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With the steady rise of the use of AI in bio-technical applications and the widespread adoption of genomics sequencing, an increasing amount of AI-based algorithms and tools is entering the research and production stage affecting critical decision-making streams like drug discovery and clinical outcomes. This paper demonstrates the vulnerability of AI models often utilized downstream tasks on recognized public genomics datasets. We undermine model robustness by deploying an attack that focuses on input transformation while mimicking the real data and confusing the model decision-making, ultimately yielding a pronounced deterioration in model performance. Further, we enhance our approach by generating poisoned data using a variational autoencoder-based model. Our empirical findings unequivocally demonstrate a decline in model performance, underscored by diminished accuracy and an upswing in false positives and false negatives. Furthermore, we analyze the resulting adversarial samples via spectral analysis yielding conclusions for countermeasures against such attacks.

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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: · 動態結構 · Learning · 可理解性 · 相關系數 ·
2024 年 3 月 2 日

Exploring molecular spaces is crucial for advancing our understanding of chemical properties and reactions, leading to groundbreaking innovations in materials science, medicine, and energy. This paper explores an approach for active learning in molecular discovery using Deep Kernel Learning (DKL), a novel approach surpassing the limits of classical Variational Autoencoders (VAEs). Employing the QM9 dataset, we contrast DKL with traditional VAEs, which analyze molecular structures based on similarity, revealing limitations due to sparse regularities in latent spaces. DKL, however, offers a more holistic perspective by correlating structure with properties, creating latent spaces that prioritize molecular functionality. This is achieved by recalculating embedding vectors iteratively, aligning with the experimental availability of target properties. The resulting latent spaces are not only better organized but also exhibit unique characteristics such as concentrated maxima representing molecular functionalities and a correlation between predictive uncertainty and error. Additionally, the formation of exclusion regions around certain compounds indicates unexplored areas with potential for groundbreaking functionalities. This study underscores DKL's potential in molecular research, offering new avenues for understanding and discovering molecular functionalities beyond classical VAE limitations.

Efficient and accurate extraction of microstructures in micrographs of materials is essential in process optimization and the exploration of structure-property relationships. Deep learning-based image segmentation techniques that rely on manual annotation are laborious and time-consuming and hardly meet the demand for model transferability and generalization on various source images. Segment Anything Model (SAM), a large visual model with powerful deep feature representation and zero-shot generalization capabilities, has provided new solutions for image segmentation. In this paper, we propose MatSAM, a general and efficient microstructure extraction solution based on SAM. A simple yet effective point-based prompt generation strategy is designed, grounded on the distribution and shape of microstructures. Specifically, in an unsupervised and training-free way, it adaptively generates prompt points for different microscopy images, fuses the centroid points of the coarsely extracted region of interest (ROI) and native grid points, and integrates corresponding post-processing operations for quantitative characterization of microstructures of materials. For common microstructures including grain boundary and multiple phases, MatSAM achieves superior zero-shot segmentation performance to conventional rule-based methods and is even preferable to supervised learning methods evaluated on 16 microscopy datasets whose micrographs are imaged by the optical microscope (OM) and scanning electron microscope (SEM). Especially, on 4 public datasets, MatSAM shows unexpected competitive segmentation performance against their specialist models. We believe that, without the need for human labeling, MatSAM can significantly reduce the cost of quantitative characterization and statistical analysis of extensive microstructures of materials, and thus accelerate the design of new materials.

Drawing inspiration from the success of diffusion models in various domains, numerous research papers proposed methods for adapting them to text data. Despite these efforts, none of them has managed to achieve the quality of the large language models. In this paper, we conduct a comprehensive analysis of key components of the text diffusion models and introduce a novel approach named Text Encoding Diffusion Model (TEncDM). Instead of the commonly used token embedding space, we train our model in the space of the language model encodings. Additionally, we propose to use a Transformer-based decoder that utilizes contextual information for text reconstruction. We also analyse self-conditioning and find that it increases the magnitude of the model outputs, allowing the reduction of the number of denoising steps at the inference stage. Evaluation of TEncDM on two downstream text generation tasks, QQP and XSum, demonstrates its superiority over existing non-autoregressive models.

We present a data structure to randomly sample rows from the Khatri-Rao product of several matrices according to the exact distribution of its leverage scores. Our proposed sampler draws each row in time logarithmic in the height of the Khatri-Rao product and quadratic in its column count, with persistent space overhead at most the size of the input matrices. As a result, it tractably draws samples even when the matrices forming the Khatri-Rao product have tens of millions of rows each. When used to sketch the linear least squares problems arising in CANDECOMP / PARAFAC tensor decomposition, our method achieves lower asymptotic complexity per solve than recent state-of-the-art methods. Experiments on billion-scale sparse tensors validate our claims, with our algorithm achieving higher accuracy than competing methods as the decomposition rank grows.

We present a novel approach to cooperative aerial transportation through a team of drones, using optimal control theory and a hierarchical control strategy. We assume the drones are connected to the payload through rigid attachments, essentially transforming the whole system into a larger flying object with "thrust modules" at the attachment locations of the drones. We investigate the optimal arrangement of the thrust modules around the payload, so that the resulting system is robust to disturbances. We choose the $\mathcal{H}_2$ norm as a measure of robustness, and propose an iterative optimization routine to compute the optimal layout of the vehicles around the object. We experimentally validate our approach using four drones and comparing the disturbance rejection performances achieved by two different layouts (the optimal one and a sub-optimal one), and observe that the results match our predictions.

Advancing robotic grasping and manipulation requires the ability to test algorithms and/or train learning models on large numbers of grasps. Towards the goal of more advanced grasping, we present the Grasp Reset Mechanism (GRM), a fully automated apparatus for conducting large-scale grasping trials. The GRM automates the process of resetting a grasping environment, repeatably placing an object in a fixed location and controllable 1-D orientation. It also collects data and swaps between multiple objects enabling robust dataset collection with no human intervention. We also present a standardized state machine interface for control, which allows for integration of most manipulators with minimal effort. In addition to the physical design and corresponding software, we include a dataset of 1,020 grasps. The grasps were created with a Kinova Gen3 robot arm and Robotiq 2F-85 Adaptive Gripper to enable training of learning models and to demonstrate the capabilities of the GRM. The dataset includes ranges of grasps conducted across four objects and a variety of orientations. Manipulator states, object pose, video, and grasp success data are provided for every trial.

In pace with developments in the research field of artificial intelligence, knowledge graphs (KGs) have attracted a surge of interest from both academia and industry. As a representation of semantic relations between entities, KGs have proven to be particularly relevant for natural language processing (NLP), experiencing a rapid spread and wide adoption within recent years. Given the increasing amount of research work in this area, several KG-related approaches have been surveyed in the NLP research community. However, a comprehensive study that categorizes established topics and reviews the maturity of individual research streams remains absent to this day. Contributing to closing this gap, we systematically analyzed 507 papers from the literature on KGs in NLP. Our survey encompasses a multifaceted review of tasks, research types, and contributions. As a result, we present a structured overview of the research landscape, provide a taxonomy of tasks, summarize our findings, and highlight directions for future work.

A fundamental goal of scientific research is to learn about causal relationships. However, despite its critical role in the life and social sciences, causality has not had the same importance in Natural Language Processing (NLP), which has traditionally placed more emphasis on predictive tasks. This distinction is beginning to fade, with an emerging area of interdisciplinary research at the convergence of causal inference and language processing. Still, research on causality in NLP remains scattered across domains without unified definitions, benchmark datasets and clear articulations of the remaining challenges. In this survey, we consolidate research across academic areas and situate it in the broader NLP landscape. We introduce the statistical challenge of estimating causal effects, encompassing settings where text is used as an outcome, treatment, or as a means to address confounding. In addition, we explore potential uses of causal inference to improve the performance, robustness, fairness, and interpretability of NLP models. We thus provide a unified overview of causal inference for the computational linguistics 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.

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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