termed dual-stream multi-dependency graph neural network (DM-GNN), to enable precise cancer patient survival analysis. Specifically, DM-GNN is structured with the feature updating and global analysis branches to better model each WSI as two graphs based on morphological affinity and global co-activating dependencies. As these two dependencies depict each WSI from distinct but complementary perspectives, the two designed branches of DM-GNN can jointly achieve the multi-view modeling of complex correlations between the patches. Moreover, DM-GNN is also capable of boosting the utilization of dependency information during graph construction by introducing the affinity-guided attention recalibration module as the readout function. This novel module offers increased robustness against feature perturbation, thereby ensuring more reliable and stable predictions. Extensive benchmarking experiments on five TCGA datasets demonstrate that DM-GNN outperforms other state-of-the-art methods and offers interpretable prediction insights based on the morphological depiction of high-attention patches. Overall, DM-GNN represents a powerful and auxiliary tool for personalized cancer prognosis from histopathology images and has great potential to assist clinicians in making personalized treatment decisions and improving patient outcomes.

Inclusion dependencies (INDs) are widely used in data management tasks. The discovery techniques of INDs have thus received a lot of attention, for discovering INDs valid in data. However, real-world data quality issues may lead to partial violations of INDs. This paper makes the first effort to provide a comprehensive study on the discovery of approximate INDs (AINDs), aiming to identify INDs with error rates below a given threshold. This paper introduces a new definition of AIND based on deletion semantics, in addition to the existing definition based on insertion semantics. A discovery method is developed that can be configured to identify AINDs based on either of these semantics. The method combines partitioning techniques to handle tables that cannot all fit into memory simultaneously, with novel approaches to quantify AIND violations based on partitioned tables. To improve efficiency, the method employs a novel three-layer filtering structure and techniques that can potentially prune invalid candidate AINDs and identify valid AINDs without necessarily processing all tuples. We conduct an extensive experimental evaluation and verify the following: the proposed method significantly outperforms existing methods for AIND discovery based on insertion semantics, the AIND discoveries with insertion and deletion semantics can provide complementary results, and our discovery method can effectively deal with dirty dataset containing various types of errors.

N4-acetylcytidine (ac4C) is a post-transcriptional modification in mRNA that is critical in mRNA translation in terms of stability and regulation. In the past few years, numerous approaches employing convolutional neural networks (CNN) and Transformer have been proposed for the identification of ac4C sites, with each variety of approaches processing distinct characteristics. CNN-based methods excel at extracting local features and positional information, whereas Transformer-based ones stands out in establishing long-range dependencies and generating global representations. Given the importance of both local and global features in mRNA ac4C sites identification, we propose a novel method termed TransC-ac4C which combines CNN and Transformer together for enhancing the feature extraction capability and improving the identification accuracy. Five different feature encoding strategies (One-hot, NCP, ND, EIIP, and K-mer) are employed to generate the mRNA sequence representations, in which way the sequence attributes and physical and chemical properties of the sequences can be embedded. To strengthen the relevance of features, we construct a novel feature fusion method. Firstly, the CNN is employed to process five single features, stitch them together and feed them to the Transformer layer. Then, our approach employs CNN to extract local features and Transformer subsequently to establish global long-range dependencies among extracted features. We use 5-fold cross-validation to evaluate the model, and the evaluation indicators are significantly improved. The prediction accuracy of the two datasets is as high as 81.42% and 80.69%, respectively. It demonstrates the stronger competitiveness and generalization performance of our model.

RNA N6-methyladenosine is a prevalent and abundant type of RNA modification that exerts significant influence on diverse biological processes. To date, numerous computational approaches have been developed for predicting methylation, with most of them ignoring the correlations of different encoding strategies and failing to explore the adaptability of various attention mechanisms for methylation identification. To solve the above issues, we proposed an innovative framework for predicting RNA m6A modification site, termed BLAM6A-Merge. Specifically, it utilized a multimodal feature fusion strategy to combine the classification results of four features and Blastn tool. Apart from this, different attention mechanisms were employed for extracting higher-level features on specific features after the screening process. Extensive experiments on 12 benchmarking datasets demonstrated that BLAM6A-Merge achieved superior performance (average AUC: 0.849 for the full transcript mode and 0.784 for the mature mRNA mode). Notably, the Blastn tool was employed for the first time in the identification of methylation sites.

Cancer is one of the most challenging health problems worldwide. Accurate cancer survival prediction is vital for clinical decision making. Many deep learning methods have been proposed to understand the association between patients’ genomic features and survival time. In most cases, the gene expression matrix is fed directly to the deep learning model. However, this approach completely ignores the interactions between biomolecules, and the resulting models can only learn the expression levels of genes to predict patient survival. In essence, the interaction between biomolecules is the key to determining the direction and function of biological processes. Proteins are the building blocks and principal undertakings of life activities, and as such, their complex interaction network is potentially informative for deep learning methods. Therefore, a more reliable approach is to have the neural network learn both gene expression data and protein interaction networks. We propose a new computational approach, termed CRESCENT, which is a protein-protein interaction (PPI) prior knowledge graph-based convolutional neural network (GCN) to improve cancer survival prediction. CRESCENT relies on the gene expression networks rather than gene expression levels to predict patient survival. The performance of CRESCENT is evaluated on a large-scale pan-cancer dataset consisting of 5991 patients from 16 different types of cancers. Extensive benchmarking experiments demonstrate that our proposed method is competitive in terms of the evaluation metric of the time-dependent concordance index(${C}^{td}$) when compared with several existing state-of-the-art approaches. Experiments also show that incorporating the network structure between genomic features effectively improves cancer survival prediction.

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.

MOTIVATION: Identifying drug-protein interactions (DPIs) is a critical step in drug repositioning, which allows reuse of approved drugs that may be effective for treating a different disease and thereby alleviates the challenges of new drug development. Despite the fact that a great variety of computational approaches for DPI prediction have been proposed, key challenges, such as extendable and unbiased similarity calculation, heterogeneous information utilization, and reliable negative sample selection, remain to be addressed. RESULTS: To address these issues, we propose a novel, unified multi-view graph autoencoder framework, termed MULGA, for both DPI and drug repositioning predictions. MULGA is featured by: (i) a multi-view learning technique to effectively learn authentic drug affinity and target affinity matrices; (ii) a graph autoencoder to infer missing DPI interactions; and (iii) a new "guilty-by-association"-based negative sampling approach for selecting highly reliable non-DPIs. Benchmark experiments demonstrate that MULGA outperforms state-of-the-art methods in DPI prediction and the ablation studies verify the effectiveness of each proposed component. Importantly, we highlight the top drugs shortlisted by MULGA that target the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SAR-CoV-2), offering additional insights into and potentially useful treatment option for COVID-19. Together with the availability of datasets and source codes, we envision that MULGA can be explored as a useful tool for DPI prediction and drug repositioning. AVAILABILITY AND IMPLEMENTATION: MULGA is publicly available for academic purposes at https://github.com/jianiM/MULGA/.

MOTIVATION: The rapid accumulation of high-throughput sequence data demands the development of effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotation simply focus on the use of protein-level information but ignore inter-relationships among annotations. RESULTS: Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs and advances in natural language processing algorithms for the functional annotation of proteins. PFresGO employs a self-attention operation to capture the inter-relationships of GO terms, updates its embedding accordingly and uses a cross-attention operation to project protein representations and GO embedding into a common latent space to identify global protein sequence patterns and local functional residues. We demonstrate that PFresGO consistently achieves superior performance across GO categories when compared with 'state-of-the-art' methods. Importantly, we show that PFresGO can identify functionally important residues in protein sequences by assessing the distribution of attention weightings. PFresGO should serve as an effective tool for the accurate functional annotation of proteins and functional domains within proteins. AVAILABILITY AND IMPLEMENTATION: PFresGO is available for academic purposes at https://github.com/BioColLab/PFresGO. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Multiple instance learning (MIL) is a powerful technique to classify whole slide images (WSIs) for diagnostic pathology. The key challenge of MIL on WSI classification is to discover the critical instances that trigger the bag label. However, tumor heterogeneity significantly hinders the algorithm's performance. RESULTS: Here, we propose a novel multiplex-detection-based multiple instance learning (MDMIL) which targets tumor heterogeneity by multiplex detection strategy and feature constraints among samples. Specifically, the internal query generated after the probability distribution analysis and the variational query optimized throughout the training process are utilized to detect potential instances in the form of internal and external assistance, respectively. The multiplex detection strategy significantly improves the instance-mining capacity of the deep neural network. Meanwhile, a memory-based contrastive loss is proposed to reach consistency on various phenotypes in the feature space. The novel network and loss function jointly achieve high robustness towards tumor heterogeneity. We conduct experiments on three computational pathology datasets, e.g. CAMELYON16, TCGA-NSCLC, and TCGA-RCC. Benchmarking experiments on the three datasets illustrate that our proposed MDMIL approach achieves superior performance over several existing state-of-the-art methods. AVAILABILITY AND IMPLEMENTATION: MDMIL is available for academic purposes at https://github.com/ZacharyWang-007/MDMIL.

MOTIVATION: RNA N6-methyladenosine (m6A) in Homo sapiens plays vital roles in a variety of biological functions. Precise identification of m6A modifications is thus essential to elucidation of their biological functions and underlying molecular-level mechanisms. Currently available high-throughput single-nucleotide-resolution m6A modification data considerably accelerated the identification of RNA modification sites through the development of data-driven computational methods. Nevertheless, existing methods have limitations in terms of the coverage of single-nucleotide-resolution cell lines and have poor capability in model interpretations, thereby having limited applicability. RESULTS: In this study, we present CLSM6A, comprising a set of deep learning-based models designed for predicting single-nucleotide-resolution m6A RNA modification sites across eight different cell lines and three tissues. Extensive benchmarking experiments are conducted on well-curated datasets and accordingly, CLSM6A achieves superior performance than current state-of-the-art methods. Furthermore, CLSM6A is capable of interpreting the prediction decision-making process by excavating critical motifs activated by filters and pinpointing highly concerned positions in both forward and backward propagations. CLSM6A exhibits better portability on similar cross-cell line/tissue datasets, reveals a strong association between highly activated motifs and high-impact motifs, and demonstrates complementary attributes of different interpretation strategies. AVAILABILITY AND IMPLEMENTATION: The webserver is available at http://csbio.njust.edu.cn/bioinf/clsm6a. The datasets and code are available at https://github.com/zhangying-njust/CLSM6A/.

In recent years, deep learning-based dehazing models have presented a momentum of dramatic growth. Unfortunately, most deep learning-based approaches heavily rely on synthetically hazed images for model training, which makes these methods brittle to restore hazy images taken from real-world scenes, due to the sample distribution discrepancy between synthetic and realistic images. Although some attempts have been made to overcome this difficulty by augmenting image spatial features with spectral features, the power of the spectral features still remains underutilized. In this paper, we propose the Spectral Dual-Channel Encoding (SDCE) framework for high-quality image dehazing, by unleashing the power of spectral feature encoding. We argue that hazes impose more adverse impacts on high-frequency image features (e.g., outlines and textures) than low-frequency features (e.g., colors), with theoretical and empirical justifications. To better restore hazed high- and low-frequency features, we decompose the hazed images into high- and low-frequency feature components with spectral dual-channel encoding and respectively design effective neural network architectures to recover hazed images on the two feature components. To be specific, we recover the low-frequency feature components with an encoder-decoder, while we specially design a high-frequency aggregation component (HFAC) to recover hazed images on high-frequency feature components, by referring to neighboring feature distributions. We conduct extensive experiments on four real-world image dehazing benchmarks. The experimental results show that our proposed SDCE framework outperforms the state-of-the-art baselines significantly, with an average 4.4% improvement in PSNR and an average 7.7% gain in SSIM.

Occluded person re-identification (ReID) aims at matching occluded person images to holistic ones across different camera views. Target Pedestrians (TP) are often disturbed by Non-Pedestrian Occlusions (NPO) and Non-Target Pedestrians (NTP). Previous methods mainly focus on increasing the model's robustness against NPO while ignoring feature contamination from NTP. In this paper, we propose a novel Feature Erasing and Diffusion Network (FED) to simultaneously handle challenges from NPO and NTP. Specifically, aided by the NPO augmentation strategy that simulates NPO on holistic pedestrian images and gen-erates precise occlusion masks, NPO features are explicitly eliminated by our proposed Occlusion Erasing Module (OEM). Subsequently, we diffuse the pedestrian representations with other memorized features to synthesize the NTP characteristics in the feature space through the novel Feature Diffusion Module (FDM). With the guidance of the occlusion scores from OEM, the feature diffusion process is conducted on visible body parts, thereby improving the quality of the synthesized NTP characteristics. We can greatly improve the model's perception ability towards TP and alleviate the influence of NPO and NTP by jointly optimizing OEM and FDM. Furthermore, the proposed FDM works as an auxiliary module for training and will not be engaged in the inference phase, thus with high flexibility. Experiments on occluded and holistic person ReID benchmarks demonstrate the superiority of FED over state-of-the-art methods.

Subcellular localization of messenger RNAs (mRNAs) plays a key role in the spatial regulation of gene activity. The functions of mRNAs have been shown to be closely linked with their localizations. As such, understanding of the subcellular localizations of mRNAs can help elucidate gene regulatory networks. Despite several computational methods that have been developed to predict mRNA localizations within cells, there is still much room for improvement in predictive performance, especially for the multiple-location prediction. In this study, we proposed a novel multi-label multi-class predictor, termed Clarion, for mRNA subcellular localization prediction. Clarion was developed based on a manually curated benchmark dataset and leveraged the weighted series method for multi-label transformation. Extensive benchmarking tests demonstrated Clarion achieved competitive predictive performance and the weighted series method plays a crucial role in securing superior performance of Clarion. In addition, the independent test results indicate that Clarion outperformed the state-of-the-art methods and can secure accuracy of 81.47, 91.29, 79.77, 92.10, 89.15, 83.74, 80.74, 79.23 and 84.74% for chromatin, cytoplasm, cytosol, exosome, membrane, nucleolus, nucleoplasm, nucleus and ribosome, respectively. The webserver and local stand-alone tool of Clarion is freely available at http://monash.bioweb.cloud.edu.au/Clarion/.

We present a versatile model, FaceAnime, for various video generation tasks from still images. Video generation from a single face image is an interesting problem and usually tackled by utilizing Generative Adversarial Networks (GANs) to integrate information from the input face image and a sequence of sparse facial landmarks. However, the generated face images usually suffer from quality loss, image distortion, identity change, and expression mismatching due to the weak representation capacity of the facial landmarks. In this paper, we propose to “imagine” a face video from a single face image according to the reconstructed 3D face dynamics, aiming to generate a realistic and identity-preserving face video, with precisely predicted pose and facial expression. The 3D dynamics reveal changes of the facial expression and motion, and can serve as a strong prior knowledge for guiding highly realistic face video generation. In particular, we explore face video prediction and exploit a well-designed 3D dynamic prediction network to predict a 3D dynamic sequence for a single face image. The 3D dynamics are then further rendered by the sparse texture mapping algorithm to recover structural details and sparse textures for generating face frames. Our model is versatile for various AR/VR and entertainment applications, such as face video retargeting and face video prediction. Superior experimental results have well demonstrated its effectiveness in generating high-fidelity, identity-preserving, and visually pleasant face video clips from a single source face image.

Video-based person re-identification (Re-ID) aims at retrieving the person through the video sequences across non-overlapping cameras. Some characteristics of pedestrians are not consecutive across frames due to the variations of viewpoints, postures, and occlusions over time. However, existing methods ignore such data peculiarity and the networks tend to only learn those salient consecutive characteristics among frames in video sequences. As a result, the learned representations fail to cover all the characteristics of pedestrians, thus lacking integrity and discrimination. To tackle this problem, we present a novel deep architecture termed Hierarchical Mining Network (HMN), which mines as many pedestrians’ characteristics by referring to the temporal and intra-class knowledge. It consists of a novel Attentive Temporal Module (ATM) and a Dynamic Supervising Branch (DSB), with a Balancing Triplet Loss (BTL) assisting the training. The proposed ATM, with pedestrian perceiving capacity, is capable of evaluating each activation of features through temporal analysis, so that the temporally scattered characteristics of pedestrians can be better aggregated and the contaminated ones can be eliminated. Then, the DSB along with the BTL further enhances the integrity of representations by multiple supervision. Specifically, the DSB perceives the diversities of intra-class samples in each mini-batch and generates targeted supervising signals for them, in which process the BTL guarantees the signals with smaller intra-class variations and larger inter-class variations. Comprehensive experiments on two video-based datasets, i.e., MARS, and DukeMTMC-VideoReID, demonstrate the contribution of each component and the superiority of the proposed HMN over the state-of-the-arts. Benchmarking our model on three popular image-based datasets, i.e., Market1501, DukeMTMC-Reid, and MSMT17 additionally verifies the promising generalizability of the proposed DSB and BTL.

As more and more patients choose online consultation, the information in the Question and Answering(Q&A) community is widely studied. Through automatic extraction of medical inquiry information entities, and establishing a neural network model, the input of basic patient information and disease information can be extracted. In order to provide an effective method for exploring medical named entity recognition in the medical community. Entity annotation is performed for the medical community Q&A pairs, and a BiLSTM-CRF network model is established for training to realize the identification of medical entities which are crawled from Q&A community. This paper introduces the principles and process of BiLSTM-CRF model, illustrates our experiment, including the data sources, experiment environment, evaluation index. This paper chooses four models of HMM, CRF, BiLSTM and BiLSTM-CRF for experiments. Finally, the experimental results are compared which verifies the effectiveness of the BiLSTM-CRF model. Realizing the recognition and extraction of diabetes-related entities in the medical field.

Video-based person re-identification (ReID) is an important task, which has received much attention in recent years due to its efficiency in the field of surveillance. Researchers have employed many effective approaches for video-based person ReID, but there are still two problems. Firstly, the same pedestrian in the video sequences differs in size. Secondly, traditional RNNs can only process one-dimension features, which are not suitable for dealing with video sequences. To solve above problems, we propose a new network called Multi-scale Spatial-Temporal Network (MSTN), which combines multi-scale feature extractor and CLSTM together to tackle the discrepant sizes of pedestrians and extract more representative temporal information for the video sequences. We conduct the experiments on the iLIDS-VID, PRID-2011 and MARS datasets, and our approach outperforms state-of-the-art methods by a large margin.

We deal with the selective classification problem (supervised-learning problem with a rejection option), where we want to achieve the best performance at a certain level of coverage of the data. We transform the original $m$-class classification problem to (m+1)-class where the (m+1)-th class represents the model abstaining from making a prediction due to disconfidence. Inspired by portfolio theory, we propose a loss function for the selective classification problem based on the doubling rate of gambling. Minimizing this loss function corresponds naturally to maximizing the return of a horse race, where a player aims to balance between betting on an outcome (making a prediction) when confident and reserving one's winnings (abstaining) when not confident. This loss function allows us to train neural networks and characterize the disconfidence of prediction in an end-to-end fashion. In comparison with previous methods, our method requires almost no modification to the model inference algorithm or model architecture. Experiments show that our method can identify uncertainty in data points, and achieves strong results on SVHN and CIFAR10 at various coverages of the data.

We consider the problem of grasping concave objects, i.e., objects whose surface includes regions with negative curvature. When a multifingered hand is used to restrain these objects, these areas can be advantageously used to determine grasps capable of more robustly resisting to external disturbance wrenches. We propose a new grasp quality metric specifically suited for this case, and we use it to inform a grasp planner searching the space of possible grasps. Our findings are validated both in simulation and on a real robot system executing a bin picking task. Experimental validation shows that our method is more effective than those not explicitly considering negative curvature.