Batch effects are inevitable in large-scale metabolomics. Prior to formal data analysis, batch effect correction (BEC) is applied to prevent from obscuring biological variations, and batch effect evaluation (BEE) is used for correction assessment. However, existing BEE algorithms neglect covariances between the variables, and existing BEC algorithms might fail to adequately correct the covariances. Therefore, we resort to recent advancements in high-dimensional statistics, and respectively propose "quality control-based simultaneous tests (QC-ST)" and "covariance correction (CoCo)". Validated by the simulation data, QC-ST can simultaneously detect the statistical significance of QC samples' mean vectors and covariance matrices across different batches, and has a satisfactory statistical performance in empirical sizes, empirical powers, and computational speed. Then, we apply four QC-based BEC algorithms to two large cohort datasets, and find that extreme gradient boost (XGBoost) performs best in relative standard deviation (RSD) and dispersion-ratio (D-ratio). After prepositive BEC, if QC-ST still suggests that batch effects between some two batches are significant, CoCo should be implemented. And after CoCo (if necessary), the four metrics (i.e., RSD, D-ratio, classification performance, and QC-ST) might be further improved. In summary, under the guidance of QC-ST, we can develop a matching strategy to integrate multiple BEC algorithms more rationally and flexibly, and minimize batch effects for reliable biological conclusions.
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The success of AI models relies on the availability of large, diverse, and high-quality datasets, which can be challenging to obtain due to data scarcity, privacy concerns, and high costs. Synthetic data has emerged as a promising solution by generating artificial data that mimics real-world patterns. This paper provides an overview of synthetic data research, discussing its applications, challenges, and future directions. We present empirical evidence from prior art to demonstrate its effectiveness and highlight the importance of ensuring its factuality, fidelity, and unbiasedness. We emphasize the need for responsible use of synthetic data to build more powerful, inclusive, and trustworthy language models.
Multi-modal 3D scene understanding has gained considerable attention due to its wide applications in many areas, such as autonomous driving and human-computer interaction. Compared to conventional single-modal 3D understanding, introducing an additional modality not only elevates the richness and precision of scene interpretation but also ensures a more robust and resilient understanding. This becomes especially crucial in varied and challenging environments where solely relying on 3D data might be inadequate. While there has been a surge in the development of multi-modal 3D methods over past three years, especially those integrating multi-camera images (3D+2D) and textual descriptions (3D+language), a comprehensive and in-depth review is notably absent. In this article, we present a systematic survey of recent progress to bridge this gap. We begin by briefly introducing a background that formally defines various 3D multi-modal tasks and summarizes their inherent challenges. After that, we present a novel taxonomy that delivers a thorough categorization of existing methods according to modalities and tasks, exploring their respective strengths and limitations. Furthermore, comparative results of recent approaches on several benchmark datasets, together with insightful analysis, are offered. Finally, we discuss the unresolved issues and provide several potential avenues for future research.
Multi-modal fusion is a fundamental task for the perception of an autonomous driving system, which has recently intrigued many researchers. However, achieving a rather good performance is not an easy task due to the noisy raw data, underutilized information, and the misalignment of multi-modal sensors. In this paper, we provide a literature review of the existing multi-modal-based methods for perception tasks in autonomous driving. Generally, we make a detailed analysis including over 50 papers leveraging perception sensors including LiDAR and camera trying to solve object detection and semantic segmentation tasks. Different from traditional fusion methodology for categorizing fusion models, we propose an innovative way that divides them into two major classes, four minor classes by a more reasonable taxonomy in the view of the fusion stage. Moreover, we dive deep into the current fusion methods, focusing on the remaining problems and open-up discussions on the potential research opportunities. In conclusion, what we expect to do in this paper is to present a new taxonomy of multi-modal fusion methods for the autonomous driving perception tasks and provoke thoughts of the fusion-based techniques in the future.
Link prediction on knowledge graphs (KGs) is a key research topic. Previous work mainly focused on binary relations, paying less attention to higher-arity relations although they are ubiquitous in real-world KGs. This paper considers link prediction upon n-ary relational facts and proposes a graph-based approach to this task. The key to our approach is to represent the n-ary structure of a fact as a small heterogeneous graph, and model this graph with edge-biased fully-connected attention. The fully-connected attention captures universal inter-vertex interactions, while with edge-aware attentive biases to particularly encode the graph structure and its heterogeneity. In this fashion, our approach fully models global and local dependencies in each n-ary fact, and hence can more effectively capture associations therein. Extensive evaluation verifies the effectiveness and superiority of our approach. It performs substantially and consistently better than current state-of-the-art across a variety of n-ary relational benchmarks. Our code is publicly available.
Video instance segmentation (VIS) is the task that requires simultaneously classifying, segmenting and tracking object instances of interest in video. Recent methods typically develop sophisticated pipelines to tackle this task. Here, we propose a new video instance segmentation framework built upon Transformers, termed VisTR, which views the VIS task as a direct end-to-end parallel sequence decoding/prediction problem. Given a video clip consisting of multiple image frames as input, VisTR outputs the sequence of masks for each instance in the video in order directly. At the core is a new, effective instance sequence matching and segmentation strategy, which supervises and segments instances at the sequence level as a whole. VisTR frames the instance segmentation and tracking in the same perspective of similarity learning, thus considerably simplifying the overall pipeline and is significantly different from existing approaches. Without bells and whistles, VisTR achieves the highest speed among all existing VIS models, and achieves the best result among methods using single model on the YouTube-VIS dataset. For the first time, we demonstrate a much simpler and faster video instance segmentation framework built upon Transformers, achieving competitive accuracy. We hope that VisTR can motivate future research for more video understanding tasks.
Graph neural networks (GNNs) have been proven to be effective in various network-related tasks. Most existing GNNs usually exploit the low-frequency signals of node features, which gives rise to one fundamental question: is the low-frequency information all we need in the real world applications? In this paper, we first present an experimental investigation assessing the roles of low-frequency and high-frequency signals, where the results clearly show that exploring low-frequency signal only is distant from learning an effective node representation in different scenarios. How can we adaptively learn more information beyond low-frequency information in GNNs? A well-informed answer can help GNNs enhance the adaptability. We tackle this challenge and propose a novel Frequency Adaptation Graph Convolutional Networks (FAGCN) with a self-gating mechanism, which can adaptively integrate different signals in the process of message passing. For a deeper understanding, we theoretically analyze the roles of low-frequency signals and high-frequency signals on learning node representations, which further explains why FAGCN can perform well on different types of networks. Extensive experiments on six real-world networks validate that FAGCN not only alleviates the over-smoothing problem, but also has advantages over the state-of-the-arts.
Most object recognition approaches predominantly focus on learning discriminative visual patterns while overlooking the holistic object structure. Though important, structure modeling usually requires significant manual annotations and therefore is labor-intensive. In this paper, we propose to "look into object" (explicitly yet intrinsically model the object structure) through incorporating self-supervisions into the traditional framework. We show the recognition backbone can be substantially enhanced for more robust representation learning, without any cost of extra annotation and inference speed. Specifically, we first propose an object-extent learning module for localizing the object according to the visual patterns shared among the instances in the same category. We then design a spatial context learning module for modeling the internal structures of the object, through predicting the relative positions within the extent. These two modules can be easily plugged into any backbone networks during training and detached at inference time. Extensive experiments show that our look-into-object approach (LIO) achieves large performance gain on a number of benchmarks, including generic object recognition (ImageNet) and fine-grained object recognition tasks (CUB, Cars, Aircraft). We also show that this learning paradigm is highly generalizable to other tasks such as object detection and segmentation (MS COCO). Project page: //github.com/JDAI-CV/LIO.
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.
Top-down visual attention mechanisms have been used extensively in image captioning and visual question answering (VQA) to enable deeper image understanding through fine-grained analysis and even multiple steps of reasoning. In this work, we propose a combined bottom-up and top-down attention mechanism that enables attention to be calculated at the level of objects and other salient image regions. This is the natural basis for attention to be considered. Within our approach, the bottom-up mechanism (based on Faster R-CNN) proposes image regions, each with an associated feature vector, while the top-down mechanism determines feature weightings. Applying this approach to image captioning, our results on the MSCOCO test server establish a new state-of-the-art for the task, achieving CIDEr / SPICE / BLEU-4 scores of 117.9, 21.5 and 36.9, respectively. Demonstrating the broad applicability of the method, applying the same approach to VQA we obtain first place in the 2017 VQA Challenge.
While existing machine learning models have achieved great success for sentiment classification, they typically do not explicitly capture sentiment-oriented word interaction, which can lead to poor results for fine-grained analysis at the snippet level (a phrase or sentence). Factorization Machine provides a possible approach to learning element-wise interaction for recommender systems, but they are not directly applicable to our task due to the inability to model contexts and word sequences. In this work, we develop two Position-aware Factorization Machines which consider word interaction, context and position information. Such information is jointly encoded in a set of sentiment-oriented word interaction vectors. Compared to traditional word embeddings, SWI vectors explicitly capture sentiment-oriented word interaction and simplify the parameter learning. Experimental results show that while they have comparable performance with state-of-the-art methods for document-level classification, they benefit the snippet/sentence-level sentiment analysis.
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