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The Segment Anything Model (SAM) has recently emerged as a groundbreaking model in the field of image segmentation. Nevertheless, both the original SAM and its medical adaptations necessitate slice-by-slice annotations, which directly increase the annotation workload with the size of the dataset. We propose MedLSAM to address this issue, ensuring a constant annotation workload irrespective of dataset size and thereby simplifying the annotation process. Our model introduces a few-shot localization framework capable of localizing any target anatomical part within the body. To achieve this, we develop a Localize Anything Model for 3D Medical Images (MedLAM), utilizing two self-supervision tasks: relative distance regression (RDR) and multi-scale similarity (MSS) across a comprehensive dataset of 14,012 CT scans. We then establish a methodology for accurate segmentation by integrating MedLAM with SAM. By annotating only six extreme points across three directions on a few templates, our model can autonomously identify the target anatomical region on all data scheduled for annotation. This allows our framework to generate a 2D bounding box for every slice of the image, which are then leveraged by SAM to carry out segmentations. We conducted experiments on two 3D datasets covering 38 organs and found that MedLSAM matches the performance of SAM and its medical adaptations while requiring only minimal extreme point annotations for the entire dataset. Furthermore, MedLAM has the potential to be seamlessly integrated with future 3D SAM models, paving the way for enhanced performance. Our code is public at \href{//github.com/openmedlab/MedLSAM}{//github.com/openmedlab/MedLSAM}.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · MoDELS · Performer · 自動問答 · 變換 ·
2023 年 8 月 18 日

Foundation models (FMs) have exhibited remarkable performance across a wide range of downstream tasks in various domains. Nevertheless, general-purpose FMs often face challenges when confronted with domain-specific problems, due to their limited access to the proprietary training data in a particular domain. In life science, a large portion of biomedical knowledge is encapsulated within heterogeneous biological data, such as molecular structures, wet-lab experiment results, and knowledge bases, which exhibit significant modality gaps with human natural language. In this paper, we introduce BioMedGPT, an open multimodal generative pre-trained transformer (GPT) for biomedicine, to bridge the gap between biomedical data and natural language. BioMedGPT allows users to easily "communicate" with various biological modalities through free text, which is the first of its kind. BioMedGPT aligns different biological modalities with the text modality via a large generative language model, namely, BioMedGPT-LM. We publish BioMedGPT-10B, which unifies the feature spaces of molecules, proteins, and natural language via encoding and alignment. Through fine-tuning, BioMedGPT-10B outperforms or is on par with human and significantly larger general-purpose foundation models on the biomedical QA task. It also demonstrates promising performance in the molecule QA and protein QA tasks, which could greatly accelerate the discovery of new drugs and therapeutic targets. In addition, BioMedGPT-LM-7B is the first large generative language model based on Llama2 in the biomedical domain, therefore is commercial friendly. Both BioMedGPT-10B and BioMedGPT-LM-7B are open-sourced to the research community. We also publish the datasets that are meticulously curated for the alignment of multi-modalities, i.e., PubChemQA and UniProtQA. All the models, codes, and datasets are publicly available.

Large Language Models (LLMs) have emerged as powerful tools capable of accomplishing a broad spectrum of tasks. Their abilities span numerous areas, and one area where they have made a significant impact is in the domain of code generation. In this context, we view LLMs as mutation and crossover tools. Meanwhile, Quality-Diversity (QD) algorithms are known to discover diverse and robust solutions. By merging the code-generating abilities of LLMs with the diversity and robustness of QD solutions, we introduce LLMatic, a Neural Architecture Search (NAS) algorithm. While LLMs struggle to conduct NAS directly through prompts, LLMatic uses a procedural approach, leveraging QD for prompts and network architecture to create diverse and highly performant networks. We test LLMatic on the CIFAR-10 image classification benchmark, demonstrating that it can produce competitive networks with just $2,000$ searches, even without prior knowledge of the benchmark domain or exposure to any previous top-performing models for the benchmark.

Diffusion model (DM) has achieved SOTA performance by modeling the image synthesis process into a sequential application of a denoising network. However, different from image synthesis, image restoration (IR) has a strong constraint to generate results in accordance with ground-truth. Thus, for IR, traditional DMs running massive iterations on a large model to estimate whole images or feature maps is inefficient. To address this issue, we propose an efficient DM for IR (DiffIR), which consists of a compact IR prior extraction network (CPEN), dynamic IR transformer (DIRformer), and denoising network. Specifically, DiffIR has two training stages: pretraining and training DM. In pretraining, we input ground-truth images into CPEN$_{S1}$ to capture a compact IR prior representation (IPR) to guide DIRformer. In the second stage, we train the DM to directly estimate the same IRP as pretrained CPEN$_{S1}$ only using LQ images. We observe that since the IPR is only a compact vector, DiffIR can use fewer iterations than traditional DM to obtain accurate estimations and generate more stable and realistic results. Since the iterations are few, our DiffIR can adopt a joint optimization of CPEN$_{S2}$, DIRformer, and denoising network, which can further reduce the estimation error influence. We conduct extensive experiments on several IR tasks and achieve SOTA performance while consuming less computational costs. Code is available at \url{//github.com/Zj-BinXia/DiffIR}.

Graph Neural Network (GNN) has demonstrated extraordinary performance in classifying graph properties. However, due to the selection bias of training and testing data (e.g., training on small graphs and testing on large graphs, or training on dense graphs and testing on sparse graphs), distribution deviation is widespread. More importantly, we often observe \emph{hybrid structure distribution shift} of both scale and density, despite of one-sided biased data partition. The spurious correlations over hybrid distribution deviation degrade the performance of previous GNN methods and show large instability among different datasets. To alleviate this problem, we propose \texttt{OOD-GMixup} to jointly manipulate the training distribution with \emph{controllable data augmentation} in metric space. Specifically, we first extract the graph rationales to eliminate the spurious correlations due to irrelevant information. Secondly, we generate virtual samples with perturbation on graph rationale representation domain to obtain potential OOD training samples. Finally, we propose OOD calibration to measure the distribution deviation of virtual samples by leveraging Extreme Value Theory, and further actively control the training distribution by emphasizing the impact of virtual OOD samples. Extensive studies on several real-world datasets on graph classification demonstrate the superiority of our proposed method over state-of-the-art baselines.

With continuous progression of Moore's Law, integrated circuit (IC) device complexity is also increasing. Scanning Electron Microscope (SEM) image based extensive defect inspection and accurate metrology extraction are two main challenges in advanced node (2 nm and beyond) technology. Deep learning (DL) algorithm based computer vision approaches gained popularity in semiconductor defect inspection over last few years. In this research work, a new semiconductor defect inspection framework "SEMI-DiffusionInst" is investigated and compared to previous frameworks. To the best of the authors' knowledge, this work is the first demonstration to accurately detect and precisely segment semiconductor defect patterns by using a diffusion model. Different feature extractor networks as backbones and data sampling strategies are investigated towards achieving a balanced trade-off between precision and computing efficiency. Our proposed approach outperforms previous work on overall mAP and performs comparatively better or as per for almost all defect classes (per class APs). The bounding box and segmentation mAPs achieved by the proposed SEMI-DiffusionInst model are improved by 3.83% and 2.10%, respectively. Among individual defect types, precision on line collapse and thin bridge defects are improved approximately 15\% on detection task for both defect types. It has also been shown that by tuning inference hyperparameters, inference time can be improved significantly without compromising model precision. Finally, certain limitations and future work strategy to overcome them are discussed.

Chinese Spelling Check (CSC) refers to the detection and correction of spelling errors in Chinese texts. In practical application scenarios, it is important to make CSC models have the ability to correct errors across different domains. In this paper, we propose a retrieval-augmented spelling check framework called RSpell, which searches corresponding domain terms and incorporates them into CSC models. Specifically, we employ pinyin fuzzy matching to search for terms, which are combined with the input and fed into the CSC model. Then, we introduce an adaptive process control mechanism to dynamically adjust the impact of external knowledge on the model. Additionally, we develop an iterative strategy for the RSpell framework to enhance reasoning capabilities. We conducted experiments on CSC datasets in three domains: law, medicine, and official document writing. The results demonstrate that RSpell achieves state-of-the-art performance in both zero-shot and fine-tuning scenarios, demonstrating the effectiveness of the retrieval-augmented CSC framework. Our code is available at //github.com/47777777/Rspell.

Recently, Zero-Shot Node Classification (ZNC) has been an emerging and crucial task in graph data analysis. This task aims to predict nodes from unseen classes which are unobserved in the training process. Existing work mainly utilizes Graph Neural Networks (GNNs) to associate features' prototypes and labels' semantics thus enabling knowledge transfer from seen to unseen classes. However, the multi-faceted semantic orientation in the feature-semantic alignment has been neglected by previous work, i.e. the content of a node usually covers diverse topics that are relevant to the semantics of multiple labels. It's necessary to separate and judge the semantic factors that tremendously affect the cognitive ability to improve the generality of models. To this end, we propose a Knowledge-Aware Multi-Faceted framework (KMF) that enhances the richness of label semantics via the extracted KG (Knowledge Graph)-based topics. And then the content of each node is reconstructed to a topic-level representation that offers multi-faceted and fine-grained semantic relevancy to different labels. Due to the particularity of the graph's instance (i.e., node) representation, a novel geometric constraint is developed to alleviate the problem of prototype drift caused by node information aggregation. Finally, we conduct extensive experiments on several public graph datasets and design an application of zero-shot cross-domain recommendation. The quantitative results demonstrate both the effectiveness and generalization of KMF with the comparison of state-of-the-art baselines.

Generalization to out-of-distribution (OOD) data is a capability natural to humans yet challenging for machines to reproduce. This is because most learning algorithms strongly rely on the i.i.d.~assumption on source/target data, which is often violated in practice due to domain shift. Domain generalization (DG) aims to achieve OOD generalization by using only source data for model learning. Since first introduced in 2011, research in DG has made great progresses. In particular, intensive research in this topic has led to a broad spectrum of methodologies, e.g., those based on domain alignment, meta-learning, data augmentation, or ensemble learning, just to name a few; and has covered various vision applications such as object recognition, segmentation, action recognition, and person re-identification. In this paper, for the first time a comprehensive literature review is provided to summarize the developments in DG for computer vision over the past decade. Specifically, we first cover the background by formally defining DG and relating it to other research fields like domain adaptation and transfer learning. Second, we conduct a thorough review into existing methods and present a categorization based on their methodologies and motivations. Finally, we conclude this survey with insights and discussions on future research directions.

Graph Neural Networks (GNNs) are widely used for analyzing graph-structured data. Most GNN methods are highly sensitive to the quality of graph structures and usually require a perfect graph structure for learning informative embeddings. However, the pervasiveness of noise in graphs necessitates learning robust representations for real-world problems. To improve the robustness of GNN models, many studies have been proposed around the central concept of Graph Structure Learning (GSL), which aims to jointly learn an optimized graph structure and corresponding representations. Towards this end, in the presented survey, we broadly review recent progress of GSL methods for learning robust representations. Specifically, we first formulate a general paradigm of GSL, and then review state-of-the-art methods classified by how they model graph structures, followed by applications that incorporate the idea of GSL in other graph tasks. Finally, we point out some issues in current studies and discuss future directions.

Graph Neural Networks (GNNs) have been shown to be effective models for different predictive tasks on graph-structured data. Recent work on their expressive power has focused on isomorphism tasks and countable feature spaces. We extend this theoretical framework to include continuous features - which occur regularly in real-world input domains and within the hidden layers of GNNs - and we demonstrate the requirement for multiple aggregation functions in this context. Accordingly, we propose Principal Neighbourhood Aggregation (PNA), a novel architecture combining multiple aggregators with degree-scalers (which generalize the sum aggregator). Finally, we compare the capacity of different models to capture and exploit the graph structure via a novel benchmark containing multiple tasks taken from classical graph theory, alongside existing benchmarks from real-world domains, all of which demonstrate the strength of our model. With this work, we hope to steer some of the GNN research towards new aggregation methods which we believe are essential in the search for powerful and robust models.

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