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Rapid and accurate identification of Venous thromboembolism (VTE), a severe cardiovascular condition including deep vein thrombosis (DVT) and pulmonary embolism (PE), is important for effective treatment. Leveraging Natural Language Processing (NLP) on radiology reports, automated methods have shown promising advancements in identifying VTE events from retrospective data cohorts or aiding clinical experts in identifying VTE events from radiology reports. However, effectively training Deep Learning (DL) and the NLP models is challenging due to limited labeled medical text data, the complexity and heterogeneity of radiology reports, and data imbalance. This study proposes novel method combinations of DL methods, along with data augmentation, adaptive pre-trained NLP model selection, and a clinical expert NLP rule-based classifier, to improve the accuracy of VTE identification in unstructured (free-text) radiology reports. Our experimental results demonstrate the model's efficacy, achieving an impressive 97\% accuracy and 97\% F1 score in predicting DVT, and an outstanding 98.3\% accuracy and 98.4\% F1 score in predicting PE. These findings emphasize the model's robustness and its potential to significantly contribute to VTE research.

Melanoma, a dangerous type of skin cancer resulting from abnormal skin cell growth, can be treated if detected early. Various approaches using Fully Convolutional Networks (FCNs) have been proposed, with the U-Net architecture being prominent To aid in its diagnosis through automatic skin lesion segmentation. However, the symmetrical U-Net model's reliance on convolutional operations hinders its ability to capture long-range dependencies crucial for accurate medical image segmentation. Several Transformer-based U-Net topologies have recently been created to overcome this limitation by replacing CNN blocks with different Transformer modules to capture local and global representations. Furthermore, the U-shaped structure is hampered by semantic gaps between the encoder and decoder. This study intends to increase the network's feature re-usability by carefully building the skip connection path. Integrating an already calculated attention affinity within the skip connection path improves the typical concatenation process utilized in the conventional skip connection path. As a result, we propose a U-shaped hierarchical Transformer-based structure for skin lesion segmentation and an Inter-scale Context Fusion (ISCF) method that uses attention correlations in each stage of the encoder to adaptively combine the contexts from each stage to mitigate semantic gaps. The findings from two skin lesion segmentation benchmarks support the ISCF module's applicability and effectiveness. The code is publicly available at \url{//github.com/saniaesk/skin-lesion-segmentation}

Various types of social biases have been reported with pretrained Masked Language Models (MLMs) in prior work. However, multiple underlying factors are associated with an MLM such as its model size, size of the training data, training objectives, the domain from which pretraining data is sampled, tokenization, and languages present in the pretrained corpora, to name a few. It remains unclear as to which of those factors influence social biases that are learned by MLMs. To study the relationship between model factors and the social biases learned by an MLM, as well as the downstream task performance of the model, we conduct a comprehensive study over 39 pretrained MLMs covering different model sizes, training objectives, tokenization methods, training data domains and languages. Our results shed light on important factors often neglected in prior literature, such as tokenization or model objectives.

Accident of struck-by machines is one of the leading causes of casualties on construction sites. Monitoring workers' proximities to avoid human-machine collisions has aroused great concern in construction safety management. Existing methods are either too laborious and costly to apply extensively, or lacking spatial perception for accurate monitoring. Therefore, this study proposes a novel framework for proximity monitoring using only an ordinary 2D camera to realize real-time human-machine collision warning, which is designed to integrate a monocular 3D object detection model to perceive spatial information from 2D images and a post-processing classification module to identify the proximity as four predefined categories: Dangerous, Potentially Dangerous, Concerned, and Safe. A virtual dataset containing 22000 images with 3D annotations is constructed and publicly released to facilitate the system development and evaluation. Experimental results show that the trained 3D object detection model achieves 75% loose AP within 20 meters. Besides, the implemented system is real-time and camera carrier-independent, achieving an F1 of roughly 0.8 within 50 meters under specified settings for machines of different sizes. This study preliminarily reveals the potential and feasibility of proximity monitoring using only a 2D camera, providing a new promising and economical way for early warning of human-machine collisions.

Multi-Arm, Multi-Stage (MAMS) clinical trial designs allow for multiple therapies to be compared across a spectrum of clinical trial phases. MAMS designs can be categorized into several overarching design groups, including adaptive designs (AD) and multi-arm (MA) designs. Factorial clinical trials designs represent an additional group of designs which can provide increased efficiency relative to fixed, traditional designs. In this work, we explore design choices associated with Factorial Adaptive Multi-Arm Multi-Stage (FAST) designs, which represent the combination of factorial and MAMS designs. This category of trial can potentially offer benefits similar to both MAMS and factorial designs. This work is motivated by a proposed clinical trial under development.

To achieve reliable and precise scene understanding, autonomous vehicles typically incorporate multiple sensing modalities to capitalize on their complementary attributes. However, existing cross-modal 3D detectors do not fully utilize the image domain information to address the bottleneck issues of the LiDAR-based detectors. This paper presents a new cross-modal 3D object detector, namely UPIDet, which aims to unleash the potential of the image branch from two aspects. First, UPIDet introduces a new 2D auxiliary task called normalized local coordinate map estimation. This approach enables the learning of local spatial-aware features from the image modality to supplement sparse point clouds. Second, we discover that the representational capability of the point cloud backbone can be enhanced through the gradients backpropagated from the training objectives of the image branch, utilizing a succinct and effective point-to-pixel module. Extensive experiments and ablation studies validate the effectiveness of our method. Notably, we achieved the top rank in the highly competitive cyclist class of the KITTI benchmark at the time of submission. The source code is available at //github.com/Eaphan/UPIDet.

Protein structure-based property prediction has emerged as a promising approach for various biological tasks, such as protein function prediction and sub-cellular location estimation. The existing methods highly rely on experimental protein structure data and fail in scenarios where these data are unavailable. Predicted protein structures from AI tools (e.g., AlphaFold2) were utilized as alternatives. However, we observed that current practices, which simply employ accurately predicted structures during inference, suffer from notable degradation in prediction accuracy. While similar phenomena have been extensively studied in general fields (e.g., Computer Vision) as model robustness, their impact on protein property prediction remains unexplored. In this paper, we first investigate the reason behind the performance decrease when utilizing predicted structures, attributing it to the structure embedding bias from the perspective of structure representation learning. To study this problem, we identify a Protein 3D Graph Structure Learning Problem for Robust Protein Property Prediction (PGSL-RP3), collect benchmark datasets, and present a protein Structure embedding Alignment Optimization framework (SAO) to mitigate the problem of structure embedding bias between the predicted and experimental protein structures. Extensive experiments have shown that our framework is model-agnostic and effective in improving the property prediction of both predicted structures and experimental structures. The benchmark datasets and codes will be released to benefit the community.

The recent proliferation of knowledge graphs (KGs) coupled with incomplete or partial information, in the form of missing relations (links) between entities, has fueled a lot of research on knowledge base completion (also known as relation prediction). Several recent works suggest that convolutional neural network (CNN) based models generate richer and more expressive feature embeddings and hence also perform well on relation prediction. However, we observe that these KG embeddings treat triples independently and thus fail to cover the complex and hidden information that is inherently implicit in the local neighborhood surrounding a triple. To this effect, our paper proposes a novel attention based feature embedding that captures both entity and relation features in any given entity's neighborhood. Additionally, we also encapsulate relation clusters and multihop relations in our model. Our empirical study offers insights into the efficacy of our attention based model and we show marked performance gains in comparison to state of the art methods on all datasets.

Attention mechanism has been used as an ancillary means to help RNN or CNN. However, the Transformer (Vaswani et al., 2017) recently recorded the state-of-the-art performance in machine translation with a dramatic reduction in training time by solely using attention. Motivated by the Transformer, Directional Self Attention Network (Shen et al., 2017), a fully attention-based sentence encoder, was proposed. It showed good performance with various data by using forward and backward directional information in a sentence. But in their study, not considered at all was the distance between words, an important feature when learning the local dependency to help understand the context of input text. We propose Distance-based Self-Attention Network, which considers the word distance by using a simple distance mask in order to model the local dependency without losing the ability of modeling global dependency which attention has inherent. Our model shows good performance with NLI data, and it records the new state-of-the-art result with SNLI data. Additionally, we show that our model has a strength in long sentences or documents.