Dataset

In fungi, fusion between individuals leads to localized cell death, a phenomenon termed heterokaryon incompatibility. Generally, the genes responsible for this incompatibility are observed to be under balancing selection resulting from negative frequency-dependent selection. Here, we assess this phenomenon in Aspergillus fumigatus, a human pathogenic fungus with a very low level of linkage disequilibrium as well as an extremely high crossover rate. Using complementation of auxotrophic mutations as an assay for hyphal compatibility, we screened sexual progeny for compatibility to identify genes involved in this process, called het genes...

Organ-specific gene expression datasets that include hundreds to thousands of experiments allow the reconstruction of organ-level gene regulatory networks (GRNs). However, creating such datasets is greatly hampered by the requirements of extensive and tedious manual curation. Here, we trained a supervised classification model that can accurately classify the organ-of-origin for a plant transcriptome. This K-Nearest Neighbor-based multiclass classifier was used to create organ-specific gene expression datasets for the leaf, root, shoot, flower, and seed in Arabidopsis thaliana ...

Platelet products are both expensive and have very short shelf lives. As usage rates for platelets are highly variable, the effective management of platelet demand and supply is very important yet challenging. The primary goal of this paper is to present an efficient forecasting model for platelet demand at Canadian Blood Services (CBS). To accomplish this goal, five different demand forecasting methods, ARIMA (Auto Regressive Integrated Moving Average), Prophet, lasso regression (least absolute shrinkage and selection operator), random forest, and LSTM (Long Short-Term Memory) networks are utilized and evaluated via a rolling window method...

Increasing evidence indicates that terminally differentiated neurons in the brain may recommit to a cell cycle-like process during neuronal aging and under disease conditions. Because of the rare existence and random localization of these cells in the brain, their molecular profiles and disease-specific heterogeneities remain unclear. Through a bioinformatics approach that allows integrated analyses of multiple single-nucleus transcriptome datasets from human brain samples, these rare cell populations were identified and selected for further characterization...

OBJECTIVES: Recovery from traumatic brain injury (TBI) is extremely difficult to predict, with TBI severity usually demonstrating weak predictive validity for functional or other outcomes. A possible explanation may lie in the statistical phenomenon called suppression, according to which a third variable masks the true association between predictor and outcome, making it appear weaker than it actually is. Age at injury is a strong candidate as a suppressor because of its well-established main and moderating effects on TBI outcomes...

We endeavor on a rarely explored task named thermal infrared video denoising. Perception in the thermal infrared significantly enhances the capabilities of machine vision. Nonetheless, noise in imaging systems is one of the factors that hampers the large-scale application of equipment. Existing thermal infrared denoising methods, primarily focusing on the image level, inadequately utilize time-domain information and insufficiently conduct investigation of system-level mixed noise, presenting the inferior ability in the video-recorded era; while video denoising methods, commonly applied to RGB cameras, exhibit uncertain effectiveness owing to substantial dissimilarities in the noise models and modalities between RGB and thermal infrared images...

Textbook question answering (TQA) task aims to infer answers for given questions from a multimodal context, including text and diagrams. The existing studies have aggregated intramodal semantics extracted from a single modality but have yet to capture the intermodal semantics between different modalities. A major challenge in learning intermodal semantics is maintaining lossless intramodal semantics while bridging the gap of semantics caused by heterogeneity. In this article, we propose an intermodal relation-aware heterogeneous graph network (IMR-HGN) to extract the intermodal semantics for TQA, which aggregates different modalities while learning features rather than representing them independently...

Despite its significant progress, cross-modal retrieval still suffers from one-to-many matching cases, where the multiplicity of semantic instances in another modality could be acquired by a given query. However, existing approaches usually map heterogeneous data into the learned space as deterministic point vectors. In spite of their remarkable performance in matching the most similar instance, such deterministic point embedding suffers from the insufficient representation of rich semantics in one-to-many correspondence...

As an emerging decentralized machine learning technique, federated learning organizes collaborative training and preserves the privacy and security of participants. However, untrustworthy devices, typically Byzantine attackers, pose a significant challenge to federated learning since they can upload malicious parameters to corrupt the global model. To defend against such attacks, we propose a novel robust aggregation method-maximum correntropy aggregation (MCA), which applies the maximum correntropy criterion (MCC) to derive a central value from parameters...

Contrastive learning (CL) has emerged as a powerful approach for self-supervised learning. However, it suffers from sampling bias, which hinders its performance. While the mainstream solutions, hard negative mining (HNM) and supervised CL (SCL), have been proposed to mitigate this critical issue, they do not effectively address graph CL (GCL). To address it, we propose graph positive sampling (GPS) and three contrastive objectives. The former is a novel learning paradigm designed to leverage the inherent properties of graphs for improved GCL models, which utilizes four complementary similarity measurements, including node centrality, topological distance, neighborhood overlapping, and semantic distance, to select positive counterparts for each node...

In zero-shot learning (ZSL), attribute knowledge plays a vital role in transferring knowledge from seen classes to unseen classes. However, most existing ZSL methods learn biased attribute knowledge, which usually results in biased attribute prediction and a decline in zero-shot recognition performance. To solve this problem and learn unbiased attribute knowledge, we propose a visual attribute Transformer for zero-shot recognition (ZS-VAT), which is an effective and interpretable Transformer designed specifically for ZSL...

High-efficiency deep learning (DL) models are necessary not only to facilitate their use in devices with limited resources but also to improve resources required for training. Convolutional neural networks (ConvNets) typically exert severe demands on local device resources and this conventionally limits their adoption within mobile and embedded platforms. This brief presents work toward utilizing static convolutional filters generated from the space of local binary patterns (LBPs) and Haar features to design efficient ConvNet architectures...

Knowledge tracing (KT) refers to predicting learners' performance in the future according to their historical responses, which has become an essential task in intelligent tutoring systems. Most deep learning-based methods usually model the learners' knowledge states via recurrent neural networks (RNNs) or attention mechanisms. Recently emerging graph neural networks (GNNs) assist the KT model to capture the relationships such as question-skill and question-learner. However, non-pairwise and complex higher-order information among responses is ignored...

Cross-modal hashing (CMH) has attracted considerable attention in recent years. Almost all existing CMH methods primarily focus on reducing the modality gap and semantic gap, i.e., aligning multi-modal features and their semantics in Hamming space, without taking into account the space gap, i.e., difference between the real number space and the Hamming space. In fact, the space gap can affect the performance of CMH methods. In this paper, we analyze and demonstrate how the space gap affects the existing CMH methods, which therefore raises two problems: solution space compression and loss function oscillation...

Deep Neural Networks (DNNs) are known to be vulnerable to both backdoor and adversarial attacks. In the literature, these two types of attacks are commonly treated as distinct robustness problems and solved separately, since they belong to training-time and inference-time attacks respectively. However, this paper revealed that there is an intriguing connection between them: (1) planting a backdoor into a model will significantly affect the model's adversarial examples; (2) for an infected model, its adversarial examples have similar features as the triggered images...

Emotion recognition from electroencephalogram (EEG) signals is a critical domain in biomedical research with applications ranging from mental disorder regulation to human-computer interaction. In this paper, we address two fundamental aspects of EEG emotion recognition: continuous regression of emotional states and discrete classification of emotions. While classification methods have garnered significant attention, regression methods remain relatively under-explored. To bridge this gap, we introduce MASA-TCN, a novel unified model that leverages the spatial learning capabilities of Temporal Convolutional Networks (TCNs) for EEG emotion regression and classification tasks...

Proximal femoral fracture segmentation in computed tomography (CT) is essential in the preoperative planning of orthopedic surgeons. Recently, numerous deep learning-based approaches have been proposed for segmenting various structures within CT scans. Nevertheless, distinguishing various attributes between fracture fragments and soft tissue regions in CT scans frequently poses challenges, which have received comparatively limited research attention. Besides, the cornerstone of contemporary deep learning methodologies is the availability of annotated data, while detailed CT annotations remain scarce...

MOTIVATION: Antibody therapeutic candidates must exhibit not only tight binding to their target but also good developability properties, especially low risk of immunogenicity. RESULTS: In this work, we fit a simple generative model, SAM, to sixty million human heavy and seventy million human light chains. We show that the probability of a sequence calculated by the model distinguishes human sequences from other species with the same or better accuracy on a variety of benchmark datasets containing >400 million sequences than any other model in the literature, outperforming large language models (LLMs) by large margins...

PURPOSE: This study aimed to assess the performance of a deep learning algorithm (YOLOv5) in detecting different mandibular fracture types in panoramic images. METHODS: This study utilized a dataset of panoramic radiographic images with mandibular fractures. The dataset was divided into training, validation, and testing sets, with 60%, 20%, and 20% of the images, respectively. An equal number of control panoramic radiographs, which did not contain any fractures, were also randomly distributed among the three sets...

PURPOSE: Obtaining large volumes of medical images, required for deep learning development, can be challenging in rare pathologies. Image augmentation and preprocessing offer viable solutions. This work explores the case of necrotising enterocolitis (NEC), a rare but life-threatening condition affecting premature neonates, with challenging radiological diagnosis. We investigate data augmentation and preprocessing techniques and propose two optimised pipelines for developing reliable computer-aided diagnosis models on a limited NEC dataset...