The secondary structure of ribonucleic acid (RNA) is more stable and accessible in the cell than its tertiary structure, making it essential for functional prediction. Although deep learning has shown promising results in this field, current methods suffer from poor generalization and high complexity. In this work, we reformulate the RNA secondary structure prediction as a K-Rook problem, thereby simplifying the prediction process into probabilistic matching within a finite solution space. Building on this innovative perspective, we introduce RFold, a simple yet effective method that learns to predict the most matching K-Rook solution from the given sequence. RFold employs a bi-dimensional optimization strategy that decomposes the probabilistic matching problem into row-wise and column-wise components to reduce the matching complexity, simplifying the solving process while guaranteeing the validity of the output. Extensive experiments demonstrate that RFold achieves competitive performance and about eight times faster inference efficiency than the state-of-the-art approaches. The code and Colab demo are available in \href{//github.com/A4Bio/RFold}{//github.com/A4Bio/RFold}.
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Complex human activity recognition (CHAR) remains a pivotal challenge within ubiquitous computing, especially in the context of smart environments. Existing studies typically require meticulous labeling of both atomic and complex activities, a task that is labor-intensive and prone to errors due to the scarcity and inaccuracies of available datasets. Most prior research has focused on datasets that either precisely label atomic activities or, at minimum, their sequence approaches that are often impractical in real world settings.In response, we introduce VCHAR (Variance-Driven Complex Human Activity Recognition), a novel framework that treats the outputs of atomic activities as a distribution over specified intervals. Leveraging generative methodologies, VCHAR elucidates the reasoning behind complex activity classifications through video-based explanations, accessible to users without prior machine learning expertise. Our evaluation across three publicly available datasets demonstrates that VCHAR enhances the accuracy of complex activity recognition without necessitating precise temporal or sequential labeling of atomic activities. Furthermore, user studies confirm that VCHAR's explanations are more intelligible compared to existing methods, facilitating a broader understanding of complex activity recognition among non-experts.
Electroencephalography (EEG), a medical imaging technique that captures scalp electrical activity of brain structures via electrodes, has been widely used in affective computing. The spatial domain of EEG is rich in affective information.However, few of the existing studies have simultaneously analyzed EEG signals from multiple perspectives of geometric and anatomical structures in spatial domain. In this paper, we propose a multi-view Graph Transformer (MVGT) based on spatial relations, which integrates information from the temporal, frequency and spatial domains, including geometric and anatomical structures, so as to enhance the expressive power of the model comprehensively.We incorporate the spatial information of EEG channels into the model as encoding, thereby improving its ability to perceive the spatial structure of the channels. Meanwhile, experimental results based on publicly available datasets demonstrate that our proposed model outperforms state-of-the-art methods in recent years. In addition, the results also show that the MVGT could extract information from multiple domains and capture inter-channel relationships in EEG emotion recognition tasks effectively.
Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.
Federated learning has emerged as a compelling paradigm for medical image segmentation, particularly in light of increasing privacy concerns. However, most of the existing research relies on relatively stringent assumptions regarding the uniformity and completeness of annotations across clients. Contrary to this, this paper highlights a prevalent challenge in medical practice: incomplete annotations. Such annotations can introduce incorrectly labeled pixels, potentially undermining the performance of neural networks in supervised learning. To tackle this issue, we introduce a novel solution, named FedIA. Our insight is to conceptualize incomplete annotations as noisy data (i.e., low-quality data), with a focus on mitigating their adverse effects. We begin by evaluating the completeness of annotations at the client level using a designed indicator. Subsequently, we enhance the influence of clients with more comprehensive annotations and implement corrections for incomplete ones, thereby ensuring that models are trained on accurate data. Our method's effectiveness is validated through its superior performance on two extensively used medical image segmentation datasets, outperforming existing solutions. The code is available at //github.com/HUSTxyy/FedIA.
Acupuncture is a widely adopted medical practice that involves inserting thin needles into specific points on the body to alleviate pain and treat various health conditions. Current learning practices heavily rely on 2D atlases and practice on peers, which are notably less intuitive and pose risks, particularly in sensitive areas such as the eyes. To address these challenges, we introduce AcuVR, a Virtual Reality (VR) based system designed to add a layer of interactivity and realism. This innovation aims to reduce the risks associated with practicing acupuncture techniques while offering more effective learning strategies. Furthermore, AcuVR incorporates medical imaging and standardized anatomy models, enabling the simulation of customized acupuncture scenarios. This feature represents a significant advancement beyond the limitations of conventional resources such as atlases and textbooks, facilitating a more immersive and personalized learning experience. The evaluation study with eight acupuncture students and practitioners revealed high participant satisfaction and pointed to the effectiveness and potential of AcuVR as a valuable addition to acupuncture training.
Python's dynamic typing system offers flexibility and expressiveness but can lead to type-related errors, prompting the need for automated type inference to enhance type hinting. While existing learning-based approaches show promising inference accuracy, they struggle with practical challenges in comprehensively handling various types, including complex generic types and (unseen) user-defined types. In this paper, we introduce TIGER, a two-stage generating-then-ranking (GTR) framework, designed to effectively handle Python's diverse type categories. TIGER leverages fine-tuned pre-trained code models to train a generative model with a span masking objective and a similarity model with a contrastive training objective. This approach allows TIGER to generate a wide range of type candidates, including complex generics in the generating stage, and accurately rank them with user-defined types in the ranking stage. Our evaluation on the ManyTypes4Py dataset shows TIGER's advantage over existing methods in various type categories, notably improving accuracy in inferring user-defined and unseen types by 11.2% and 20.1% respectively in Top-5 Exact Match. Moreover, the experimental results not only demonstrate TIGER's superior performance and efficiency, but also underscore the significance of its generating and ranking stages in enhancing automated type inference.
In causal inference, estimating heterogeneous treatment effects (HTE) is critical for identifying how different subgroups respond to interventions, with broad applications in fields such as precision medicine and personalized advertising. Although HTE estimation methods aim to improve accuracy, how to provide explicit subgroup descriptions remains unclear, hindering data interpretation and strategic intervention management. In this paper, we propose CURLS, a novel rule learning method leveraging HTE, which can effectively describe subgroups with significant treatment effects. Specifically, we frame causal rule learning as a discrete optimization problem, finely balancing treatment effect with variance and considering the rule interpretability. We design an iterative procedure based on the minorize-maximization algorithm and solve a submodular lower bound as an approximation for the original. Quantitative experiments and qualitative case studies verify that compared with state-of-the-art methods, CURLS can find subgroups where the estimated and true effects are 16.1% and 13.8% higher and the variance is 12.0% smaller, while maintaining similar or better estimation accuracy and rule interpretability. Code is available at //osf.io/zwp2k/.
External influences such as traffic and environmental factors induce vibrations in structures, leading to material degradation over time. These vibrations result in cracks due to the material's lack of plasticity compromising structural integrity. Detecting such damage requires the installation of vibration sensors to capture the internal dynamics. However, distinguishing relevant eigenmodes from external noise necessitates the use of Deep Learning models. The detection of changes in eigenmodes can be used to anticipate these shifts in material properties and to discern between normal and anomalous structural behavior. Eigenmodes, representing characteristic vibration patterns, provide insights into structural dynamics and deviations from expected states. Thus, we propose ModeConv to automatically capture and analyze changes in eigenmodes, facilitating effective anomaly detection in structures and material properties. In the conducted experiments, ModeConv demonstrates computational efficiency improvements, resulting in reduced runtime for model calculations. The novel ModeConv neural network layer is tailored for temporal graph neural networks, in which every node represents one sensor. ModeConv employs a singular value decomposition based convolutional filter design for complex numbers and leverages modal transformation in lieu of Fourier or Laplace transformations in spectral graph convolutions. We include a mathematical complexity analysis illustrating the runtime reduction.
In multi-turn dialog, utterances do not always take the full form of sentences \cite{Carbonell1983DiscoursePA}, which naturally makes understanding the dialog context more difficult. However, it is essential to fully grasp the dialog context to generate a reasonable response. Hence, in this paper, we propose to improve the response generation performance by examining the model's ability to answer a reading comprehension question, where the question is focused on the omitted information in the dialog. Enlightened by the multi-task learning scheme, we propose a joint framework that unifies these two tasks, sharing the same encoder to extract the common and task-invariant features with different decoders to learn task-specific features. To better fusing information from the question and the dialog history in the encoding part, we propose to augment the Transformer architecture with a memory updater, which is designed to selectively store and update the history dialog information so as to support downstream tasks. For the experiment, we employ human annotators to write and examine a large-scale dialog reading comprehension dataset. Extensive experiments are conducted on this dataset, and the results show that the proposed model brings substantial improvements over several strong baselines on both tasks. In this way, we demonstrate that reasoning can indeed help better response generation and vice versa. We release our large-scale dataset for further research.
We propose a novel attention gate (AG) model for medical imaging that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules of cascaded convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN architectures such as the U-Net model with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed Attention U-Net architecture is evaluated on two large CT abdominal datasets for multi-class image segmentation. Experimental results show that AGs consistently improve the prediction performance of U-Net across different datasets and training sizes while preserving computational efficiency. The code for the proposed architecture is publicly available.
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