A survey on semi-supervised learning

Demystifying unsupervised learning: how it helps and hurts

Humans and machines rarely have access to explicit external feedback or supervision, yet manage to learn. Most modern machine learning systems succeed because they benefit from unsupervised data. Humans are also expected to benefit and yet, mysteriously, empirical results are mixed. Does unsupervised learning help humans or not? Here, we argue that the mixed results are not conflicting answers to this question, but reflect that humans self-reinforce their predictions in the absence of supervision, which can help or hurt depending on whether predictions and task align. We use this framework to synthesize empirical results across various domains to clarify when unsupervised learning will help or hurt. This provides new insights into the fundamentals of learning with implications for instruction and lifelong learning.

Advances in artificial intelligence for meibomian gland evaluation: A comprehensive review

Meibomian gland dysfunction (MGD) is increasingly recognized as a critical contributor to evaporative dry eye, significantly impacting visual quality. With a global prevalence estimated at 35.8 %, it presents substantial challenges for clinicians. Conventional manual evaluation techniques for MGD face limitations characterized by inefficiencies, high subjectivity, limited big data processing capabilities, and a dearth of quantitative analytical tools. With rapidly advancing artificial intelligence (AI) techniques revolutionizing ophthalmology, studies are now leveraging sophisticated AI methodologies--including computer vision, unsupervised learning, and supervised learning--to facilitate comprehensive analyses of meibomian gland (MG) evaluations. These evaluations employ various techniques, including slit lamp examination, infrared imaging, confocal microscopy, and optical coherence tomography. This paradigm shift promises enhanced accuracy and consistency in disease evaluation and severity classification. While AI has achieved preliminary strides in meibomian gland evaluation, ongoing advancements in system development and clinical validation are imperative. We review the evolution of MG evaluation, juxtapose AI-driven methods with traditional approaches, elucidate the specific roles of diverse AI technologies, and explore their practical applications using various evaluation techniques. Moreover, we delve into critical considerations for the clinical deployment of AI technologies and envisages future prospects, providing novel insights into MG evaluation and fostering technological and clinical progress in this arena.

From zero to hero: Harnessing transformers for biomedical named entity recognition in zero- and few-shot contexts

Supervised named entity recognition (NER) in the biomedical domain depends on large sets of annotated texts with the given named entities. The creation of such datasets can be time-consuming and expensive, while extraction of new entities requires additional annotation tasks and retraining the model. This paper proposes a method for zero- and few-shot NER in the biomedical domain to address these challenges. The method is based on transforming the task of multi-class token classification into binary token classification and pre-training on a large number of datasets and biomedical entities, which allows the model to learn semantic relations between the given and potentially novel named entity labels. We have achieved average F1 scores of 35.44% for zero-shot NER, 50.10% for one-shot NER, 69.94% for 10-shot NER, and 79.51% for 100-shot NER on 9 diverse evaluated biomedical entities with fine-tuned PubMedBERT-based model. The results demonstrate the effectiveness of the proposed method for recognizing new biomedical entities with no or limited number of examples, outperforming previous transformer-based methods, and being comparable to GPT3-based models using models with over 1000 times fewer parameters. We make models and developed code publicly available.

Taming Overconfident Prediction on Unlabeled Data From Hindsight

Minimizing prediction uncertainty on unlabeled data is a key factor to achieve good performance in semi-supervised learning (SSL). The prediction uncertainty is typically expressed as the entropy computed by the transformed probabilities in output space. Most existing works distill low-entropy prediction by either accepting the determining class (with the largest probability) as the true label or suppressing subtle predictions (with the smaller probabilities). Unarguably, these distillation strategies are usually heuristic and less informative for model training. From this discernment, this article proposes a dual mechanism, named adaptive sharpening (ADS), which first applies a soft-threshold to adaptively mask out determinate and negligible predictions, and then seamlessly sharpens the informed predictions, distilling certain predictions with the informed ones only. More importantly, we theoretically analyze the traits of ADS by comparing it with various distillation strategies. Numerous experiments verify that ADS significantly improves state-of-the-art SSL methods by making it a plug-in. Our proposed ADS forges a cornerstone for future distillation-based SSL research.

Machine learning and artificial intelligence within pediatric autoimmune diseases: applications, challenges, future perspective

INTRODUCTION

Autoimmune disorders affect 4.5% to 9.4% of children, significantly reducing their quality of life. The diagnosis and prognosis of autoimmune diseases are uncertain because of the variety of onset and development. Machine learning can identify clinically relevant patterns from vast amounts of data. Hence, its introduction has been beneficial in the diagnosis and management of patients.

AREAS COVERED

This narrative review was conducted through searching various electronic databases, including PubMed, Scopus, and Web of Science. This study thoroughly explores the current knowledge and identifies the remaining gaps in the applications of machine learning specifically in the context of pediatric autoimmune and related diseases.

EXPERT OPINION

Machine learning algorithms have the potential to completely change how pediatric autoimmune disorders are identified, treated, and managed. Machine learning can assist physicians in making more precise and fast judgments, identifying new biomarkers and therapeutic targets, and personalizing treatment strategies for each patient by utilizing massive datasets and powerful analytics.

A simulation data-driven semi-supervised framework based on MK-KNN graph and ESSGAT for bearing fault diagnosis

Current supervised intelligent fault diagnosis relies on abundant labeled data. However, collecting and labeling data are typically both expensive and time-consuming. Fault diagnosis with unlabeled data remains a significant challenge. To address this issue, a simulation data-driven semi-supervised framework based on multi-kernel K-nearest neighbor (MK-KNN) and edge self-supervised graph attention network (ESSGAT) is proposed. The novel MK-KNN establishes the neighborhood relationships between simulation data and real data. The developed multi-kernel function mitigates the risks of overfitting and underfitting, thereby enhancing the robustness of the simulation-real graphs. The designed ESSGAT employs two forms of self-supervised attention to predict the presence of edges, increasing the weights of crucial neighboring nodes in the MK-KNN graph. The performance of the proposed method is evaluated using a public bearing dataset and a self-constructed dataset of high-speed train axle box bearings. The results show that the proposed method achieves better diagnostic performance compared with other state-of-the-art graph construction methods and graph convolutional networks.

Machine learning algorithms and biomarkers identification for pancreatic cancer diagnosis using multi-omics data integration

PURPOSE

Pancreatic cancer is a lethal type of cancer with most of the cases being diagnosed in an advanced stage and poor prognosis. Developing new diagnostic and prognostic markers for pancreatic cancer can significantly improve early detection and patient outcomes. These biomarkers can potentially revolutionize medical practice by enabling personalized, more effective, targeted treatments, ultimately improving patient outcomes.

METHODS

The search strategy was developed following PRISMA guidelines. A comprehensive search was performed across four electronic databases: PubMed, Scopus, EMBASE, and Web of Science, covering all English publications up to September 2022. The Newcastle-Ottawa Scale (NOS) was utilized to assess bias, categorizing studies as "good," "fair," or "poor" quality based on their NOS scores. Descriptive statistics for all included studies were compiled and reviewed, along with the NOS scores for each study to indicate their quality assessment.

RESULTS

Our results showed that SVM and RF are the most widely used algorithms in machine learning and data analysis, particularly for biomarker identification. SVM, a supervised learning algorithm, is employed for both classification and regression by mapping data points in high-dimensional space to identify the optimal separating hyperplane between classes.

CONCLUSIONS

The application of machine-learning algorithms in the search for novel biomarkers in pancreatic cancer represents a significant advancement in the field. By harnessing the power of artificial intelligence, researchers are poised to make strides towards earlier detection and more effective treatment, ultimately improving patient outcomes in this challenging disease.

SMS Scam Detection Application Based on Optical Character Recognition for Image Data Using Unsupervised and Deep Semi-Supervised Learning

The growing problem of unsolicited text messages (smishing) and data irregularities necessitates stronger spam detection solutions. This paper explores the development of a sophisticated model designed to identify smishing messages by understanding the complex relationships among words, images, and context-specific factors, areas that remain underexplored in existing research. To address this, we merge a UCI spam dataset of regular text messages with real-world spam data, leveraging OCR technology for comprehensive analysis. The study employs a combination of traditional machine learning models, including K-means, Non-Negative Matrix Factorization, and Gaussian Mixture Models, along with feature extraction techniques such as TF-IDF and PCA. Additionally, deep learning models like RNN-Flatten, LSTM, and Bi-LSTM are utilized. The selection of these models is driven by their complementary strengths in capturing both the linear and non-linear relationships inherent in smishing messages. Machine learning models are chosen for their efficiency in handling structured text data, while deep learning models are selected for their superior ability to capture sequential dependencies and contextual nuances. The performance of these models is rigorously evaluated using metrics like accuracy, precision, recall, and F1 score, enabling a comparative analysis between the machine learning and deep learning approaches. Notably, the K-means feature extraction with vectorizer achieved 91.01% accuracy, and the KNN-Flatten model reached 94.13% accuracy, emerging as the top performer. The rationale behind highlighting these models is their potential to significantly improve smishing detection rates. For instance, the high accuracy of the KNN-Flatten model suggests its applicability in real-time spam detection systems, but its computational complexity might limit scalability in large-scale deployments. Similarly, while K-means with vectorizer excels in accuracy, it may struggle with the dynamic and evolving nature of smishing attacks, necessitating continual retraining.

Turbocharging protein binding site prediction with geometric attention, inter-resolution transfer learning, and homology-based augmentation

BACKGROUND

Locating small molecule binding sites in target proteins, in the resolution of either pocket or residue, is critical in many drug-discovery scenarios. Since it is not always easy to find such binding sites using conventional methods, different deep learning methods to predict binding sites out of protein structures have been developed in recent years. The existing deep learning based methods have several limitations, including (1) the inefficiency of the CNN-only architecture, (2) loss of information due to excessive post-processing, and (3) the under-utilization of available data sources.

METHODS

We present a new model architecture and training method that resolves the aforementioned problems. First, by layering geometric self-attention units on top of residue-level 3D CNN outputs, our model overcomes the problems of CNN-only architectures. Second, by configuring the fundamental units of computation as residues and pockets instead of voxels, our method reduced the information loss from post-processing. Lastly, by employing inter-resolution transfer learning and homology-based augmentation, our method maximizes the utilization of available data sources to a significant extent.

RESULTS

The proposed method significantly outperformed all state-of-the-art baselines regarding both resolutions-pocket and residue. An ablation study demonstrated the indispensability of our proposed architecture, as well as transfer learning and homology-based augmentation, for achieving optimal performance. We further scrutinized our model's performance through a case study involving human serum albumin, which demonstrated our model's superior capability in identifying multiple binding sites of the protein, outperforming the existing methods.

CONCLUSIONS

We believe that our contribution to the literature is twofold. Firstly, we introduce a novel computational method for binding site prediction with practical applications, substantiated by its strong performance across diverse benchmarks and case studies. Secondly, the innovative aspects in our method- specifically, the design of the model architecture, inter-resolution transfer learning, and homology-based augmentation-would serve as useful components for future work.

The changing scenario of drug discovery using AI to deep learning: Recent advancement, success stories, collaborations, and challenges

Due to the transformation of artificial intelligence (AI) tools and technologies, AI-driven drug discovery has come to the forefront. It reduces the time and expenditure. Due to these advantages, pharmaceutical industries are concentrating on AI-driven drug discovery. Several drug molecules have been discovered using AI-based techniques and tools, and several newly AI-discovered drug molecules have already entered clinical trials. In this review, we first present the data and their resources in the pharmaceutical sector for AI-driven drug discovery and illustrated some significant algorithms or techniques used for AI and ML which are used in this field. We gave an overview of the deep neural network (NN) models and compared them with artificial NNs. Then, we illustrate the recent advancement of the landscape of drug discovery using AI to deep learning, such as the identification of drug targets, prediction of their structure, estimation of drug-target interaction, estimation of drug-target binding affinity, design of de novo drug, prediction of drug toxicity, estimation of absorption, distribution, metabolism, excretion, toxicity; and estimation of drug-drug interaction. Moreover, we highlighted the success stories of AI-driven drug discovery and discussed several collaboration and the challenges in this area. The discussions in the article will enrich the pharmaceutical industry.

Application of artificial intelligence tools in wastewater and waste gas treatment systems: Recent advances and prospects

The non-linear complex relationships among the process variables in wastewater and waste gas treatment systems possess a significant challenge for real-time systems modelling. Data driven artificial intelligence (AI) tools are increasingly being adopted to predict the process performance, cost-effective process monitoring, and the control of different waste treatment systems, including those involving resource recovery. This review presents an in-depth analysis of the applications of emerging AI tools in physico-chemical and biological processes for the treatment of air pollutants, water and wastewater, and resource recovery processes. Additionally, the successful implementation of AI-controlled wastewater and waste gas treatment systems, along with real-time monitoring at the industrial scale are discussed.

A Futuristic Development in 3D Printing Technique Using Nanomaterials with a Step Toward 4D Printing

3D bioprinting has shown great promise in tissue engineering and regenerative medicine for creating patient-specific tissue scaffolds and medicinal devices. The quickness, accurate imaging, and design targeting of this emerging technology have excited biomedical engineers and translational medicine researchers. Recently, scaffolds made from 3D bioprinted tissue have become more clinically effective due to nanomaterials and nanotechnology. Because of quantum confinement effects and high surface area/volume ratios, nanomaterials and nanotechnological techniques have unique physical, chemical, and biological features. The use of nanomaterials and 3D bioprinting has led to scaffolds with improved physicochemical and biological properties. Nanotechnology and nanomaterials affect 3D bioprinted tissue engineered scaffolds for regenerative medicine and tissue engineering. Biomaterials and cells that respond to stimuli change the structural shape in 4D bioprinting. With such dynamic designs, tissue architecture can change morphologically. New 4D bioprinting techniques will aid in bioactuation, biorobotics, and biosensing. The potential of 4D bioprinting in biomedical technologies is also discussed in this article.

Machine learning assisted sorting of active microswimmers

Active matter systems, being in a non-equilibrium state, exhibit complex behaviors, such as self-organization, giving rise to emergent phenomena. There are many examples of active particles with biological origins, including bacteria and spermatozoa, or with artificial origins, such as self-propelled swimmers and Janus particles. The ability to manipulate active particles is vital for their effective application, e.g., separating motile spermatozoa from nonmotile and dead ones, to increase fertilization chance. In this study, we proposed a mechanism-an apparatus-to sort and demix active particles based on their motility values (Péclet number). Initially, using Brownian simulations, we demonstrated the feasibility of sorting self-propelled particles. Following this, we employed machine learning methods, supplemented with data from comprehensive simulations that we conducted for this study, to model the complex behavior of active particles. This enabled us to sort them based on their Péclet number. Finally, we evaluated the performance of the developed models and showed their effectiveness in demixing and sorting the active particles. Our findings can find applications in various fields, including physics, biology, and biomedical science, where the sorting and manipulation of active particles play a pivotal role.

A Semi-Supervised Transformer-Based Deep Learning Framework for Automated Tooth Segmentation and Identification on Panoramic Radiographs

Automated tooth segmentation and identification on dental radiographs are crucial steps in establishing digital dental workflows. While deep learning networks have been developed for these tasks, their performance has been inferior in partially edentulous individuals. This study proposes a novel semi-supervised Transformer-based framework (SemiTNet), specifically designed to improve tooth segmentation and identification performance on panoramic radiographs, particularly in partially edentulous cases, and establish an open-source dataset to serve as a unified benchmark. A total of 16,317 panoramic radiographs (1589 labeled and 14,728 unlabeled images) were collected from various datasets to create a large-scale dataset (TSI15k). The labeled images were divided into training and test sets at a 7:1 ratio, while the unlabeled images were used for semi-supervised learning. The SemiTNet was developed using a semi-supervised learning method with a label-guided teacher-student knowledge distillation strategy, incorporating a Transformer-based architecture. The performance of SemiTNet was evaluated on the test set using the intersection over union (IoU), Dice coefficient, precision, recall, and F1 score, and compared with five state-of-the-art networks. Paired t-tests were performed to compare the evaluation metrics between SemiTNet and the other networks. SemiTNet outperformed other networks, achieving the highest accuracy for tooth segmentation and identification, while requiring minimal model size. SemiTNet's performance was near-perfect for fully dentate individuals (all metrics over 99.69%) and excellent for partially edentulous individuals (all metrics over 93%). In edentulous cases, SemiTNet obtained statistically significantly higher tooth identification performance than all other networks. The proposed SemiTNet outperformed previous high-complexity, state-of-the-art networks, particularly in partially edentulous cases. The established open-source TSI15k dataset could serve as a unified benchmark for future studies.

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.

Using clinical text to refine unspecific condition codes in Dutch general practitioner EHR data

OBJECTIVE

Observational studies using electronic health record (EHR) databases often face challenges due to unspecific clinical codes that can obscure detailed medical information, hindering precise data analysis. In this study, we aimed to assess the feasibility of refining these unspecific condition codes into more specific codes in a Dutch general practitioner (GP) EHR database by leveraging the available clinical free text.

METHODS

We utilized three approaches for text classification-search queries, semi-supervised learning, and supervised learning-to improve the specificity of ten unspecific International Classification of Primary Care (ICPC-1) codes. Two text representations and three machine learning algorithms were evaluated for the (semi-)supervised models. Additionally, we measured the improvement achieved by the refinement process on all code occurrences in the database.

RESULTS

The classification models performed well for most codes. In general, no single classification approach consistently outperformed the others. However, there were variations in the relative performance of the classification approaches within each code and in the use of different text representations and machine learning algorithms. Class imbalance and limited training data affected the performance of the (semi-)supervised models, yet the simple search queries remained particularly effective. Ultimately, the developed models improved the specificity of over half of all the unspecific code occurrences in the database.

CONCLUSIONS

Our findings show the feasibility of using information from clinical text to improve the specificity of unspecific condition codes in observational healthcare databases, even with a limited range of machine-learning techniques and modest annotated training sets. Future work could investigate transfer learning, integration of structured data, alternative semi-supervised methods, and validation of models across healthcare settings. The improved level of detail enriches the interpretation of medical information and can benefit observational research and patient care.

Multi-source fully test-time adaptation

Deep neural networks have significantly advanced various fields. However, these models often encounter difficulties in achieving effective generalization when the distribution of test samples varies from that of the training samples. Recently, some fully test-time adaptation methods have been proposed to adapt the trained model with the unlabeled test samples before prediction to enhance the test performance. Despite achieving remarkable results, these methods only involve one trained model, which could only provide certain side information for the test samples. In real-world scenarios, there could be multiple available trained models that are beneficial to the test samples and are complementary to each other. Consequently, to better utilize these trained models, in this paper, we propose the problem of multi-source fully test-time adaptation to adapt multiple trained models to the test samples. To address this problem, we introduce a simple yet effective method utilizing a weighted aggregation scheme and introduce two unsupervised losses. The former could adaptively assign a higher weight to a more relevant model, while the latter could jointly adapt models with online unlabeled samples. Extensive experiments on three image classification datasets show that the proposed method achieves better results than baseline methods, demonstrating the superiority in adapting to multiple models.

Performance evaluation of semi-supervised learning frameworks for multi-class weed detection

Precision weed management (PWM), driven by machine vision and deep learning (DL) advancements, not only enhances agricultural product quality and optimizes crop yield but also provides a sustainable alternative to herbicide use. However, existing DL-based algorithms on weed detection are mainly developed based on supervised learning approaches, typically demanding large-scale datasets with manual-labeled annotations, which can be time-consuming and labor-intensive. As such, label-efficient learning methods, especially semi-supervised learning, have gained increased attention in the broader domain of computer vision and have demonstrated promising performance. These methods aim to utilize a small number of labeled data samples along with a great number of unlabeled samples to develop high-performing models comparable to the supervised learning counterpart trained on a large amount of labeled data samples. In this study, we assess the effectiveness of a semi-supervised learning framework for multi-class weed detection, employing two well-known object detection frameworks, namely FCOS (Fully Convolutional One-Stage Object Detection) and Faster-RCNN (Faster Region-based Convolutional Networks). Specifically, we evaluate a generalized student-teacher framework with an improved pseudo-label generation module to produce reliable pseudo-labels for the unlabeled data. To enhance generalization, an ensemble student network is employed to facilitate the training process. Experimental results show that the proposed approach is able to achieve approximately 76% and 96% detection accuracy as the supervised methods with only 10% of labeled data in CottonWeedDet3 and CottonWeedDet12, respectively. We offer access to the source code (https://github.com/JiajiaLi04/SemiWeeds), contributing a valuable resource for ongoing semi-supervised learning research in weed detection and beyond.

Investigating Contrastive Pair Learning's Frontiers in Supervised, Semisupervised, and Self-Supervised Learning

In recent years, contrastive learning has been a highly favored method for self-supervised representation learning, which significantly improves the unsupervised training of deep image models. Self-supervised learning is a subset of unsupervised learning in which the learning process is supervised by creating pseudolabels from the data themselves. Using supervised final adjustments after unsupervised pretraining is one way to take the most valuable information from a vast collection of unlabeled data and teach from a small number of labeled instances. This study aims firstly to compare contrastive learning with other traditional learning models; secondly to demonstrate by experimental studies the superiority of contrastive learning during classification; thirdly to fine-tune performance using pretrained models and appropriate hyperparameter selection; and finally to address the challenge of using contrastive learning techniques to produce data representations with semantic meaning that are independent of irrelevant factors like position, lighting, and background. Relying on contrastive techniques, the model efficiently captures meaningful representations by discerning similarities and differences between modified copies of the same image. The proposed strategy, involving unsupervised pretraining followed by supervised fine-tuning, improves the robustness, accuracy, and knowledge extraction of deep image models. The results show that even with a modest 5% of data labeled, the semisupervised model achieves an accuracy of 57.72%. However, the use of supervised learning with a contrastive approach and careful hyperparameter tuning increases accuracy to 85.43%. Further adjustment of the hyperparameters resulted in an excellent accuracy of 88.70%.

Progress and Opportunities for Machine Learning in Materials and Processes of Additive Manufacturing

In recent years, there has been widespread adoption of machine learning (ML) technologies to unravel intricate relationships among diverse parameters in various additive manufacturing (AM) techniques. These ML models excel at recognizing complex patterns from extensive, well-curated datasets, thereby unveiling latent knowledge crucial for informed decision-making during the AM process. The collaborative synergy between ML and AM holds the potential to revolutionize the design and production of AM-printed parts. This review delves into the challenges and opportunities emerging at the intersection of these two dynamic fields. It provides a comprehensive analysis of the publication landscape for ML-related research in the field of AM, explores common ML applications in AM research (such as quality control, process optimization, design optimization, microstructure analysis, and material formulation), and concludes by presenting an outlook that underscores the utilization of advanced ML models, the development of emerging sensors, and ML applications in emerging AM-related fields. Notably, ML has garnered increased attention in AM due to its superior performance across various AM-related applications. It is envisioned that the integration of ML into AM processes will significantly enhance 3D printing capabilities across diverse AM-related research areas.

CarcassFormer: an end-to-end transformer-based framework for simultaneous localization, segmentation and classification of poultry carcass defect

In the food industry, assessing the quality of poultry carcasses during processing is a crucial step. This study proposes an effective approach for automating the assessment of carcass quality without requiring skilled labor or inspector involvement. The proposed system is based on machine learning (ML) and computer vision (CV) techniques, enabling automated defect detection and carcass quality assessment. To this end, an end-to-end framework called CarcassFormer is introduced. It is built upon a Transformer-based architecture designed to effectively extract visual representations while simultaneously detecting, segmenting, and classifying poultry carcass defects. Our proposed framework is capable of analyzing imperfections resulting from production and transport welfare issues, as well as processing plant stunner, scalder, picker, and other equipment malfunctions. To benchmark the framework, a dataset of 7,321 images was initially acquired, which contained both single and multiple carcasses per image. In this study, the performance of the CarcassFormer system is compared with other state-of-the-art (SOTA) approaches for both classification, detection, and segmentation tasks. Through extensive quantitative experiments, our framework consistently outperforms existing methods, demonstrating re- markable improvements across various evaluation metrics such as AP, AP@50, and AP@75. Furthermore, the qualitative results highlight the strengths of CarcassFormer in capturing fine details, including feathers, and accurately localizing and segmenting carcasses with high precision. To facilitate further research and collaboration, the source code and trained models will be made publicly available upon acceptance.

AI-Powered Microfluidics: Shaping the Future of Phenotypic Drug Discovery

Phenotypic drug discovery (PDD), which involves harnessing biological systems directly to uncover effective drugs, has undergone a resurgence in recent years. The rapid advancement of artificial intelligence (AI) over the past few years presents numerous opportunities for augmenting phenotypic drug screening on microfluidic platforms, leveraging its predictive capabilities, data analysis, efficient data processing, etc. Microfluidics coupled with AI is poised to revolutionize the landscape of phenotypic drug discovery. By integrating advanced microfluidic platforms with AI algorithms, researchers can rapidly screen large libraries of compounds, identify novel drug candidates, and elucidate complex biological pathways with unprecedented speed and efficiency. This review provides an overview of recent advances and challenges in AI-based microfluidics and their applications in drug discovery. We discuss the synergistic combination of microfluidic systems for high-throughput screening and AI-driven analysis for phenotype characterization, drug-target interactions, and predictive modeling. In addition, we highlight the potential of AI-powered microfluidics to achieve an automated drug screening system. Overall, AI-powered microfluidics represents a promising approach to shaping the future of phenotypic drug discovery by enabling rapid, cost-effective, and accurate identification of therapeutically relevant compounds.

Enhanced Domain Adaptation for Foot Ulcer Segmentation Through Mixing Self-Trained Weak Labels

Wound management requires the measurement of the wound parameters such as its shape and area. However, computerized analysis of the wound suffers the challenge of inexact segmentation of the wound images due to limited or inaccurate labels. It is a common scenario that the source domain provides an abundance of labeled data, while the target domain provides only limited labels. To overcome this, we propose a novel approach that combines self-training learning and mixup augmentation. The neural network is trained on the source domain to generate weak labels on the target domain via the self-training process. In the second stage, generated labels are mixed up with labels from the source domain to retrain the neural network and enhance generalization across diverse datasets. The efficacy of our approach was evaluated using the DFUC 2022, FUSeg, and RMIT datasets, demonstrating substantial improvements in segmentation accuracy and robustness across different data distributions. Specifically, in single-domain experiments, segmentation on the DFUC 2022 dataset scored a dice score of 0.711, while the score on the FUSeg dataset achieved 0.859. For domain adaptation, when these datasets were used as target datasets, the dice scores were 0.714 for DFUC 2022 and 0.561 for FUSeg.

Multi-omics based artificial intelligence for cancer research

With significant advancements of next generation sequencing technologies, large amounts of multi-omics data, including genomics, epigenomics, transcriptomics, proteomics, and metabolomics, have been accumulated, offering an unprecedented opportunity to explore the heterogeneity and complexity of cancer across various molecular levels and scales. One of the promising aspects of multi-omics lies in its capacity to offer a holistic view of the biological networks and pathways underpinning cancer, facilitating a deeper understanding of its development, progression, and response to treatment. However, the exponential growth of data generated by multi-omics studies present significant analytical challenges. Processing, analyzing, integrating, and interpreting these multi-omics datasets to extract meaningful insights is an ambitious task that stands at the forefront of current cancer research. The application of artificial intelligence (AI) has emerged as a powerful solution to these challenges, demonstrating exceptional capabilities in deciphering complex patterns and extracting valuable information from large-scale, intricate omics datasets. This review delves into the synergy of AI and multi-omics, highlighting its revolutionary impact on oncology. We dissect how this confluence is reshaping the landscape of cancer research and clinical practice, particularly in the realms of early detection, diagnosis, prognosis, treatment and pathology. Additionally, we elaborate the latest AI methods for multi-omics integration to provide a comprehensive insight of the complex biological mechanisms and inherent heterogeneity of cancer. Finally, we discuss the current challenges of data harmonization, algorithm interpretability, and ethical considerations. Addressing these challenges necessitates a multidisciplinary collaboration, paving the promising way for more precise, personalized, and effective treatments for cancer patients.

Artificial Intelligence-Based Microfluidic Platform for Detecting Contaminants in Water: A Review

Water pollution greatly impacts humans and ecosystems, so a series of policies have been enacted to control it. The first step in performing pollution control is to detect contaminants in the water. Various methods have been proposed for water quality testing, such as spectroscopy, chromatography, and electrochemical techniques. However, traditional testing methods require the utilization of laboratory equipment, which is large and not suitable for real-time testing in the field. Microfluidic devices can overcome the limitations of traditional testing instruments and have become an efficient and convenient tool for water quality analysis. At the same time, artificial intelligence is an ideal means of recognizing, classifying, and predicting data obtained from microfluidic systems. Microfluidic devices based on artificial intelligence and machine learning are being developed with great significance for the next generation of water quality monitoring systems. This review begins with a brief introduction to the algorithms involved in artificial intelligence and the materials used in the fabrication and detection techniques of microfluidic platforms. Then, the latest research development of combining the two for pollutant detection in water bodies, including heavy metals, pesticides, micro- and nanoplastics, and microalgae, is mainly introduced. Finally, the challenges encountered and the future directions of detection methods based on industrial intelligence and microfluidic chips are discussed.

Federated learning for medical image analysis: A survey

Machine learning in medical imaging often faces a fundamental dilemma, namely, the small sample size problem. Many recent studies suggest using multi-domain data pooled from different acquisition sites/centers to improve statistical power. However, medical images from different sites cannot be easily shared to build large datasets for model training due to privacy protection reasons. As a promising solution, federated learning, which enables collaborative training of machine learning models based on data from different sites without cross-site data sharing, has attracted considerable attention recently. In this paper, we conduct a comprehensive survey of the recent development of federated learning methods in medical image analysis. We have systematically gathered research papers on federated learning and its applications in medical image analysis published between 2017 and 2023. Our search and compilation were conducted using databases from IEEE Xplore, ACM Digital Library, Science Direct, Springer Link, Web of Science, Google Scholar, and PubMed. In this survey, we first introduce the background of federated learning for dealing with privacy protection and collaborative learning issues. We then present a comprehensive review of recent advances in federated learning methods for medical image analysis. Specifically, existing methods are categorized based on three critical aspects of a federated learning system, including client end, server end, and communication techniques. In each category, we summarize the existing federated learning methods according to specific research problems in medical image analysis and also provide insights into the motivations of different approaches. In addition, we provide a review of existing benchmark medical imaging datasets and software platforms for current federated learning research. We also conduct an experimental study to empirically evaluate typical federated learning methods for medical image analysis. This survey can help to better understand the current research status, challenges, and potential research opportunities in this promising research field.

Stepwise Transfer Learning for Expert-level Pediatric Brain Tumor MRI Segmentation in a Limited Data Scenario

Purpose To develop, externally test, and evaluate clinical acceptability of a deep learning pediatric brain tumor segmentation model using stepwise transfer learning. Materials and Methods In this retrospective study, the authors leveraged two T2-weighted MRI datasets (May 2001 through December 2015) from a national brain tumor consortium (n = 184; median age, 7 years [range, 1-23 years]; 94 male patients) and a pediatric cancer center (n = 100; median age, 8 years [range, 1-19 years]; 47 male patients) to develop and evaluate deep learning neural networks for pediatric low-grade glioma segmentation using a stepwise transfer learning approach to maximize performance in a limited data scenario. The best model was externally tested on an independent test set and subjected to randomized blinded evaluation by three clinicians, wherein they assessed clinical acceptability of expert- and artificial intelligence (AI)-generated segmentations via 10-point Likert scales and Turing tests. Results The best AI model used in-domain stepwise transfer learning (median Dice score coefficient, 0.88 [IQR, 0.72-0.91] vs 0.812 [IQR, 0.56-0.89] for baseline model; P = .049). With external testing, the AI model yielded excellent accuracy using reference standards from three clinical experts (median Dice similarity coefficients: expert 1, 0.83 [IQR, 0.75-0.90]; expert 2, 0.81 [IQR, 0.70-0.89]; expert 3, 0.81 [IQR, 0.68-0.88]; mean accuracy, 0.82). For clinical benchmarking (n = 100 scans), experts rated AI-based segmentations higher on average compared with other experts (median Likert score, 9 [IQR, 7-9] vs 7 [IQR 7-9]) and rated more AI segmentations as clinically acceptable (80.2% vs 65.4%). Experts correctly predicted the origin of AI segmentations in an average of 26.0% of cases. Conclusion Stepwise transfer learning enabled expert-level automated pediatric brain tumor autosegmentation and volumetric measurement with a high level of clinical acceptability. Keywords: Stepwise Transfer Learning, Pediatric Brain Tumors, MRI Segmentation, Deep Learning Supplemental material is available for this article. © RSNA, 2024.

A survey of label-noise deep learning for medical image analysis

Several factors are associated with the success of deep learning. One of the most important reasons is the availability of large-scale datasets with clean annotations. However, obtaining datasets with accurate labels in the medical imaging domain is challenging. The reliability and consistency of medical labeling are some of these issues, and low-quality annotations with label noise usually exist. Because noisy labels reduce the generalization performance of deep neural networks, learning with noisy labels is becoming an essential task in medical image analysis. Literature on this topic has expanded in terms of volume and scope. However, no recent surveys have collected and organized this knowledge, impeding the ability of researchers and practitioners to utilize it. In this work, we presented an up-to-date survey of label-noise learning for medical image domain. We reviewed extensive literature, illustrated some typical methods, and showed unified taxonomies in terms of methodological differences. Subsequently, we conducted the methodological comparison and demonstrated the corresponding advantages and disadvantages. Finally, we discussed new research directions based on the characteristics of medical images. Our survey aims to provide researchers and practitioners with a solid understanding of existing medical label-noise learning, such as the main algorithms developed over the past few years, which could help them investigate new methods to combat with the negative effects of label noise.

Diabetes management in the era of artificial intelligence

Artificial intelligence is growing quickly, and its application in the global diabetes pandemic has the potential to completely change the way this chronic illness is identified and treated. Machine learning methods have been used to construct algorithms supporting predictive models for the risk of getting diabetes or its complications. Social media and Internet forums also increase patient participation in diabetes care. Diabetes resource usage optimisation has benefited from technological improvements. As a lifestyle therapy intervention, digital therapies have made a name for themselves in the treatment of diabetes. Artificial intelligence will cause a paradigm shift in diabetes care, moving away from current methods and toward the creation of focused, data-driven precision treatment.

A semi-supervised segmentation method for microscopic hyperspectral pathological images based on multi-consistency learning

Pathological images are considered the gold standard for clinical diagnosis and cancer grading. Automatic segmentation of pathological images is a fundamental and crucial step in constructing powerful computer-aided diagnostic systems. Medical microscopic hyperspectral pathological images can provide additional spectral information, further distinguishing different chemical components of biological tissues, offering new insights for accurate segmentation of pathological images. However, hyperspectral pathological images have higher resolution and larger area, and their annotation requires more time and clinical experience. The lack of precise annotations limits the progress of research in pathological image segmentation. In this paper, we propose a novel semi-supervised segmentation method for microscopic hyperspectral pathological images based on multi-consistency learning (MCL-Net), which combines consistency regularization methods with pseudo-labeling techniques. The MCL-Net architecture employs a shared encoder and multiple independent decoders. We introduce a Soft-Hard pseudo-label generation strategy in MCL-Net to generate pseudo-labels that are closer to real labels for pathological images. Furthermore, we propose a multi-consistency learning strategy, treating pseudo-labels generated by the Soft-Hard process as real labels, by promoting consistency between predictions of different decoders, enabling the model to learn more sample features. Extensive experiments in this paper demonstrate the effectiveness of the proposed method, providing new insights for the segmentation of microscopic hyperspectral tissue pathology images.

Semi-supervised learning methods for weed detection in turf

BACKGROUND

Accurate weed detection is a prerequisite for precise automatic precision herbicide application. Previous research has adopted the laborious and time-consuming approach of manually labeling and processing large image data sets to develop deep neural networks for weed detection. This research introduces a novel semi-supervised learning (SSL) approach for detecting weeds in turf. The performance of SSL was compared with that of ResNet50, a fully supervised learning (FSL) method, in detecting and differentiating sub-images containing weeds from those containing only turfgrass.

RESULTS

Compared with ResNet50, the evaluated SSL methods, Π-model, Mean Teacher, and FixMatch, increased the classification accuracy by 2.8%, 0.7%, and 3.9%, respectively, when only 100 labeled images per class were utilized. FixMatch was the most efficient and reliable model, as it exhibited higher accuracy (≥0.9530) and F1 scores (≥0.951) with fewer labeled data (50 per class) in the validation and testing data sets than the other neural networks evaluated.

CONCLUSION

These results reveal that the SSL deep neural networks are capable of being highly accurate while requiring fewer labeled training images, thus being more time- and labor-efficient than the FSL method. © 2024 Society of Chemical Industry.

MutexMatch: Semi-Supervised Learning With Mutex-Based Consistency Regularization

The core issue in semi-supervised learning (SSL) lies in how to effectively leverage unlabeled data, whereas most existing methods tend to put a great emphasis on the utilization of high-confidence samples yet seldom fully explore the usage of low-confidence samples. In this article, we aim to utilize low-confidence samples in a novel way with our proposed mutex-based consistency regularization, namely MutexMatch. Specifically, the high-confidence samples are required to exactly predict "what it is" by the conventional true-positive classifier (TPC), while low-confidence samples are employed to achieve a simpler goal-to predict with ease "what it is not" by the true-negative classifier (TNC). In this sense, we not only mitigate the pseudo-labeling errors but also make full use of the low-confidence unlabeled data by the consistency of dissimilarity degree. MutexMatch achieves superior performance on multiple benchmark datasets, i.e., Canadian Institute for Advanced Research (CIFAR)-10, CIFAR-100, street view house numbers (SVHN), self-taught learning 10 (STL-10), and mini-ImageNet. More importantly, our method further shows superiority when the amount of labeled data is scarce, e.g., 92.23% accuracy with only 20 labeled data on CIFAR-10. Code has been released at https://github.com/NJUyued/MutexMatch4SSL.

A deep-learning strategy to identify cell types across species from high-density extracellular recordings

High-density probes allow electrophysiological recordings from many neurons simultaneously across entire brain circuits but don't reveal cell type. Here, we develop a strategy to identify cell types from extracellular recordings in awake animals, revealing the computational roles of neurons with distinct functional, molecular, and anatomical properties. We combine optogenetic activation and pharmacology using the cerebellum as a testbed to generate a curated ground-truth library of electrophysiological properties for Purkinje cells, molecular layer interneurons, Golgi cells, and mossy fibers. We train a semi-supervised deep-learning classifier that predicts cell types with greater than 95% accuracy based on waveform, discharge statistics, and layer of the recorded neuron. The classifier's predictions agree with expert classification on recordings using different probes, in different laboratories, from functionally distinct cerebellar regions, and across animal species. Our classifier extends the power of modern dynamical systems analyses by revealing the unique contributions of simultaneously-recorded cell types during behavior.

scTPC: a novel semisupervised deep clustering model for scRNA-seq data

MOTIVATION

Continuous advancements in single-cell RNA sequencing (scRNA-seq) technology have enabled researchers to further explore the study of cell heterogeneity, trajectory inference, identification of rare cell types, and neurology. Accurate scRNA-seq data clustering is crucial in single-cell sequencing data analysis. However, the high dimensionality, sparsity, and presence of "false" zero values in the data can pose challenges to clustering. Furthermore, current unsupervised clustering algorithms have not effectively leveraged prior biological knowledge, making cell clustering even more challenging.

RESULTS

This study investigates a semisupervised clustering model called scTPC, which integrates the triplet constraint, pairwise constraint, and cross-entropy constraint based on deep learning. Specifically, the model begins by pretraining a denoising autoencoder based on a zero-inflated negative binomial distribution. Deep clustering is then performed in the learned latent feature space using triplet constraints and pairwise constraints generated from partial labeled cells. Finally, to address imbalanced cell-type datasets, a weighted cross-entropy loss is introduced to optimize the model. A series of experimental results on 10 real scRNA-seq datasets and five simulated datasets demonstrate that scTPC achieves accurate clustering with a well-designed framework.

AVAILABILITY AND IMPLEMENTATION

scTPC is a Python-based algorithm, and the code is available from https://github.com/LF-Yang/Code or https://zenodo.org/records/10951780.

Forest fire susceptibility assessment under small sample scenario: A semi-supervised learning approach using transductive support vector machine

Forest fires threaten global ecosystems, socio-economic structures, and public safety. Accurately assessing forest fire susceptibility is critical for effective environmental management. Supervised learning methods dominate this assessment, relying on a substantial dataset of forest fire occurrences for model training. However, obtaining precise forest fire location data remains challenging. To address this issue, semi-supervised learning emerges as a viable solution, leveraging both a limited set of collected samples and unlabeled data containing environmental factors for training. Our study employed the transductive support vector machine (TSVM), a key semi-supervised learning method, to assess forest fire susceptibility in scenarios with limited samples. We conducted a comparative analysis, evaluating its performance against widely used supervised learning methods. The assessment area for forest fire susceptibility lies in Dayu County, Jiangxi Province, China, renowned for its vast forest cover and frequent fire incidents. We analyzed and generated maps depicting forest fire susceptibility, evaluating prediction accuracies for both supervised and semi-supervised learning methods across various small sample scenarios (e.g., 4, 8, 12, 16, 20, 24, 28, and 32 samples). Our findings indicate that TSVM exhibits superior prediction accuracy compared to supervised learning with limited samples, yielding more plausible forest fire susceptibility maps. For instance, at sample sizes of 4, 16, and 28, TSVM achieves prediction accuracies of approximately 0.8037, 0.9257, and 0.9583, respectively. In contrast, random forests, the top performers in supervised learning, demonstrate accuracies of approximately 0.7424, 0.8916, and 0.9431, respectively, for the same small sample sizes. Additionally, we discussed three key aspects: TSVM parameter configuration, the impact of unlabeled sample size, and performance within typical sample sizes. Our findings support semi-supervised learning as a promising approach compared to supervised learning for forest fire susceptibility assessment and mapping, particularly in scenarios with small sample sizes.

Human-in-the-Loop: Visual Analytics for Building Models Recognizing Behavioral Patterns in Time Series

Detecting complex behavioral patterns in temporal data, such as moving object trajectories, often relies on precise formal specifications derived from vague domain concepts. However, such methods are sensitive to noise and minor fluctuations, leading to missed pattern occurrences. Conversely, machine learning (ML) approaches require abundant labeled examples, posing practical challenges. Our visual analytics approach enables domain experts to derive, test, and combine interval-based features to discriminate patterns and generate training data for ML algorithms. Visual aids enhance recognition and characterization of expected patterns and discovery of unexpected ones. Case studies demonstrate feasibility and effectiveness of the approach, which offers a novel framework for integrating human expertise and analytical reasoning with ML techniques, advancing data analytics.

Manifold Peaks Nonnegative Matrix Factorization

Nonnegative matrix factorization (NMF) has attracted increasing interest for its high interpretability in recent years. It is shown that the NMF is closely related to fuzzy k -means clustering, where the basis matrix represents the cluster centroids. However, most of the existing NMF-based clustering algorithms often have their decomposed centroids deviate away from the data manifold, which potentially undermines the clustering results, especially when the datasets lie on complicated geometric structures. In this article, we present a manifold peaks NMF (MPNMF) for data clustering. The proposed approach has the following advantages: 1) it selects a number of MPs to characterize the backbone of the data manifold; 2) it enforces the centroids to lie on the original data manifold, by restricting each centroid to be a conic combination of a small number of nearby MPs; 3) it generalizes the graph smoothness regularization to guide the local graph construction; and 4) it solves a general problem of quadratic regularized nonnegative least squares (NNLSs) with group l0 -norm constraint and further develops an efficient optimization algorithm to solve the objective function of the MPNMF. Extensive experiments on both synthetic and real-world datasets demonstrate the effectiveness of the proposed approach.

Expanding the Horizons of Machine Learning in Nanomaterials to Chiral Nanostructures

Machine learning holds significant research potential in the field of nanotechnology, enabling nanomaterial structure and property predictions, facilitating materials design and discovery, and reducing the need for time-consuming and labor-intensive experiments and simulations. In contrast to their achiral counterparts, the application of machine learning for chiral nanomaterials is still in its infancy, with a limited number of publications to date. This is despite the great potential of machine learning to advance the development of new sustainable chiral materials with high values of optical activity, circularly polarized luminescence, and enantioselectivity, as well as for the analysis of structural chirality by electron microscopy. In this review, an analysis of machine learning methods used for studying achiral nanomaterials is provided, subsequently offering guidance on adapting and extending this work to chiral nanomaterials. An overview of chiral nanomaterials within the framework of synthesis-structure-property-application relationships is presented and insights on how to leverage machine learning for the study of these highly complex relationships are provided. Some key recent publications are reviewed and discussed on the application of machine learning for chiral nanomaterials. Finally, the review captures the key achievements, ongoing challenges, and the prospective outlook for this very important research field.

Linear semantic transformation for semi-supervised medical image segmentation

Medical image segmentation is a focus research and foundation in developing intelligent medical systems. Recently, deep learning for medical image segmentation has become a standard process and succeeded significantly, promoting the development of reconstruction, and surgical planning of disease diagnosis. However, semantic learning is often inefficient owing to the lack of supervision of feature maps, resulting in that high-quality segmentation models always rely on numerous and accurate data annotations. Learning robust semantic representation in latent spaces remains a challenge. In this paper, we propose a novel semi-supervised learning framework to learn vital attributes in medical images, which constructs generalized representation from diverse semantics to realize medical image segmentation. We first build a self-supervised learning part that achieves context recovery by reconstructing space and intensity of medical images, which conduct semantic representation for feature maps. Subsequently, we combine semantic-rich feature maps and utilize simple linear semantic transformation to convert them into image segmentation. The proposed framework was tested using five medical segmentation datasets. Quantitative assessments indicate the highest scores of our method on IXI (73.78%), ScaF (47.50%), COVID-19-Seg (50.72%), PC-Seg (65.06%), and Brain-MR (72.63%) datasets. Finally, we compared our method with the latest semi-supervised learning methods and obtained 77.15% and 75.22% DSC values, respectively, ranking first on two representative datasets. The experimental results not only proved that the proposed linear semantic transformation was effectively applied to medical image segmentation, but also presented its simplicity and ease-of-use to pursue robust segmentation in semi-supervised learning. Our code is now open at: https://github.com/QingYunA/Linear-Semantic-Transformation-for-Semi-Supervised-Medical-Image-Segmentation.

Semi-supervised medical image classification via distance correlation minimization and graph attention regularization

We propose a novel semi-supervised learning method to leverage unlabeled data alongside minimal annotated data and improve medical imaging classification performance in realistic scenarios with limited labeling budgets to afford data annotations. Our method introduces distance correlation to minimize correlations between feature representations from different views of the same image encoded with non-coupled deep neural networks architectures. In addition, it incorporates a data-driven graph-attention based regularization strategy to model affinities among images within the unlabeled data by exploiting their inherent relational information in the feature space. We conduct extensive experiments on four medical imaging benchmark data sets involving X-ray, dermoscopic, magnetic resonance, and computer tomography imaging on single and multi-label medical imaging classification scenarios. Our experiments demonstrate the effectiveness of our method in achieving very competitive performance and outperforming several state-of-the-art semi-supervised learning methods. Furthermore, they confirm the suitability of distance correlation as a versatile dependence measure and the benefits of the proposed graph-attention based regularization for semi-supervised learning in medical imaging analysis.

Machine learning methods for predicting guide RNA effects in CRISPR epigenome editing experiments

CRISPR epigenomic editing technologies enable functional interrogation of non-coding elements. However, current computational methods for guide RNA (gRNA) design do not effectively predict the power potential, molecular and cellular impact to optimize for efficient gRNAs, which are crucial for successful applications of these technologies. We present "launch-dCas9" (machine LeArning based UNified CompreHensive framework for CRISPR-dCas9) to predict gRNA impact from multiple perspectives, including cell fitness, wildtype abundance (gauging power potential), and gene expression in single cells. Our launchdCas9, built and evaluated using experiments involving >1 million gRNAs targeted across the human genome, demonstrates relatively high prediction accuracy (AUC up to 0.81) and generalizes across cell lines. Method-prioritized top gRNA(s) are 4.6-fold more likely to exert effects, compared to other gRNAs in the same cis-regulatory region. Furthermore, launchdCas9 identifies the most critical sequence-related features and functional annotations from >40 features considered. Our results establish launch-dCas9 as a promising approach to design gRNAs for CRISPR epigenomic experiments.

Improving Graph Convolutional Network with Learnable Edge Weights and Edge-Node Co-Embedding for Graph Anomaly Detection

The era of Industry 4.0 is gradually transforming our society into a data-driven one, which can help us uncover valuable information from accumulated data, thereby improving the level of social governance. The detection of anomalies, is crucial for maintaining societal trust and fairness, yet it poses significant challenges due to the ubiquity of anomalies and the difficulty in identifying them accurately. This paper aims to enhance the performance of the current Graph Convolutional Network (GCN)-based Graph Anomaly Detection (GAD) algorithm on datasets with extremely low proportions of anomalous labels. This goal is achieved through modifying the GCN network structure and conducting feature extraction, thus fully utilizing three types of information in the graph: node label information, node feature information, and edge information. Firstly, we theoretically demonstrate the relationship between label propagation and feature convolution, indicating that the Label Propagation Algorithm (LPA) can serve as a regularization penalty term for GCN, aiding in training and enabling learnable edge weights, providing a basis for incorporating node label information into GCN networks. Secondly, we introduce a method to aggregate node and edge features, thereby incorporating edge information into GCN networks. Finally, we design different GCN trainable weights for node features and co-embedding features. This design allows different features to be projected into different spaces, greatly enhancing model expressiveness. Experimental results on the DGraph dataset demonstrate superior AUC performance compared to baseline models, highlighting the feasibility and efficacy of the proposed approach in addressing GAD tasks in the scene with extremely low proportions of anomalous data.

Decoding Nanomaterial-Biosystem Interactions through Machine Learning

The interactions between biosystems and nanomaterials regulate most of their theranostic and nanomedicine applications. These nanomaterial-biosystem interactions are highly complex and influenced by a number of entangled factors, including but not limited to the physicochemical features of nanomaterials, the types and characteristics of the interacting biosystems, and the properties of the surrounding microenvironments. Over the years, different experimental approaches coupled with computational modeling have revealed important insights into these interactions, although many outstanding questions remain unanswered. The emergence of machine learning has provided a timely and unique opportunity to revisit nanomaterial-biosystem interactions and to further push the boundary of this field. This minireview highlights the development and use of machine learning to decode nanomaterial-biosystem interactions and provides our perspectives on the current challenges and potential opportunities in this field.

Cross-prediction-powered inference

While reliable data-driven decision-making hinges on high-quality labeled data, the acquisition of quality labels often involves laborious human annotations or slow and expensive scientific measurements. Machine learning is becoming an appealing alternative as sophisticated predictive techniques are being used to quickly and cheaply produce large amounts of predicted labels; e.g., predicted protein structures are used to supplement experimentally derived structures, predictions of socioeconomic indicators from satellite imagery are used to supplement accurate survey data, and so on. Since predictions are imperfect and potentially biased, this practice brings into question the validity of downstream inferences. We introduce cross-prediction: a method for valid inference powered by machine learning. With a small labeled dataset and a large unlabeled dataset, cross-prediction imputes the missing labels via machine learning and applies a form of debiasing to remedy the prediction inaccuracies. The resulting inferences achieve the desired error probability and are more powerful than those that only leverage the labeled data. Closely related is the recent proposal of prediction-powered inference [A. N. Angelopoulos, S. Bates, C. Fannjiang, M. I. Jordan, T. Zrnic, Science 382, 669-674 (2023)], which assumes that a good pretrained model is already available. We show that cross-prediction is consistently more powerful than an adaptation of prediction-powered inference in which a fraction of the labeled data is split off and used to train the model. Finally, we observe that cross-prediction gives more stable conclusions than its competitors; its CIs typically have significantly lower variability.

GUIDE: Training Deep Graph Neural Networks via Guided Dropout Over Edges

Graph neural networks (GNNs) have made great progress in graph-based semi-supervised learning (GSSL). However, most existing GNNs are confronted with the oversmoothing issue that limits their expressive ability. A key factor that leads to this problem is the excessive aggregation of information from other classes when updating the node representation. To alleviate this limitation, we propose an effective method called GUIded Dropout over Edges (GUIDE) for training deep GNNs. The core of the method is to reduce the influence of nodes from other classes by removing a certain number of inter-class edges. In GUIDE, we drop edges according to the edge strength, which is defined as the time an edge acts as a bridge along the shortest path between node pairs. We find that the stronger the edge strength, the more likely it is to be an inter-class edge. In this way, GUIDE can drop more inter-class edges and keep more intra-class edges. Therefore, nodes in the same community or class are more similar, whereas different classes are more separated in the embedded space. In addition, we perform some theoretical analysis of the proposed method, which explains why it is effective in alleviating the oversmoothing problem. To validate its rationality and effectiveness, we conduct experiments on six public benchmarks with different GNNs backbones. Experimental results demonstrate that GUIDE consistently outperforms state-of-the-art methods in both shallow and deep GNNs.

Separated collaborative learning for semi-supervised prostate segmentation with multi-site heterogeneous unlabeled MRI data

Segmenting prostate from magnetic resonance imaging (MRI) is a critical procedure in prostate cancer staging and treatment planning. Considering the nature of labeled data scarcity for medical images, semi-supervised learning (SSL) becomes an appealing solution since it can simultaneously exploit limited labeled data and a large amount of unlabeled data. However, SSL relies on the assumption that the unlabeled images are abundant, which may not be satisfied when the local institute has limited image collection capabilities. An intuitive solution is to seek support from other centers to enrich the unlabeled image pool. However, this further introduces data heterogeneity, which can impede SSL that works under identical data distribution with certain model assumptions. Aiming at this under-explored yet valuable scenario, in this work, we propose a separated collaborative learning (SCL) framework for semi-supervised prostate segmentation with multi-site unlabeled MRI data. Specifically, on top of the teacher-student framework, SCL exploits multi-site unlabeled data by: (i) Local learning, which advocates local distribution fitting, including the pseudo label learning that reinforces confirmation of low-entropy easy regions and the cyclic propagated real label learning that leverages class prototypes to regularize the distribution of intra-class features; (ii) External multi-site learning, which aims to robustly mine informative clues from external data, mainly including the local-support category mutual dependence learning, which takes the spirit that mutual information can effectively measure the amount of information shared by two variables even from different domains, and the stability learning under strong adversarial perturbations to enhance robustness to heterogeneity. Extensive experiments on prostate MRI data from six different clinical centers show that our method can effectively generalize SSL on multi-site unlabeled data and significantly outperform other semi-supervised segmentation methods. Besides, we validate the extensibility of our method on the multi-class cardiac MRI segmentation task with data from four different clinical centers.

TNCB: Tri-Net With Cross-Balanced Pseudo Supervision for Class Imbalanced Medical Image Classification

In clinical settings, the implementation of deep neural networks is impeded by the prevalent problems of label scarcity and class imbalance in medical images. To mitigate the need for labeled data, semi-supervised learning (SSL) has gained traction. However, existing SSL schemes exhibit certain limitations. 1) They commonly fail to address the class imbalance problem. Training with imbalanced data makes the model's prediction biased towards majority classes, consequently introducing prediction bias. 2) They usually suffer from training bias arising from unreasonable training strategies, such as strong coupling between the generation and utilization of pseudo labels. To address these problems, we propose a novel SSL framework called Tri-Net with Cross-Balanced pseudo supervision (TNCB). Specifically, two student networks focusing on different learning tasks and a teacher network equipped with an adaptive balancer are designed. This design enables the teacher model to pay more focus on minority classes, thereby reducing prediction bias. Additionally, we propose a virtual optimization strategy to further enhance the teacher model's resistance to class imbalance. Finally, to fully exploit valuable knowledge from unlabeled images, we employ cross-balanced pseudo supervision, where an adaptive cross loss function is introduced to reduce training bias. Extensive evaluation on four datasets with different diseases, image modalities, and imbalance ratios consistently demonstrate the superior performance of TNCB over state-of-the-art SSL methods. These results indicate the effectiveness and robustness of TNCB in addressing imbalanced medical image classification challenges.

Deep learning methods in metagenomics: a review

The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.

Collaborative Multiple Players to Address Label Sparsity in Quality Prediction of Batch Processes

For decades, soft sensors have been extensively renowned for their efficiency in real-time tracking of expensive variables for advanced process control. However, despite the diverse efforts lavished on enhancing their models, the issue of label sparsity when modeling the soft sensors has always posed challenges across various processes. In this paper, a fledgling technique, called co-training, is studied for leveraging only a small ratio of labeled data, to hone and formulate a more advantageous framework in soft sensor modeling. Dissimilar to the conventional routine where only two players are employed, we investigate the efficient number of players in batch processes, making a multiple-player learning scheme to assuage the sparsity issue. Meanwhile, a sliding window spanning across both time and batch direction is used to aggregate the samples for prediction, and account for the unique 2D correlations among the general batch process data. Altogether, the forged framework can outperform the other prevalent methods, especially when the ratio of unlabeled data is climbing up, and two case studies are showcased to demonstrate its effectiveness.

Handling the Challenges of Small-Scale Labeled Data and Class Imbalances in Classifying the N and K Statuses of Rubber Leaves Using Hyperspectroscopy Techniques

The nutritional status of rubber trees (Hevea brasiliensis) is inseparable from the production of natural rubber. Nitrogen (N) and potassium (K) levels in rubber leaves are 2 crucial criteria that reflect the nutritional status of the rubber tree. Advanced hyperspectral technology can evaluate N and K statuses in leaves rapidly. However, high bias and uncertain results will be generated when using a small size and imbalance dataset to train a spectral estimaion model. A typical solution of laborious long-term nutrient stress and high-intensive data collection deviates from rapid and flexible advantages of hyperspectral tech. Therefore, a less intensive and streamlined method, remining information from hyperspectral image data, was assessed. From this new perspective, a semisupervised learning (SSL) method and resampling techniques were employed for generating pseudo-labeling data and class rebalancing. Subsequently, a 5-classification spectral model of the N and K statuses of rubber leaves was established. The SSL model based on random forest classifiers and mean sampling techniques yielded optimal classification results both on imbalance/balance dataset (weighted average precision 67.8/78.6%, macro averaged precision 61.2/74.4%, and weighted recall 65.7/78.5% for the N status). All data and code could be viewed on the:Github https://github.com/WeehowTang/SSL-rebalancingtest. Ultimately, we proposed an efficient way to rapidly and accurately monitor the N and K levels in rubber leaves, especially in the scenario of small annotation and imbalance categories ratios.