We introduce CartiMorph, a framework for automated knee articular cartilage morphometrics. It takes an image as input and generates quantitative metrics for cartilage subregions, including the percentage of full-thickness cartilage loss (FCL), mean thickness, surface area, and volume. CartiMorph leverages the power of deep learning models for hierarchical image feature representation. Deep learning models were trained and validated for tissue segmentation, template construction, and template-to-image registration. We established methods for surface-normal-based cartilage thickness mapping, FCL estimation, and rule-based cartilage parcellation. Our cartilage thickness map showed less error in thin and peripheral regions. We evaluated the effectiveness of the adopted segmentation model by comparing the quantitative metrics obtained from model segmentation and those from manual segmentation. The root-mean-squared deviation of the FCL measurements was less than 8%, and strong correlations were observed for the mean thickness (Pearson's correlation coefficient $\rho \in [0.82,0.97]$), surface area ($\rho \in [0.82,0.98]$) and volume ($\rho \in [0.89,0.98]$) measurements. We compared our FCL measurements with those from a previous study and found that our measurements deviated less from the ground truths. We observed superior performance of the proposed rule-based cartilage parcellation method compared with the atlas-based approach. CartiMorph has the potential to promote imaging biomarkers discovery for knee osteoarthritis.
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The Conformer has become the most popular encoder model for automatic speech recognition (ASR). It adds convolution modules to a transformer to learn both local and global dependencies. In this work we describe a faster, more memory-efficient, and better-performing transformer, called Zipformer. Modeling changes include: 1) a U-Net-like encoder structure where middle stacks operate at lower frame rates; 2) reorganized block structure with more modules, within which we re-use attention weights for efficiency; 3) a modified form of LayerNorm called BiasNorm allows us to retain some length information; 4) new activation functions SwooshR and SwooshL work better than Swish. We also propose a new optimizer, called ScaledAdam, which scales the update by each tensor's current scale to keep the relative change about the same, and also explictly learns the parameter scale. It achieves faster convergence and better performance than Adam. Extensive experiments on LibriSpeech, Aishell-1, and WenetSpeech datasets demonstrate the effectiveness of our proposed Zipformer over other state-of-the-art ASR models. Our code is publicly available at //github.com/k2-fsa/icefall.
The Graded of Membership (GoM) model is a powerful tool for inferring latent classes in categorical data, which enables subjects to belong to multiple latent classes. However, its application is limited to categorical data with nonnegative integer responses, making it inappropriate for datasets with continuous or negative responses. To address this limitation, this paper proposes a novel model named the Weighted Grade of Membership (WGoM) model. Compared with GoM, our WGoM relaxes GoM's distribution constraint on the generation of a response matrix and it is more general than GoM. We then propose an algorithm to estimate the latent mixed memberships and the other WGoM parameters. We derive the error bounds of the estimated parameters and show that the algorithm is statistically consistent. The algorithmic performance is validated in both synthetic and real-world datasets. The results demonstrate that our algorithm is accurate and efficient, indicating its high potential for practical applications. This paper makes a valuable contribution to the literature by introducing a novel model that extends the applicability of the GoM model and provides a more flexible framework for analyzing categorical data with weighted responses.
Recently, a myriad of conditional image generation and editing models have been developed to serve different downstream tasks, including text-to-image generation, text-guided image editing, subject-driven image generation, control-guided image generation, etc. However, we observe huge inconsistencies in experimental conditions: datasets, inference, and evaluation metrics - render fair comparisons difficult. This paper proposes ImagenHub, which is a one-stop library to standardize the inference and evaluation of all the conditional image generation models. Firstly, we define seven prominent tasks and curate high-quality evaluation datasets for them. Secondly, we built a unified inference pipeline to ensure fair comparison. Thirdly, we design two human evaluation scores, i.e. Semantic Consistency and Perceptual Quality, along with comprehensive guidelines to evaluate generated images. We train expert raters to evaluate the model outputs based on the proposed metrics. Our human evaluation achieves a high inter-worker agreement of Krippendorff's alpha on 76% models with a value higher than 0.4. We comprehensively evaluated a total of around 30 models and observed three key takeaways: (1) the existing models' performance is generally unsatisfying except for Text-guided Image Generation and Subject-driven Image Generation, with 74% models achieving an overall score lower than 0.5. (2) we examined the claims from published papers and found 83% of them hold with a few exceptions. (3) None of the existing automatic metrics has a Spearman's correlation higher than 0.2 except subject-driven image generation. Moving forward, we will continue our efforts to evaluate newly published models and update our leaderboard to keep track of the progress in conditional image generation.
Finding the optimal design of experiments in the Bayesian setting typically requires estimation and optimization of the expected information gain functional. This functional consists of one outer and one inner integral, separated by the logarithm function applied to the inner integral. When the mathematical model of the experiment contains uncertainty about the parameters of interest and nuisance uncertainty, (i.e., uncertainty about parameters that affect the model but are not themselves of interest to the experimenter), two inner integrals must be estimated. Thus, the already considerable computational effort required to determine good approximations of the expected information gain is increased further. The Laplace approximation has been applied successfully in the context of experimental design in various ways, and we propose two novel estimators featuring the Laplace approximation to alleviate the computational burden of both inner integrals considerably. The first estimator applies Laplace's method followed by a Laplace approximation, introducing a bias. The second estimator uses two Laplace approximations as importance sampling measures for Monte Carlo approximations of the inner integrals. Both estimators use Monte Carlo approximation for the remaining outer integral estimation. We provide three numerical examples demonstrating the applicability and effectiveness of our proposed estimators.
The ability of Deep Learning to process and extract relevant information in complex brain dynamics from raw EEG data has been demonstrated in various recent works. Deep learning models, however, have also been shown to perform best on large corpora of data. When processing EEG, a natural approach is to combine EEG datasets from different experiments to train large deep-learning models. However, most EEG experiments use custom channel montages, requiring the data to be transformed into a common space. Previous methods have used the raw EEG signal to extract features of interest and focused on using a common feature space across EEG datasets. While this is a sensible approach, it underexploits the potential richness of EEG raw data. Here, we explore using spatial attention applied to EEG electrode coordinates to perform channel harmonization of raw EEG data, allowing us to train deep learning on EEG data using different montages. We test this model on a gender classification task. We first show that spatial attention increases model performance. Then, we show that a deep learning model trained on data using different channel montages performs significantly better than deep learning models trained on fixed 23- and 128-channel data montages.
We present a versatile open-source pipeline for simulating inhomogeneous reaction-diffusion processes in highly resolved, image-based geometries of porous media with reactive boundaries. Resolving realistic pore-scale geometries in numerical models is challenging and computationally demanding, as the scale differences between the sizes of the interstitia and the whole system can lead to prohibitive memory requirements. The present pipeline combines a level-set method with geometry-adapted sparse block grids on GPUs to efficiently simulate reaction-diffusion processes in image-based geometries. We showcase the method by applying it to fertilizer diffusion in soil, heat transfer in porous ceramics, and determining effective diffusion coefficients and tortuosity. The present approach enables solving reaction-diffusion partial differential equations in real-world geometries applicable to porous media across fields such as engineering, environmental science, and biology.
Achieving accurate approximations to solutions of large linear systems is crucial, especially when those systems utilize real-world data. A consequence of using real-world data is that there will inevitably be missingness. Current approaches for dealing with missing data, such as deletion and imputation, can introduce bias. Recent studies proposed an adaptation of stochastic gradient descent (SGD) in specific missing-data models. In this work, we propose a new algorithm, $\ell$-tuple mSGD, for the setting in which data is missing in a block-wise, tuple pattern. We prove that our proposed method uses unbiased estimates of the gradient of the least squares objective in the presence of tuple missing data. We also draw connections between $\ell$-tuple mSGD and previously established SGD-type methods for missing data. Furthermore, we prove our algorithm converges when using updating step sizes and empirically demonstrate the convergence of $\ell$-tuple mSGD on synthetic data. Lastly, we evaluate $\ell$-tuple mSGD applied to real-world continuous glucose monitoring (CGM) device data.
Generative AI has seen remarkable growth over the past few years, with diffusion models being state-of-the-art for image generation. This study investigates the use of diffusion models in generating artificial data generation for electronic circuits for enhancing the accuracy of subsequent machine learning models in tasks such as performance assessment, design, and testing when training data is usually known to be very limited. We utilize simulations in the HSPICE design environment with 22nm CMOS technology nodes to obtain representative real training data for our proposed diffusion model. Our results demonstrate the close resemblance of synthetic data using diffusion model to real data. We validate the quality of generated data, and demonstrate that data augmentation certainly effective in predictive analysis of VLSI design for digital circuits.
Classification of unlabeled data is usually achieved by supervised learning from labeled samples. Although there exist many sophisticated supervised machine learning methods that can predict the missing labels with a high level of accuracy, they often lack the required transparency in situations where it is important to provide interpretable results and meaningful measures of confidence. Body fluid classification of forensic casework data is the case in point. We develop a new Biclustering Dirichlet Process for Class-assignment with Random Matrices (BDP-CaRMa), with a three-level hierarchy of clustering, and a model-based approach to classification that adapts to block structure in the data matrix. As the class labels of some observations are missing, the number of rows in the data matrix for each class is unknown. BDP-CaRMa handles this and extends existing biclustering methods by simultaneously biclustering multiple matrices each having a randomly variable number of rows. We demonstrate our method by applying it to the motivating problem, which is the classification of body fluids based on mRNA profiles taken from crime scenes. The analyses of casework-like data show that our method is interpretable and produces well-calibrated posterior probabilities. Our model can be more generally applied to other types of data with a similar structure to the forensic data.
We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.
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