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Automatic brain tumor segmentation in 2D intra-operative ultrasound images using MRI tumor annotations
Faanes, Mathilde, Helland, Ragnhild Holden, Solheim, Ole, Reinertsen, Ingerid
Automatic segmentation of brain tumors in intra-operative ultrasound (iUS) images could facilitate localization of tumor tissue during resection surgery. The lack of large annotated datasets limits the current models performances. In this paper, we investigate the use of tumor annotations in pre-operative MRI images, which are more easily accessible than annotations in iUS images, for training of deep learning models for iUS brain tumor segmentation. We used 180 annotated pre-operative MRI images with corresponding unannotated iUS images, and 29 annotated iUS images. Image registration was performed to transfer the MRI annotations to the corresponding iUS images before training models with the nnU-Net framework. To validate the use of MRI labels, the models were compared to a model trained with only US annotated tumors, and a model with both US and MRI annotated tumors. In addition, the results were compared to annotations validated by an expert neurosurgeon on the same test set to measure inter-observer variability. The results showed similar performance for a model trained with only MRI annotated tumors, compared to a model trained with only US annotated tumors. The model trained using both modalities obtained slightly better results with an average Dice score of 0.62, where external expert annotations achieved a score of 0.67. The results also showed that the deep learning models were comparable to expert annotation for larger tumors (> 200 mm2), but perform clearly worse for smaller tumors (< 200 mm2). This shows that MRI tumor annotations can be used as a substitute for US tumor annotations to train a deep learning model for automatic brain tumor segmentation in intra-operative ultrasound images. Small tumors is a limitation for the current models and will be the focus of future work. The main models are available here: https://github.com/mathildefaanes/us_brain_tumor_segmentation.
MBD: Multi b-value Denoising of Diffusion Magnetic Resonance Images
Jurek, Jakub, Materka, Andrzej, Ludwisiak, Kamil, Majos, Agata, Szczepankiewicz, Filip
We propose a novel approach to denoising diffusion magnetic resonance images (dMRI) using convolutional neural networks, that exploits the benefits of data acquired at multiple b-values to offset the need for many redundant observations. Denoising is especially relevant in dMRI since noise can have a deleterious impact on both quantification accuracy and image preprocessing. The most successful methods proposed to date, like Marchenko-Pastur Principal Component Analysis (MPPCA) denoising, are tailored to diffusion-weighting repeated for many encoding directions. They exploit high redundancy of the dataset that oversamples the diffusion-encoding direction space, since many directions have collinear components. However, there are many dMRI techniques that do not entail a large number of encoding directions or repetitions, and are therefore less suited to this approach. For example, clinical dMRI exams may include as few as three encoding directions, with low or negligible data redundancy across directions. Moreover, promising new dMRI approaches, like spherical b-tensor encoding (STE), benefit from high b-values while sensitizing the signal to diffusion along all directions in just a single shot. We introduce a convolutional neural network approach that we call multi-b-value-based denoising (MBD). MBD exploits the similarity in diffusion-weighted images (DWI) across different b-values but along the same diffusion encoding direction. It allows denoising of diffusion images with high noise variance while avoiding blurring, and using just a small number input images.
Benign Overfitting in Single-Head Attention
Magen, Roey, Shang, Shuning, Xu, Zhiwei, Frei, Spencer, Hu, Wei, Vardi, Gal
The phenomenon of benign overfitting, where a trained neural network perfectly fits noisy training data but still achieves near-optimal test performance, has been extensively studied in recent years for linear models and fully-connected/convolutional networks. In this work, we study benign overfitting in a single-head softmax attention model, which is the fundamental building block of Transformers. We prove that under appropriate conditions, the model exhibits benign overfitting in a classification setting already after two steps of gradient descent. Moreover, we show conditions where a minimum-norm/maximum-margin interpolator exhibits benign overfitting. We study how the overfitting behavior depends on the signal-to-noise ratio (SNR) of the data distribution, namely, the ratio between norms of signal and noise tokens, and prove that a sufficiently large SNR is both necessary and sufficient for benign overfitting.
DIFFnet: Diffusion parameter mapping network generalized for input diffusion gradient schemes and bvalues
Park, Juhung, Jung, Woojin, Choi, Eun-Jung, Oh, Se-Hong, Shin, Dongmyung, An, Hongjun, Lee, Jongho
In MRI, deep neural networks have been proposed to reconstruct diffusion model parameters. However, the inputs of the networks were designed for a specific diffusion gradient scheme (i.e., diffusion gradient directions and numbers) and a specific b-value that are the same as the training data. In this study, a new deep neural network, referred to as DIFFnet, is developed to function as a generalized reconstruction tool of the diffusion-weighted signals for various gradient schemes and b-values. For generalization, diffusion signals are normalized in a q-space and then projected and quantized, producing a matrix (Qmatrix) as an input for the network. To demonstrate the validity of this approach, DIFFnet is evaluated for diffusion tensor imaging (DIFFnetDTI) and for neurite orientation dispersion and density imaging (DIFFnetNODDI). In each model, two datasets with different gradient schemes and b-values are tested. The results demonstrate accurate reconstruction of the diffusion parameters at substantially reduced processing time (approximately 8.7 times and 2240 times faster processing time than conventional methods in DTI and NODDI, respectively; less than 4% mean normalized root-mean-square errors (NRMSE) in DTI and less than 8% in NODDI). The generalization capability of the networks was further validated using reduced numbers of diffusion signals from the datasets. Different from previously proposed deep neural networks, DIFFnet does not require any specific gradient scheme and b-value for its input. As a result, it can be adopted as an online reconstruction tool for various complex diffusion imaging.
Breaking the Memory Wall for AI Chip with a New Dimension
Tam, Eugene, Jiang, Shenfei, Duan, Paul, Meng, Shawn, Pang, Yue, Huang, Cayden, Han, Yi, Xie, Jacke, Cui, Yuanjun, Yu, Jinsong, Lu, Minggui
Recent advancements in deep learning have led to the widespread adoption of artificial intelligence (AI) in applications such as computer vision and natural language processing. As neural networks become deeper and larger, AI modeling demands outstrip the capabilities of conventional chip architectures. Memory bandwidth falls behind processing power. Energy consumption comes to dominate the total cost of ownership. Currently, memory capacity is insufficient to support the most advanced NLP models. In this work, we present a 3D AI chip, called Sunrise, with near-memory computing architecture to address these three challenges. This distributed, near-memory computing architecture allows us to tear down the performance-limiting memory wall with an abundance of data bandwidth. We achieve the same level of energy efficiency on 40nm technology as competing chips on 7nm technology. By moving to similar technologies as other AI chips, we project to achieve more than ten times the energy efficiency, seven times the performance of the current state-of-the-art chips, and twenty times of memory capacity as compared with the best chip in each benchmark.
Implicit Modeling with Uncertainty Estimation for Intravoxel Incoherent Motion Imaging
Zhang, Lin, Vishnevskiy, Valery, Jakab, Andras, Goksel, Orcun
Intravoxel incoherent motion (IVIM) imaging allows contrast-agent free in vivo perfusion quantification with magnetic resonance imaging (MRI). However, its use is limited by typically low accuracy due to low signal-to-noise ratio (SNR) at large gradient encoding magnitudes as well as dephasing artefacts caused by subject motion, which is particularly challenging in fetal MRI. To mitigate this problem, we propose an implicit IVIM signal acquisition model with which we learn full posterior distribution of perfusion parameters using artificial neural networks. This posterior then encapsulates the uncertainty of the inferred parameter estimates, which we validate herein via numerical experiments with rejection-based Bayesian sampling. Compared to state-of-the-art IVIM estimation method of segmented least-squares fitting, our proposed approach improves parameter estimation accuracy by 65% on synthetic anisotropic perfusion data. On paired rescans of in vivo fetal MRI, our method increases repeatability of parameter estimation in placenta by 46%.
The New NVIDIA TITAN X: The Ultimate. Period. The Official NVIDIA Blog
"1 and 4 are marketing justifications to raise prices for those who are too myopic to see the truth of it." You don't understand the market. You think it's just a gaming card with a gimmick. Search for "inside the gpu clusters that power baidu's neural networks" and read the nextplatform article. Is it a coincidence that Jen-Hsun Huang presented the Titan X to Baidu Chief Scientist Andrew Ng and not to a game developer?
Building and Refining Abstract Planning Cases by Change of Representation Language
Abstraction is one of the most promising approaches to improve the performance of problem solvers. In several domains abstraction by dropping sentences of a domain description -- as used in most hierarchical planners -- has proven useful. In this paper we present examples which illustrate significant drawbacks of abstraction by dropping sentences. To overcome these drawbacks, we propose a more general view of abstraction involving the change of representation language. We have developed a new abstraction methodology and a related sound and complete learning algorithm that allows the complete change of representation language of planning cases from concrete to abstract. However, to achieve a powerful change of the representation language, the abstract language itself as well as rules which describe admissible ways of abstracting states must be provided in the domain model. This new abstraction approach is the core of Paris (Plan Abstraction and Refinement in an Integrated System), a system in which abstract planning cases are automatically learned from given concrete cases. An empirical study in the domain of process planning in mechanical engineering shows significant advantages of the proposed reasoning from abstract cases over classical hierarchical planning.