Daily Papers

Motion artefacts in magnetic resonance brain images can have a strong impact on diagnostic confidence. The assessment of MR image quality is fundamental before proceeding with the clinical diagnosis. Motion artefacts can alter the delineation of structures such as the brain, lesions or tumours and may require a repeat scan. Otherwise, an inaccurate (e.g. correct pathology but wrong severity) or incorrect diagnosis (e.g. wrong pathology) may occur. "Image quality assessment" as a fast, automated step right after scanning can assist in deciding if the acquired images are diagnostically sufficient. An automated image quality assessment based on the structural similarity index (SSIM) regression through a residual neural network is proposed in this work. Additionally, a classification into different groups - by subdividing with SSIM ranges - is evaluated. Importantly, this method predicts SSIM values of an input image in the absence of a reference ground truth image. The networks were able to detect motion artefacts, and the best performance for the regression and classification task has always been achieved with ResNet-18 with contrast augmentation. The mean and standard deviation of residuals' distribution were mu=-0.0009 and sigma=0.0139, respectively. Whilst for the classification task in 3, 5 and 10 classes, the best accuracies were 97, 95 and 89\%, respectively. The results show that the proposed method could be a tool for supporting neuro-radiologists and radiographers in evaluating image quality quickly.

Spatial-Spectral Mamba (SSM) improves computational efficiency and captures long-range dependencies, addressing Transformer limitations. However, traditional Mamba models overlook rich spectral information in HSIs and struggle with high dimensionality and sequential data. To address these issues, we propose the SSM with multi-head self-attention and token enhancement (MHSSMamba). This model integrates spectral and spatial information by enhancing spectral tokens and using multi-head attention to capture complex relationships between spectral bands and spatial locations. It also manages long-range dependencies and the sequential nature of HSI data, preserving contextual information across spectral bands. MHSSMamba achieved remarkable classification accuracies of 97.62\% on Pavia University, 96.92\% on the University of Houston, 96.85\% on Salinas, and 99.49\% on Wuhan-longKou datasets. The source code is available at https://github.com/MHassaanButt/MHA\_SS\_Mamba{GitHub}.

The use of the structural similarity index (SSIM) is widespread. For almost two decades, it has played a major role in image quality assessment in many different research disciplines. Clearly, its merits are indisputable in the research community. However, little deep scrutiny of this index has been performed. Contrary to popular belief, there are some interesting properties of SSIM that merit such scrutiny. In this paper, we analyze the mathematical factors of SSIM and show that it can generate results, in both synthetic and realistic use cases, that are unexpected, sometimes undefined, and nonintuitive. As a consequence, assessing image quality based on SSIM can lead to incorrect conclusions and using SSIM as a loss function for deep learning can guide neural network training in the wrong direction.

Accelerating MRI scans is one of the principal outstanding problems in the MRI research community. Towards this goal, we hosted the second fastMRI competition targeted towards reconstructing MR images with subsampled k-space data. We provided participants with data from 7,299 clinical brain scans (de-identified via a HIPAA-compliant procedure by NYU Langone Health), holding back the fully-sampled data from 894 of these scans for challenge evaluation purposes. In contrast to the 2019 challenge, we focused our radiologist evaluations on pathological assessment in brain images. We also debuted a new Transfer track that required participants to submit models evaluated on MRI scanners from outside the training set. We received 19 submissions from eight different groups. Results showed one team scoring best in both SSIM scores and qualitative radiologist evaluations. We also performed analysis on alternative metrics to mitigate the effects of background noise and collected feedback from the participants to inform future challenges. Lastly, we identify common failure modes across the submissions, highlighting areas of need for future research in the MRI reconstruction community.

Linear time-invariant state space models (SSM) are a classical model from engineering and statistics, that have recently been shown to be very promising in machine learning through the Structured State Space sequence model (S4). A core component of S4 involves initializing the SSM state matrix to a particular matrix called a HiPPO matrix, which was empirically important for S4's ability to handle long sequences. However, the specific matrix that S4 uses was actually derived in previous work for a particular time-varying dynamical system, and the use of this matrix as a time-invariant SSM had no known mathematical interpretation. Consequently, the theoretical mechanism by which S4 models long-range dependencies actually remains unexplained. We derive a more general and intuitive formulation of the HiPPO framework, which provides a simple mathematical interpretation of S4 as a decomposition onto exponentially-warped Legendre polynomials, explaining its ability to capture long dependencies. Our generalization introduces a theoretically rich class of SSMs that also lets us derive more intuitive S4 variants for other bases such as the Fourier basis, and explains other aspects of training S4, such as how to initialize the important timescale parameter. These insights improve S4's performance to 86% on the Long Range Arena benchmark, with 96% on the most difficult Path-X task.

Modeling multivariate time series is a well-established problem with a wide range of applications from healthcare to financial markets. Traditional State Space Models (SSMs) are classical approaches for univariate time series modeling due to their simplicity and expressive power to represent linear dependencies. They, however, have fundamentally limited expressive power to capture non-linear dependencies, are slow in practice, and fail to model the inter-variate information flow. Despite recent attempts to improve the expressive power of SSMs by using deep structured SSMs, the existing methods are either limited to univariate time series, fail to model complex patterns (e.g., seasonal patterns), fail to dynamically model the dependencies of variate and time dimensions, and/or are input-independent. We present Chimera that uses two input-dependent 2-D SSM heads with different discretization processes to learn long-term progression and seasonal patterns. To improve the efficiency of complex 2D recurrence, we present a fast training using a new 2-dimensional parallel selective scan. We further present and discuss 2-dimensional Mamba and Mamba-2 as the spacial cases of our 2D SSM. Our experimental evaluation shows the superior performance of Chimera on extensive and diverse benchmarks, including ECG and speech time series classification, long-term and short-term time series forecasting, and time series anomaly detection.

Dynamic imaging is a beneficial tool for interventions to assess physiological changes. Nonetheless during dynamic MRI, while achieving a high temporal resolution, the spatial resolution is compromised. To overcome this spatio-temporal trade-off, this research presents a super-resolution (SR) MRI reconstruction with prior knowledge based fine-tuning to maximise spatial information while reducing the required scan-time for dynamic MRIs. An U-Net based network with perceptual loss is trained on a benchmark dataset and fine-tuned using one subject-specific static high resolution MRI as prior knowledge to obtain high resolution dynamic images during the inference stage. 3D dynamic data for three subjects were acquired with different parameters to test the generalisation capabilities of the network. The method was tested for different levels of in-plane undersampling for dynamic MRI. The reconstructed dynamic SR results after fine-tuning showed higher similarity with the high resolution ground-truth, while quantitatively achieving statistically significant improvement. The average SSIM of the lowest resolution experimented during this research (6.25~\% of the k-space) before and after fine-tuning were 0.939 pm 0.008 and 0.957 pm 0.006 respectively. This could theoretically result in an acceleration factor of 16, which can potentially be acquired in less than half a second. The proposed approach shows that the super-resolution MRI reconstruction with prior-information can alleviate the spatio-temporal trade-off in dynamic MRI, even for high acceleration factors.

Transformers have widely adopted attention networks for sequence mixing and MLPs for channel mixing, playing a pivotal role in achieving breakthroughs across domains. However, recent literature highlights issues with attention networks, including low inductive bias and quadratic complexity concerning input sequence length. State Space Models (SSMs) like S4 and others (Hippo, Global Convolutions, liquid S4, LRU, Mega, and Mamba), have emerged to address the above issues to help handle longer sequence lengths. Mamba, while being the state-of-the-art SSM, has a stability issue when scaled to large networks for computer vision datasets. We propose SiMBA, a new architecture that introduces Einstein FFT (EinFFT) for channel modeling by specific eigenvalue computations and uses the Mamba block for sequence modeling. Extensive performance studies across image and time-series benchmarks demonstrate that SiMBA outperforms existing SSMs, bridging the performance gap with state-of-the-art transformers. Notably, SiMBA establishes itself as the new state-of-the-art SSM on ImageNet and transfer learning benchmarks such as Stanford Car and Flower as well as task learning benchmarks as well as seven time series benchmark datasets. The project page is available on this website ~https://github.com/badripatro/Simba.