Annotated Data Research Articles

A plasmid-mediated type III secretion system associated with invasiveness and diarrheagenicity of Providencia rustigianii.

We have recently described a clinical isolate of Providencia rustigianii strain JH-1 carrying the genes for cytolethal distending toxin (CDT) in a conjugative plasmid. A cdtB mutant of strain JH-1, which lost CDT activity, was still found to retain invasiveness and diarrheagenicity. The strain was subjected to phenotypic and genetic analyses including whole genome sequencing (WGS) to explore the genetic determinants of the observed invasiveness and diarrheagenic properties. Analysis and annotation of WGS data revealed the presence of two distinct type III secretion systems (T3SS) in strain JH-1, one of which was located on the chromosome designated as cT3SS (3,992,833 bp) and the other on a mega-plasmid designated as pT3SS (168,819 bp). Comparative genomic analysis revealed that cT3SS is generally conserved in Providencia spp. but pT3SS was limited to a subset of Providencia spp., carrying cdt genes. Strain JH-1 was found to invade HeLa cells and induce fluid accumulation with characteristic pathological lesions in rabbit ileal loops. Remarkably, these phenomena were associated with the pT3SS but not cT3SS. The plasmid could be transferred by conjugation from strain JH-1 to other strains of P. rustigianii, Providencia rettgeri, and Escherichia coli with concomitant transfer of these virulence properties. This is the first report of a functional and mobile T3SS in P. rustigianii and its association with invasiveness and diarrheagenicity of this bacterium. These data suggest that P. rustigianii and other CDT-producing Providencia strains might carry T3SS and exert their diarrheagenic effect by exploiting the T3SS nano-machinery.IMPORTANCEThe precise mechanism of virulence of Providencia rustigianii is unclear, although some strains produce cytolethal distending toxin as a putative virulence factor. We have detected the presence of a type III secretion system (T3SS) for the first time on a plasmid in a P. rustigianii strain. Plasmid-mediated T3SS seems to be directly involved in virulence of P. rustigianii and may serve as a means of horizontal transfer of T3SS genes. Our results may have implication in understanding the mechanism of emergence of new pathogenic strains of P. rustigianii.

Crowd Counting Using Meta-Test-Time Adaptation.

Machine learning algorithms are commonly used for quickly and efficiently counting people from a crowd. Test-time adaptation methods for crowd counting adjust model parameters and employ additional data augmentation to better adapt the model to the specific conditions encountered during testing. The majority of current studies concentrate on unsupervised domain adaptation. These approaches commonly perform hundreds of epochs of training iterations, requiring a sizable number of unannotated data of every new target domain apart from annotated data of the source domain. Unlike these methods, we propose a meta-test-time adaptive crowd counting approach called CrowdTTA, which integrates the concept of test-time adaptation into the meta-learning framework and makes it easier for the counting model to adapt to the unknown test distributions. To facilitate the reliable supervision signal at the pixel level, we introduce uncertainty by inserting the dropout layer into the counting model. The uncertainty is then used to generate valuable pseudo labels, serving as effective supervisory signals for adapting the model. In the context of meta-learning, one image can be regarded as one task for crowd counting. In each iteration, our approach is a dual-level optimization process. In the inner update, we employ a self-supervised consistency loss function to optimize the model so as to simulate the parameters update process that occurs during the test phase. In the outer update, we authentically update the parameters based on the image with ground truth, improving the model's performance and making the pseudo labels more accurate in the next iteration. At test time, the input image is used for adapting the model before testing the image. In comparison to various supervised learning and domain adaptation methods, our results via extensive experiments on diverse datasets showcase the general adaptive capability of our approach across datasets with varying crowd densities and scales.

Self-Supervised Dam Deformation Anomaly Detection Based on Temporal-Spatial Contrast Learning.

The detection of anomalies in dam deformation is paramount for evaluating structural integrity and facilitating early warnings, representing a critical aspect of dam health monitoring (DHM). Conventional data-driven methods for dam anomaly detection depend extensively on historical data; however, obtaining annotated data is both expensive and labor-intensive. Consequently, methodologies that leverage unlabeled or semi-labeled data are increasingly gaining popularity. This paper introduces a spatiotemporal contrastive learning pretraining (STCLP) strategy designed to extract discriminative features from unlabeled datasets of dam deformation. STCLP innovatively combines spatial contrastive learning based on temporal contrastive learning to capture representations embodying both spatial and temporal characteristics. Building upon this, a novel anomaly detection method for dam deformation utilizing STCLP is proposed. This method transfers pretrained parameters to targeted downstream classification tasks and leverages prior knowledge for enhanced fine-tuning. For validation, an arch dam serves as the case study. The results reveal that the proposed method demonstrates excellent performance, surpassing other benchmark models.

AnnotateXR: An Extended Reality Workflow for Automating Data Annotation to Support Computer Vision Applications

Abstract Computer vision (CV) algorithms require large annotated datasets that are often labor-intensive and expensive to create. We propose AnnotateXR, an extended reality (XR) workflow to collect various high-fidelity data and auto-annotate it in a single demonstration. AnnotateXR allows users to align virtual models over physical objects, tracked with six degrees-of-freedom (6DOF) sensors. AnnotateXR utilizes a hand tracking capable XR head-mounted display coupled with 6DOF information and collision detection to enable algorithmic segmentation of different actions in videos through its digital twin. The virtual–physical mapping provides a tight bounding volume to generate semantic segmentation masks for the captured image data. Alongside supporting object and action segmentation, we also support other dimensions of annotation required by modern CV, such as human–object, object–object, and rich 3D recordings, all with a single demonstration. Our user study shows AnnotateXR produced over 112,000 annotated data points in 67 min.

Learning to learn for few-shot continual active learning

Continual learning strives to ensure stability in solving previously seen tasks while demonstrating plasticity in a novel domain. Recent advances in continual learning are mostly confined to a supervised learning setting, especially in NLP domain. In this work, we consider a few-shot continual active learning setting where labeled data are inadequate, and unlabeled data are abundant but with a limited annotation budget. We exploit meta-learning and propose a method, called Meta-Continual Active Learning. This method sequentially queries the most informative examples from a pool of unlabeled data for annotation to enhance task-specific performance and tackles continual learning problems through a meta-objective. Specifically, we employ meta-learning and experience replay to address inter-task confusion and catastrophic forgetting. We further incorporate textual augmentations to avoid memory over-fitting caused by experience replay and sample queries, thereby ensuring generalization. We conduct extensive experiments on benchmark text classification datasets from diverse domains to validate the feasibility and effectiveness of meta-continual active learning. We also analyze the impact of different active learning strategies on various meta continual learning models. The experimental results demonstrate that introducing randomness into sample selection is the best default strategy for maintaining generalization in meta-continual learning framework.

Optimizing Automated Optical Inspection: An Adaptive Fusion and Semi-Supervised Self-Learning Approach for Elevated Accuracy and Efficiency in Scenarios with Scarce Labeled Data.

In the field of automatic optical inspection (AOI), this study presents innovative strategies to enhance object detection accuracy while minimizing dependence on large annotated datasets. We initially developed a defect detection model using a dataset of 3579 images across 32 categories, created in collaboration with a major Taiwanese panel manufacturer. This model was evaluated using 12,000 ambiguously labeled images, with improvements achieved through data augmentation and annotation refinement. To address the challenges of limited labeled data, we proposed the Adaptive Fused Semi-Supervised Self-Learning (AFSL) method. This approach, designed for anchor-based object detection models, leverages a small set of labeled data alongside a larger pool of unlabeled data to enable continuous model optimization. Key components of AFSL include the Bounding Box Assigner, Adaptive Training Scheduler, and Data Allocator, which together facilitate dynamic threshold adjustments and balanced training, significantly enhancing the model's performance on AOI datasets. The AFSL method improved the mean average precision (mAP) from 43.5% to 57.1% on the COCO dataset and by 2.6% on the AOI dataset, demonstrating its effectiveness in achieving high levels of precision and efficiency in AOI with minimal labeled data.

Improved region proposal network for enhanced few-shot object detection

Despite significant success of deep learning in object detection tasks, the standard training of deep neural networks requires access to a substantial quantity of annotated images across all classes. Data annotation is an arduous and time-consuming endeavor, particularly when dealing with infrequent objects. Few-shot object detection (FSOD) methods have emerged as a solution to the limitations of classic object detection approaches based on deep learning. FSOD methods demonstrate remarkable performance by achieving robust object detection using a significantly smaller amount of training data. A challenge for FSOD is that instances from novel classes that do not belong to the fixed set of training classes appear in the background and the base model may pick them up as potential objects. These objects behave similarly to label noise because they are classified as one of the training dataset classes, leading to FSOD performance degradation. We develop a semi-supervised algorithm to detect and then utilize these unlabeled novel objects as positive samples during the FSOD training stage to improve FSOD performance. Specifically, we develop a hierarchical ternary classification region proposal network (HTRPN) to localize the potential unlabeled novel objects and assign them new objectness labels to distinguish these objects from the base training dataset classes. Our improved hierarchical sampling strategy for the region proposal network (RPN) also boosts the perception ability of the object detection model for large objects. We test our approach and COCO and PASCAL VOC baselines that are commonly used in FSOD literature. Our experimental results indicate that our method is effective and outperforms the existing state-of-the-art (SOTA) FSOD methods. Our implementation is provided as a supplement to support reproducibility of the results https://github.com/zshanggu/HTRPN.11Early partial results of this work is presented in the 2023 ICCV Workshop on Visual Continual Learning (Shangguan and Rostami, 2023).

CACER: Clinical concept Annotations for Cancer Events and Relations.

Clinical notes contain unstructured representations of patient histories, including the relationships between medical problems and prescription drugs. To investigate the relationship between cancer drugs and their associated symptom burden, we extract structured, semantic representations of medical problem and drug information from the clinical narratives of oncology notes. We present Clinical concept Annotations for Cancer Events and Relations (CACER), a novel corpus with fine-grained annotations for over 48000 medical problems and drug events and 10000 drug-problem and problem-problem relations. Leveraging CACER, we develop and evaluate transformer-based information extraction models such as Bidirectional Encoder Representations from Transformers (BERT), Fine-tuned Language Net Text-To-Text Transfer Transformer (Flan-T5), Large Language Model Meta AI (Llama3), and Generative Pre-trained Transformers-4 (GPT-4) using fine-tuning and in-context learning (ICL). In event extraction, the fine-tuned BERT and Llama3 models achieved the highest performance at 88.2-88.0 F1, which is comparable to the inter-annotator agreement (IAA) of 88.4 F1. In relation extraction, the fine-tuned BERT, Flan-T5, and Llama3 achieved the highest performance at 61.8-65.3 F1. GPT-4 with ICL achieved the worst performance across both tasks. The fine-tuned models significantly outperformed GPT-4 in ICL, highlighting the importance of annotated training data and model optimization. Furthermore, the BERT models performed similarly to Llama3. For our task, large language models offer no performance advantage over the smaller BERT models. We introduce CACER, a novel corpus with fine-grained annotations for medical problems, drugs, and their relationships in clinical narratives of oncology notes. State-of-the-art transformer models achieved performance comparable to IAA for several extraction tasks.

An efficient zero-labeling segmentation approach for pest monitoring on smartphone-based images

Timely and precise farm inspection, which involves the identification and recognition of harmful insects and diseases, is crucial for safeguarding crop production. Traditional vision-based pest recognition methods typically require extensive annotated data for each pest species and a lengthy training process. This approach is time-consuming, labor-intensive, and prone to human error. Zero-shot learning offers a potential solution by enabling pest segmentation and control without requiring explicit training data. This study supports farmers in automatically identifying ten common pests and their precise locations in real-world outdoor environments. The zero-shot pest segmentation is based on a hybrid approach combining Explainable Contrastive Language-Image Pre-training (ECLIP) and Segment-Anything (SAM). Moreover, an optimized super-resolution model and various data augmentation methods are implemented to improve the quality of the dataset. Lastly, a mask post-processing step is applied to remove highly overlapping segmented masks and noise blobs caused by the complex background. The mean Intersection over Union (mIoU) of 66.5 % on the validation set demonstrates the potential of zero-shot methods for automated pest segmentation during farm inspections. This research lays the foundation for accurate pest monitoring systems capable of adapting to new pests, ultimately improving agricultural productivity.

Application of Generative Adversarial Networks in Semi-Annotated Defect Synthesis and Detection Under Limited Resources

Defect detection is a crucial technology that is extensively employed in the manufacturing industry to monitor and ensure the quality of output. Deep learning models have shown remarkable potential for defect detection. However, the success of these models heavily relies on voluminous training data. Collecting substantial amounts of defect data is challenging in practical settings, and the tedious process of pixel-level defect annotation further complicates the task. Among the common defects encountered in manufacturing, scratches are particularly significant. To address these challenges, this study proposes a two-phase generative adversarial network (GAN) approach for synthesizing defect images and generating semi-automatic pixel-wise labels for anomaly detection. The first phase primarily focuses on synthesizing images, while the second phase involves the pixel-wise labeling of the images. The synthesized paired images generated by the GANs serve as input to the semantic network. Notably, the proposed methodology requires only a few real defect samples for training and a small amount of annotated data, making it practical and computationally efficient for implementation in the manufacturing industry. Experimental results indicate the effectiveness of the proposed deep-learning solution in defect detection, specifically in identifying scratches on various textured and patterned surfaces. A notably high detection accuracy is achieved, validating the potential of the approach in real-world manufacturing scenarios.

A general framework for generative self-supervised learning in non-invasive estimation of physiological parameters using photoplethysmography

Aligning physiological parameter labels with large-scale photoplethysmographic (PPG) data for deep learning is challenging and resource-intensive. While self-supervised representation learning (SSRL) can handle limited annotated data, the challenge lies in learning robust shared representations from vast unlabeled data and integrating various contextual cues to learn distinctive representations. To alleviate these challenges, a generative SSRL framework TS2TC is proposed to collaboratively utilize the temporal, spectrogram, and temporal-spectrogram mixed domains to explore and incorporate the unique features of PPG for universal and non-invasive physiological parameter estimation. Initially, a pretext task named Cross-Temporal Fusion Generative Anchor (CTFGA) is designed, modeling temporal dependencies and reconstructing independent segments at a coarse level to provide robust global feature extraction and local semantic contextual representation. The framework also includes sub-signals from PPG with diverse frequency scales and order derivatives reflecting hemodynamics to facilitate learning shared representations at varying semantic levels. Secondly, an advanced cognitive-inspired dual-process transfer (DPT) strategy is formulated, consisting of prior-dependent autonomous processes and posterior observation reasoning processes, to leverage the independent and integrated advantages of shared and specific representations. Furthermore, TS2TC introduces a novel bilinear temporal-spectrogram fusion method in the mixed domain, aligning latent representations from different domains, and establishing fine-grained contextual interactions at the feature level across multiple sources of information. Extensive experiments on physiological parameter estimation tasks showed that the joint performance of CTFGA and DPT outperforms standard generative learning significantly. TS2TC achieved an average 2.49% improvement in RMSE over the current state-of-the-art estimation methods with only 10% training data.

Comprehensive scRNA-seq analysis to identify new markers of M2 macrophages for predicting the prognosis of prostate cancer

Background Prostate cancer (PCa) has become the highest incidence of malignant tumor among men in the world. Tumor microenvironment (TME) is necessary for tumor growth. M2 macrophages play an important role in many solid tumors. This research aimed at the role of M2 macrophages’ prognosis value in PCa. Methods Single-cell RNA-seq (scRNA-seq) data and mRNA expression data were obtained from the Gene Expression Omnibus database (GEO) and The Cancer Genome Atlas (TCGA). Quality control, normalization, reduction, clustering, and cell annotation of scRNA-seq data were preformed using the Seruat package. The sub-populations of the tumor-associated macrophages (TAMs) were analysis and the marker genes of M2 macrophage were selected. Differentially expressed genes (DEGs) in PCa were identified using limma and the immune infiltration was detected using CIBERSORTx. Then, a weighted correlation network analysis (WGCNA) was constructed to identify the M2 macrophage-related modules and genes. Integration of the marker genes of M2 macrophage from scRNA-seq data analysis and hub genes from WGCNA to select the prognostic gene signature based on Univariate and LASSO regression analysis. The risk score was calculated, and the DEGs, biological function, immune characteristics related to risk score were explored. And a predictive nomogram was constructed. CCK8, Transwell, and wound healing were used to verify cell phenotype changes after co-cultured. Results A total of 2431 marker genes of M2 macrophage and 650 hub M2 macrophage-related genes were selected based on scRNA-seq data and WGCNA. Then, 113 M2 macrophage-related genes were obtained by overlapping the scRNA-seq data and WGCNA results. Nine M2 macrophage-related genes (SMOC2, PLPP1, HES1, STMN1, GPR160, ABCG1, MAZ, MYC, and EPCAM) were screened as prognostic gene signatures. M2 risk score was calculated, the DEGs, Immune score, stromal score, ESTIMATE score, tumor purity, and immune cell infiltration, immune checkpoint expression, and responses of immunotherapy and chemotherapy were identified. And a predictive nomogram was constructed. CCK8, Transwell invasion, and wound healing further verified that M2 macrophages promoted the proliferation, invasion, and migration of PCa (p < 0.05). Conclusions We uncovered that M2 macrophages and relevant genes played key roles in promoting the occurrence, development, and metastases of PCa and played as convincing predictors in PCa.

High-quality expert annotations enhance artificial intelligence model accuracy for osteosarcoma X-ray diagnosis.

Primary malignant bone tumors, such as osteosarcoma, significantly affect the pediatric and young adult populations, necessitating early diagnosis for effective treatment. This study developed a high-performance artificial intelligence (AI) model to detect osteosarcoma from X-ray images using highly accurate annotated data to improve diagnostic accuracy at initial consultations. Traditional models trained on unannotated data have shown limited success, with sensitivities of approximately 60%-70%. In contrast, our model used a data-centric approach with annotations from an experienced oncologist, achieving a sensitivity of 95.52%, specificity of 96.21%, and an area under the curve of 0.989. The model was trained using 468 X-ray images from 31 osteosarcoma cases and 378 normal knee images with a strategy to maximize diversity in the training and validation sets. It was evaluated using an independent dataset of 268 osteosarcoma and 554 normal knee images to ensure generalizability. By applying the U-net architecture and advanced image processing techniques such as renormalization and affine transformations, our AI model outperforms existing models, reducing missed diagnoses and enhancing patient outcomes by facilitating earlier treatment. This study highlights the importance of high-quality training data and advocates a shift towards data-centric AI development in medical imaging. These insights can be extended to other rare cancers and diseases, underscoring the potential of AI in transforming diagnostic processes in oncology. The integration of this AI model into clinical workflows could support physicians in early osteosarcoma detection, thereby improving diagnostic accuracy and patient care.

Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers

Background: With increasing rates of polypharmacy, the vigilant surveillance of clinical drug toxicity has emerged as an important With increasing rates of polypharmacy, the vigilant surveillance of clinical drug toxicity has emerged as an important concern. Named Entity Recognition (NER) stands as an indispensable undertaking, essential for the extraction of valuable insights regarding drug safety from the biomedical literature. In recent years, significant advancements have been achieved in the deep learning models on NER tasks. Nonetheless, the effectiveness of these NER techniques relies on the availability of substantial volumes of annotated data, which is labor-intensive and inefficient. Methods: This study introduces a novel approach that diverges from the conventional reliance on manually annotated data. It employs a transformer-based technique known as Positive-Unlabeled Learning (PULearning), which incorporates adaptive learning and is applied to the clinical cancer drug toxicity corpus. To improve the precision of prediction, we employ relative position embeddings within the transformer encoder. Additionally, we formulate a composite loss function that integrates two Kullback-Leibler (KL) regularizers to align with PULearning assumptions. The outcomes demonstrate that our approach attains the targeted performance for NER tasks, solely relying on unlabeled data and named entity dictionaries. Conclusion: Our model achieves an overall NER performance with an F1 of 0.819. Specifically, it attains F1 of 0.841, 0.801 and 0.815 for DRUG, CANCER, and TOXI entities, respectively. A comprehensive analysis of the results validates the effectiveness of our approach in comparison to existing PULearning methods on biomedical NER tasks. Additionally, a visualization of the associations among three identified entities is provided, offering a valuable reference for querying their interrelationships.

Fast clustering and cell-type annotation of scATAC data using pre-trained embeddings.

Data from the single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) are now widely available. One major computational challenge is dealing with high dimensionality and inherent sparsity, which is typically addressed by producing lower dimensional representations of single cells for downstream clustering tasks. Current approaches produce such individual cell embeddings directly through a one-step learning process. Here, we propose an alternative approach by building embedding models pre-trained on reference data. We argue that this provides a more flexible analysis workflow that also has computational performance advantages through transfer learning. We implemented our approach in scEmbed, an unsupervised machine-learning framework that learns low-dimensional embeddings of genomic regulatory regions to represent and analyze scATAC-seq data. scEmbed performs well in terms of clustering ability and has the key advantage of learning patterns of region co-occurrence that can be transferred to other, unseen datasets. Moreover, models pre-trained on reference data can be exploited to build fast and accurate cell-type annotation systems without the need for other data modalities. scEmbed is implemented in Python and it is available to download from GitHub. We also make our pre-trained models available on huggingface for public use. scEmbed is open source and available at https://github.com/databio/geniml. Pre-trained models from this work can be obtained on huggingface: https://huggingface.co/databio.

Predicting cell cycle stage from 3D single-cell nuclear-stained images.

The cell cycle governs the proliferation, differentiation, and regeneration of all eukaryotic cells. Profiling cell cycle dynamics is therefore central to basic and biomedical research spanning development, health, aging, and disease. However, current approaches to cell cycle profiling involve complex interventions that may confound experimental interpretation. To facilitate more efficient cell cycle annotation of microscopy data, we developed CellCycleNet, a machine learning (ML) workflow designed to simplify cell cycle staging with minimal experimenter intervention and cost. CellCycleNet accurately predicts cell cycle phase using only a fluorescent nuclear stain (DAPI) in fixed interphase cells. Using the Fucci2a cell cycle reporter system as ground truth, we collected two benchmarking image datasets and trained two ML models-a support vector machine (SVM) and a deep neural network-to classify nuclei as being in either the G1 or S/G2 phases of the cell cycle. Our results suggest that CellCycleNet outperforms state-of-the-art SVM models on each dataset individually. When trained on two image datasets simultaneously, CellCycleNet achieves the highest classification accuracy, with an improvement in AUROC of 0.08-0.09. The model also demonstrates excellent generalization across different microscopes, achieving an AUROC of 0.95. Overall, using features derived from 3D images, rather than 2D projections of those same images, significantly improves classification performance. We have released our image data, trained models, and software as a community resource.

Development and application of the GenoBaits WheatSNP16K array to accelerate wheat genetic research and breeding

Single-nucleotide polymorphisms (SNPs) are widely used as molecular markers for constructing genetic linkage maps in wheat. Compared with available SNP-based genotyping platforms, a genotyping by target sequencing (GBTS) system with capture-in-solution (liquid chip) technology has become the favored genotyping technology because it is less demanding and more cost effective, flexible, and user-friendly. In this study, a new GenoBaits WheatSNP16K (GBW16K) GBTS array was designed using datasets generated by the wheat 660K SNP array and resequencing platforms in our previous studies. The GBW16K array contains 14 868 target SNP regions that are evenly distributed across the wheat genome, and 37 669 SNPs in these regions can be identified in a diversity panel consisting of 239 wheat accessions from around the world. Principal component and neighbor-joining analyses using the called SNPs are consistent with the pedigree information and geographic distributions or ecological environments of the accessions. For the GBW16K marker panel, the average genetic diversity among the 239 accessions is 0.270, which is sufficient for linkage map construction and preliminary mapping of targeted genes or quantitative trait loci (QTLs). A genetic linkage map, constructed using the GBW16K array-based genotyping of a recombinant inbred line population derived from a cross of the CIMMYT wheat line Yaco“S” and the Chinese landrace Mingxian169, enables the identification of Yr27, Yr30, and QYr.nwafu-2BL.4 for adult-plant resistance to stripe rust from Yaco“S” and of Yr18 from Mingxian169. QYr.nwafu-2BL.4 is different from any previously reported gene/QTL. Three haplotypes and six candidate genes have been identified for QYr.nwafu-2BL.4 on the basis of haplotype analysis, micro-collinearity, gene annotation, RNA sequencing, and SNP data. This array provides a new tool for wheat genetic analysis and breeding studies and for achieving durable control of wheat stripe rust.

A Generalisable Heartbeat Classifier Leveraging Self-Supervised Learning for ECG Analysis During Magnetic Resonance Imaging.

Electrocardiogram (ECG) is acquired during Magnetic Resonance Imaging (MRI) to monitor patients and synchronize image acquisition with the heart motion. ECG signals are highly distorted during MRI due to the complex electromagnetic environment. Automated ECG analysis is therefore complicated in this context and there is no reference technique in MRI to classify pathological heartbeats. Imaging arrhythmic patients is hence difficult in MRI. Deep Learning based heartbeat classifier have been suggested but require large databases whereas existing annotated sets of ECG in MRI are very small. We proposed a Siamese network to leverage a large database of unannotated ECGs outside MRI. This was used to develop an efficient representation of ECG signals, further used to develop a heartbeat classifier. We extensively tested several data augmentations and self-supervised learning (SSL) techniques and assessed the generalization of the obtained classifier to ECG signals acquired in MRI. These augmentations included random noises and a model simulating MRI specific artefacts. SSL pretraining improved the generalizability of heartbeat classifiers in MRI (F1=0.75) compared to Deep Learning not relying on SSL (F1=0.46) and another classical machine learning approach (F1=0.40). These promising results seem to indicate that the use of SSL techniques can learn efficient ECG signal representation, and are useful for the development of Deep Learning models even when only scarce annotated medical data are available.

Few-Shot Object Detection: A Comprehensive Survey.

Humans are able to learn to recognize new objects even from a few examples. In contrast, training deep-learning-based object detectors requires huge amounts of annotated data. To avoid the need to acquire and annotate these huge amounts of data, few-shot object detection (FSOD) aims to learn from few object instances of new categories in the target domain. In this survey, we provide an overview of the state of the art in FSOD. We categorize approaches according to their training scheme and architectural layout. For each type of approach, we describe the general realization as well as concepts to improve the performance on novel categories. Whenever appropriate, we give short takeaways regarding these concepts in order to highlight the best ideas. Eventually, we introduce commonly used datasets and their evaluation protocols and analyze the reported benchmark results. As a result, we emphasize common challenges in evaluation and identify the most promising current trends in this emerging field of FSOD.

Enhancing training performance of convolutional neural network algorithm through an autoencoder-based unsupervised labeling framework for mineral exploration targeting

Convolutional neural networks (CNNs), a prominent deep learning approach, have garnered significant interest in the field of mineral potential mapping (MPM) due to their capability to capture and learn spatial features that traditional algorithms tend to overlook. The effectiveness of CNNs is closely tied to the quantity of training data available, thereby impacting the outcomes of MPM. Moreover, uncertainties arising from delineation of negative samples can compromise the reliability of MPM assessments. To deal with these challenges, we propose the utilization of an autoencoder-based anomaly detection technique for the purpose of annotating locations in an unsupervised manner. Subsequently, a CNN is trained using the unsupervised annotated data to generate a Fe prospectivity model within a specific region in Iran. To validate the effectiveness of the proposed method, we first perform an MPM with insufficient positive training samples that extract from the location of known occurrences. We then execute another MPM on a set of samples labeled based on the reconstruction error of an autoencoder network. When comparing the two prospectivity models, namely using augmented data or inadequate samples, it is evident that modeling with augmented data outperforms the MPM model trained with insufficient samples. This confirms the effectiveness of the adopted approach and shows that the unsupervised labeling technique proposed in this work can significantly improve the performance of the CNN in MPM.