Single-step retrosynthesis is a crucial task in organic chemistry and drug design, requiring the identification of required reactants to synthesize a specific compound. with the advent of computer-aided synthesis planning, there is growing interest in using machine-learning techniques to facilitate the process. Existing template-free machine learning-based models typically utilize transformer structures and represent molecules as ID sequences. However, these methods often face challenges in fully leveraging the extensive topological information of the molecule and aligning atoms between the production and reactants, leading to results that are not as competitive as those of semi-template models. Our proposed method, Node-Aligned Graph-to-Graph (NAG2G), also serves as a transformer-based template-free model but utilizes 2D molecular graphs and 3D conformation information. Furthermore, our approach simplifies the incorporation of production-reactant atom mapping alignment by leveraging node alignment to determine a specific order for node generation and generating molecular graphs in an auto-regressive manner node-by-node. This method ensures that the node generation order coincides with the node order in the input graph, overcoming the difficulty of determining a specific node generation order in an auto-regressive manner. Our extensive benchmarking results demonstrate that the proposed NAG2G can outperform the previous state-of-the-art baselines in various metrics.
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Magnetic resonance imaging (MRI) using hyperpolarized noble gases provides a way to visualize the structure and function of human lung, but the long imaging time limits its broad research and clinical applications. Deep learning has demonstrated great potential for accelerating MRI by reconstructing images from undersampled data. However, most existing deep conventional neural networks (CNN) directly apply square convolution to k-space data without considering the inherent properties of k-space sampling, limiting k-space learning efficiency and image reconstruction quality. In this work, we propose an encoding enhanced (EN2) complex CNN for highly undersampled pulmonary MRI reconstruction. EN2 employs convolution along either the frequency or phase-encoding direction, resembling the mechanisms of k-space sampling, to maximize the utilization of the encoding correlation and integrity within a row or column of k-space. We also employ complex convolution to learn rich representations from the complex k-space data. In addition, we develop a feature-strengthened modularized unit to further boost the reconstruction performance. Experiments demonstrate that our approach can accurately reconstruct hyperpolarized 129Xe and 1H lung MRI from 6-fold undersampled k-space data and provide lung function measurements with minimal biases compared with fully-sampled image. These results demonstrate the effectiveness of the proposed algorithmic components and indicate that the proposed approach could be used for accelerated pulmonary MRI in research and clinical lung disease patient care.
Mining Conditional Part Semantics with Occluded Extrapolation for Human-Object Interaction Detection
Human-Object Interaction Detection is a crucial aspect of human-centric scene understanding, with important applications in various domains. Despite recent progress in this field, recognizing subtle and detailed interactions remains challenging. Existing methods try to use human-related clues to alleviate the difficulty, but rely heavily on external annotations or knowledge, limiting their practical applicability in real-world scenarios. In this work, we propose a novel Part Semantic Network (PSN) to solve this problem. The core of PSN is a Conditional Part Attention (CPA) mechanism, where human features are taken as keys and values, and the object feature is used as query for the computation in a cross-attention mechanism. In this way, our model learns to automatically focus on the most informative human parts conditioned on the involved object, generating more semantically meaningful features for interaction recognition. Additionally, we propose an Occluded Part Extrapolation (OPE) strategy to facilitate interaction recognition under occluded scenarios, which teaches the model to extrapolate detailed features from partially occluded ones. Our method consistently outperforms prior approaches on the V-COCO and HICO-DET datasets, without external data or extra annotations. Additional ablation studies validate the effectiveness of each component of our proposed method.
Movable antenna (MA) array is a novel technology recently developed where positions of transmit/receive antennas can be flexibly adjusted in the specified region to reconfigure the wireless channel and achieve a higher capacity. In this letter, we, for the first time, investigate the MA array-assisted physical-layer security where the confidential information is transmitted from a MA array-enabled Alice to a single-antenna Bob, in the presence of multiple single-antenna and colluding eavesdroppers. We aim to maximize the achievable secrecy rate by jointly designing the transmit beamforming and positions of all antennas at Alice subject to the transmit power budget and specified regions for positions of all transmit antennas. The resulting problem is highly non-convex, for which the projected gradient ascent (PGA) and the alternating optimization methods are utilized to obtain a high-quality suboptimal solution. Simulation results demonstrate that since the additional spatial degree of freedom (DoF) can be fully exploited, the MA array significantly enhances the secrecy rate compared to the conventional fixed-position antenna (FPA) array.
Tumour-infiltrating lymphocytes (TILs) are considered as a valuable prognostic markers in both triple-negative and human epidermal growth factor receptor 2 (HER2) breast cancer. In this study, we introduce an innovative deep learning pipeline based on the Efficient-UNet architecture to compute a TILs score for breast cancer whole slide images. Our pipeline first segments tumour-stroma regions and generates a tumour bulk mask. Subsequently, it detects TILs within the tumour-associated stroma, generating a TILs score by closely mirroring the pathologist's workflow. Our method exhibits state-of-the-art performance in segmenting tumour/stroma areas and TILs detection, as demonstrated by internal cross-validation on the TiGER Challenge training dataset and evaluation on the final leaderboards. Additionally, our TILs score proves competitive in predicting survival outcomes within the same challenge, underscoring the clinical relevance and potential of our automated TILs scoring system as a breast cancer prognostic tool.
Cryogenic electron tomography (cryo-ET) is a technique for imaging biological samples such as viruses, cells, and proteins in 3D. A microscope collects a series of 2D projections of the sample, and the goal is to reconstruct the 3D density of the sample called the tomogram. This is difficult as the 2D projections have a missing wedge of information and are noisy. Tomograms reconstructed with conventional methods, such as filtered back-projection, suffer from the noise, and from artifacts and anisotropic resolution due to the missing wedge of information. To improve the visual quality and resolution of such tomograms, we propose a deep-learning approach for simultaneous denoising and missing wedge reconstruction called DeepDeWedge. DeepDeWedge is based on fitting a neural network to the 2D projections with a self-supervised loss inspired by noise2noise-like methods. The algorithm requires no training or ground truth data. Experiments on synthetic and real cryo-ET data show that DeepDeWedge achieves competitive performance for deep learning-based denoising and missing wedge reconstruction of cryo-ET tomograms.
LLaVA-Plus is a general-purpose multimodal assistant that expands the capabilities of large multimodal models. It maintains a skill repository of pre-trained vision and vision-language models and can activate relevant tools based on users' inputs to fulfill real-world tasks. LLaVA-Plus is trained on multimodal instruction-following data to acquire the ability to use tools, covering visual understanding, generation, external knowledge retrieval, and compositions. Empirical results show that LLaVA-Plus outperforms LLaVA in existing capabilities and exhibits new ones. It is distinct in that the image query is directly grounded and actively engaged throughout the entire human-AI interaction sessions, significantly improving tool use performance and enabling new scenarios.
Visual commonsense reasoning (VCR) is a challenging multi-modal task, which requires high-level cognition and commonsense reasoning ability about the real world. In recent years, large-scale pre-training approaches have been developed and promoted the state-of-the-art performance of VCR. However, the existing approaches almost employ the BERT-like objectives to learn multi-modal representations. These objectives motivated from the text-domain are insufficient for the excavation on the complex scenario of visual modality. Most importantly, the spatial distribution of the visual objects is basically neglected. To address the above issue, we propose to construct the spatial relation graph based on the given visual scenario. Further, we design two pre-training tasks named object position regression (OPR) and spatial relation classification (SRC) to learn to reconstruct the spatial relation graph respectively. Quantitative analysis suggests that the proposed method can guide the representations to maintain more spatial context and facilitate the attention on the essential visual regions for reasoning. We achieve the state-of-the-art results on VCR and two other vision-and-language reasoning tasks VQA, and NLVR.
Electric vehicle (EV) adoption in long-distance logistics faces challenges such as range anxiety and uneven distribution of charging stations. Two pivotal questions emerge: How can EVs be efficiently routed in a charging network considering range limits, charging speeds and prices? And, can the existing charging infrastructure sustain the increasing demand for EVs in long-distance logistics? This paper addresses these questions by introducing a novel theoretical and computational framework to study the EV network flow problems. We present an EV network flow model that incorporates range constraints and nonlinear charging rates, and identify conditions under which polynomial-time solutions can be obtained for optimal single EV routing, maximum flow, and minimum-cost flow problems. Our findings provide insights for optimizing EV routing in logistics, ensuring an efficient and sustainable future.
Ultrasound (US) imaging is widely used in diagnosing and staging abdominal diseases due to its lack of non-ionizing radiation and prevalent availability. However, significant inter-operator variability and inconsistent image acquisition hinder the widespread adoption of extensive screening programs. Robotic ultrasound systems have emerged as a promising solution, offering standardized acquisition protocols and the possibility of automated acquisition. Additionally, these systems enable access to 3D data via robotic tracking, enhancing volumetric reconstruction for improved ultrasound interpretation and precise disease diagnosis. However, the interpretability of 3D US reconstruction of abdominal images can be affected by the patient's breathing motion. This study introduces a method to compensate for breathing motion in 3D US compounding by leveraging implicit neural representations. Our approach employs a robotic ultrasound system for automated screenings. To demonstrate the method's effectiveness, we evaluate our proposed method for the diagnosis and monitoring of abdominal aorta aneurysms as a representative use case. Our experiments demonstrate that our proposed pipeline facilitates robust automated robotic acquisition, mitigating artifacts from breathing motion, and yields smoother 3D reconstructions for enhanced screening and medical diagnosis.
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.
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