This paper studies the open problem of conformalized entry prediction in a row/column-exchangeable matrix. The matrix setting presents novel and unique challenges, but there exists little work on this interesting topic. We meticulously define the problem, differentiate it from closely related problems, and rigorously delineate the boundary between achievable and impossible goals. We then propose two practical algorithms. The first method provides a fast emulation of the full conformal prediction, while the second method leverages the technique of algorithmic stability for acceleration. Both methods are computationally efficient and can effectively safeguard coverage validity in presence of arbitrary missing pattern. Further, we quantify the impact of missingness on prediction accuracy and establish fundamental limit results. Empirical evidence from synthetic and real-world data sets corroborates the superior performance of our proposed methods.
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Limited by imaging systems, the reconstruction of Magnetic Resonance Imaging (MRI) images from partial measurement is essential to medical imaging research. Benefiting from the diverse and complementary information of multi-contrast MR images in different imaging modalities, multi-contrast Super-Resolution (SR) reconstruction is promising to yield SR images with higher quality. In the medical scenario, to fully visualize the lesion, radiologists are accustomed to zooming the MR images at arbitrary scales rather than using a fixed scale, as used by most MRI SR methods. In addition, existing multi-contrast MRI SR methods often require a fixed resolution for the reference image, which makes acquiring reference images difficult and imposes limitations on arbitrary scale SR tasks. To address these issues, we proposed an implicit neural representations based dual-arbitrary multi-contrast MRI super-resolution method, called Dual-ArbNet. First, we decouple the resolution of the target and reference images by a feature encoder, enabling the network to input target and reference images at arbitrary scales. Then, an implicit fusion decoder fuses the multi-contrast features and uses an Implicit Decoding Function~(IDF) to obtain the final MRI SR results. Furthermore, we introduce a curriculum learning strategy to train our network, which improves the generalization and performance of our Dual-ArbNet. Extensive experiments in two public MRI datasets demonstrate that our method outperforms state-of-the-art approaches under different scale factors and has great potential in clinical practice.
The brain's white matter (WM) undergoes developmental and degenerative processes during the human lifespan. To investigate the relationship between WM anatomical regions and age, we study diffusion magnetic resonance imaging tractography that is finely parcellated into fiber clusters in the deep, superficial, and cerebellar WM. We propose a deep-learning-based age prediction model that leverages large convolutional kernels and inverted bottlenecks. We improve performance using novel discrete multi-faceted mix data augmentation and a novel prior-knowledge-based loss function that encourages age predictions in the expected range. We study a dataset of 965 healthy young adults (22-37 years) derived from the Human Connectome Project (HCP). Experimental results demonstrate that the proposed model achieves a mean absolute error of 2.59 years and outperforms compared methods. We find that the deep WM is the most informative for age prediction in this cohort, while the superficial WM is the least informative. Overall, the most predictive WM tracts are the thalamo-frontal tract from the deep WM and the intracerebellar input and Purkinje tract from the cerebellar WM.
The paradigm of self-supervision focuses on representation learning from raw data without the need of labor-consuming annotations, which is the main bottleneck of current data-driven methods. Self-supervision tasks are often used to pre-train a neural network with a large amount of unlabeled data and extract generic features of the dataset. The learned model is likely to contain useful information which can be transferred to the downstream main task and improve performance compared to random parameter initialization. In this paper, we propose a new self-supervision task called source identification (SI), which is inspired by the classic blind source separation problem. Synthetic images are generated by fusing multiple source images and the network's task is to reconstruct the original images, given the fused images. A proper understanding of the image content is required to successfully solve the task. We validate our method on two medical image segmentation tasks: brain tumor segmentation and white matter hyperintensities segmentation. The results show that the proposed SI task outperforms traditional self-supervision tasks for dense predictions including inpainting, pixel shuffling, intensity shift, and super-resolution. Among variations of the SI task fusing images of different types, fusing images from different patients performs best.
In this paper, we study the problems of detection and recovery of hidden submatrices with elevated means inside a large Gaussian random matrix. We consider two different structures for the planted submatrices. In the first model, the planted matrices are disjoint, and their row and column indices can be arbitrary. Inspired by scientific applications, the second model restricts the row and column indices to be consecutive. In the detection problem, under the null hypothesis, the observed matrix is a realization of independent and identically distributed standard normal entries. Under the alternative, there exists a set of hidden submatrices with elevated means inside the same standard normal matrix. Recovery refers to the task of locating the hidden submatrices. For both problems, and for both models, we characterize the statistical and computational barriers by deriving information-theoretic lower bounds, designing and analyzing algorithms matching those bounds, and proving computational lower bounds based on the low-degree polynomials conjecture. In particular, we show that the space of the model parameters (i.e., number of planted submatrices, their dimensions, and elevated mean) can be partitioned into three regions: the impossible regime, where all algorithms fail; the hard regime, where while detection or recovery are statistically possible, we give some evidence that polynomial-time algorithm do not exist; and finally the easy regime, where polynomial-time algorithms exist.
Conformal prediction has emerged as a rigorous means of providing deep learning models with reliable uncertainty estimates and safety guarantees. Yet, its performance is known to degrade under distribution shift and long-tailed class distributions, which are often present in real world applications. Here, we characterize the performance of several post-hoc and training-based conformal prediction methods under these settings, providing the first empirical evaluation on large-scale datasets and models. We show that across numerous conformal methods and neural network families, performance greatly degrades under distribution shifts violating safety guarantees. Similarly, we show that in long-tailed settings the guarantees are frequently violated on many classes. Understanding the limitations of these methods is necessary for deployment in real world and safety-critical applications.
Large language models(LLMs) have shown excellent text generation capabilities, but there is still much space for improvement in accuracy, sometimes with grammatical errors, semantic inaccuracies, and contextual incoherence, which seriously affect the reliability of the models. These problems may originate from the difficulties and limitations encountered in the pattern extraction stage of large language models. How to utilize the generative power of large language models to generate as many possible patterns that help solve problems and find the optimal patterns from them, so as to use patterns to guide large language models to generate good content, has become a current research hotspot. In this paper, we propose a pattern extraction and selection framework, PatternGPT, which generates rich patterns through the extraction ability of large language models and draws on the idea of federation learning, where multiple agents collaborate with each other to generate diverse patterns. High-quality patterns are selected by defining criteria and optimization algorithms to personalize the guidance of the model generation process. PatternGPT has the advantages of generating diverse and useful patterns, extending relevant knowledge, facilitating efficient pattern use and transfer, and optimizing the quality of generated results and user experience, which provides an effective method for optimizing the text generation capability of large language models and is expected to drive further development in the field of intelligent dialogue and content generation. It is expected to promote further development in the field of intelligent dialogue and content generation.
Variable selection is a procedure to attain the truly important predictors from inputs. Complex nonlinear dependencies and strong coupling pose great challenges for variable selection in high-dimensional data. In addition, real-world applications have increased demands for interpretability of the selection process. A pragmatic approach should not only attain the most predictive covariates, but also provide ample and easy-to-understand grounds for removing certain covariates. In view of these requirements, this paper puts forward an approach for transparent and nonlinear variable selection. In order to transparently decouple information within the input predictors, a three-step heuristic search is designed, via which the input predictors are grouped into four subsets: the relevant to be selected, and the uninformative, redundant, and conditionally independent to be removed. A nonlinear partial correlation coefficient is introduced to better identify the predictors which have nonlinear functional dependence with the response. The proposed method is model-free and the selected subset can be competent input for commonly used predictive models. Experiments demonstrate the superior performance of the proposed method against the state-of-the-art baselines in terms of prediction accuracy and model interpretability.
The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.
Recently many efforts have been devoted to applying graph neural networks (GNNs) to molecular property prediction which is a fundamental task for computational drug and material discovery. One of major obstacles to hinder the successful prediction of molecule property by GNNs is the scarcity of labeled data. Though graph contrastive learning (GCL) methods have achieved extraordinary performance with insufficient labeled data, most focused on designing data augmentation schemes for general graphs. However, the fundamental property of a molecule could be altered with the augmentation method (like random perturbation) on molecular graphs. Whereas, the critical geometric information of molecules remains rarely explored under the current GNN and GCL architectures. To this end, we propose a novel graph contrastive learning method utilizing the geometry of the molecule across 2D and 3D views, which is named GeomGCL. Specifically, we first devise a dual-view geometric message passing network (GeomMPNN) to adaptively leverage the rich information of both 2D and 3D graphs of a molecule. The incorporation of geometric properties at different levels can greatly facilitate the molecular representation learning. Then a novel geometric graph contrastive scheme is designed to make both geometric views collaboratively supervise each other to improve the generalization ability of GeomMPNN. We evaluate GeomGCL on various downstream property prediction tasks via a finetune process. Experimental results on seven real-life molecular datasets demonstrate the effectiveness of our proposed GeomGCL against state-of-the-art baselines.
We introduce an effective model to overcome the problem of mode collapse when training Generative Adversarial Networks (GAN). Firstly, we propose a new generator objective that finds it better to tackle mode collapse. And, we apply an independent Autoencoders (AE) to constrain the generator and consider its reconstructed samples as "real" samples to slow down the convergence of discriminator that enables to reduce the gradient vanishing problem and stabilize the model. Secondly, from mappings between latent and data spaces provided by AE, we further regularize AE by the relative distance between the latent and data samples to explicitly prevent the generator falling into mode collapse setting. This idea comes when we find a new way to visualize the mode collapse on MNIST dataset. To the best of our knowledge, our method is the first to propose and apply successfully the relative distance of latent and data samples for stabilizing GAN. Thirdly, our proposed model, namely Generative Adversarial Autoencoder Networks (GAAN), is stable and has suffered from neither gradient vanishing nor mode collapse issues, as empirically demonstrated on synthetic, MNIST, MNIST-1K, CelebA and CIFAR-10 datasets. Experimental results show that our method can approximate well multi-modal distribution and achieve better results than state-of-the-art methods on these benchmark datasets. Our model implementation is published here: //github.com/tntrung/gaan
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