PET Head Motion Estimation Using Supervised Deep Learning with Attention

Head movement poses a significant challenge in brain positron emission tomography (PET) imaging, resulting in image artifacts and tracer uptake quantification inaccuracies. Effective head motion estimation and correction are crucial for precise quantitative image analysis and accurate diagnosis of neurological disorders. Hardware-based motion tracking (HMT) has limited applicability in real-world clinical practice. To overcome this limitation, we propose a deep-learning head motion correction approach with cross-attention (DL-HMC++) to predict rigid head motion from one-second 3D PET raw data. DL-HMC++ is trained in a supervised manner by leveraging existing dynamic PET scans with gold-standard motion measurements from external HMT. We evaluate DL-HMC++ on two PET scanners (HRRT and mCT) and four radiotracers (18F-FDG, 18F-FPEB, 11C-UCB-J, and 11C-LSN3172176) to demonstrate the effectiveness and generalization of the approach in large cohort PET studies. Quantitative and qualitative results demonstrate that DL-HMC++ consistently outperforms state-of-the-art data-driven motion estimation methods, producing motion-free images with clear delineation of brain structures and reduced motion artifacts that are indistinguishable from gold-standard HMT. Brain region of interest standard uptake value analysis exhibits average difference ratios between DL-HMC++ and gold-standard HMT to be 1.2 plus-minus 0.5% for HRRT and 0.5 plus-minus 0.2% for mCT. DL-HMC++ demonstrates the potential for data-driven PET head motion correction to remove the burden of HMT, making motion correction accessible to clinical populations beyond research settings. The code is available at https://github.com/maxxxxxxcai/DL-HMC-TMI.

A Text-Image Fusion Method with Data Augmentation Capabilities for Referring Medical Image Segmentation

Deep learning relies heavily on data augmentation to mitigate limited data, especially in medical imaging. Recent multimodal learning integrates text and images for segmentation, known as referring or text-guided image segmentation. However, common augmentations like rotation and flipping disrupt spatial alignment between image and text, weakening performance. To address this, we propose an early fusion framework that combines text and visual features before augmentation, preserving spatial consistency. We also design a lightweight generator that projects text embeddings into visual space, bridging semantic gaps. Visualization of generated pseudo-images shows accurate region localization. Our method is evaluated on three medical imaging tasks and four segmentation frameworks, achieving state-of-the-art results. Code is publicly available on GitHub: https://github.com/11yxk/MedSeg_EarlyFusion.

CuMPerLay: Learning Cubical Multiparameter Persistence Vectorizations

We present CuMPerLay, a novel differentiable vectorization layer that enables the integration of Cubical Multiparameter Persistence (CMP) into deep learning pipelines. While CMP presents a natural and powerful way to topologically work with images, its use is hindered by the complexity of multifiltration structures as well as the vectorization of CMP. In face of these challenges, we introduce a new algorithm for vectorizing MP homologies of cubical complexes. Our CuMPerLay decomposes the CMP into a combination of individual, learnable single-parameter persistence, where the bifiltration functions are jointly learned. Thanks to the differentiability, its robust topological feature vectors can be seamlessly used within state-of-the-art architectures such as Swin Transformers. We establish theoretical guarantees for the stability of our vectorization under generalized Wasserstein metrics. Our experiments on benchmark medical imaging and computer vision datasets show the benefit CuMPerLay on classification and segmentation performance, particularly in limited-data scenarios. Overall, CuMPerLay offers a promising direction for integrating global structural information into deep networks for structured image analysis.

I-DCCRN-VAE: An Improved Deep Representation Learning Framework for Complex VAE-based Single-channel Speech Enhancement

Recently, a complex variational autoencoder (VAE)-based single-channel speech enhancement system based on the DCCRN architecture has been proposed. In this system, a noise suppression VAE (NSVAE) learns to extract clean speech representations from noisy speech using pretrained clean speech and noise VAEs with skip connections. In this paper, we improve DCCRN-VAE by incorporating three key modifications: 1) removing the skip connections in the pretrained VAEs to encourage more informative speech and noise latent representations; 2) using $\beta$-VAE in pretraining to better balance reconstruction and latent space regularization; and 3) a NSVAE generating both speech and noise latent representations. Experiments show that the proposed system achieves comparable performance as the DCCRN and DCCRN-VAE baselines on the matched DNS3 dataset but outperforms the baselines on mismatched datasets (WSJ0-QUT, Voicebank-DEMEND), demonstrating improved generalization ability. In addition, an ablation study shows that a similar performance can be achieved with classical fine-tuning instead of adversarial training, resulting in a simpler training pipeline.

Hybrid Explanation-Guided Learning for Transformer-Based Chest X-Ray Diagnosis

Transformer-based deep learning models have demonstrated exceptional performance in medical imaging by leveraging attention mechanisms for feature representation and interpretability. However, these models are prone to learning spurious correlations, leading to biases and limited generalization. While human-AI attention alignment can mitigate these issues, it often depends on costly manual supervision. In this work, we propose a Hybrid Explanation-Guided Learning (H-EGL) framework that combines self-supervised and human-guided constraints to enhance attention alignment and improve generalization. The self-supervised component of H-EGL leverages class-distinctive attention without relying on restrictive priors, promoting robustness and flexibility. We validate our approach on chest X-ray classification using the Vision Transformer (ViT), where H-EGL outperforms two state-of-the-art Explanation-Guided Learning (EGL) methods, demonstrating superior classification accuracy and generalization capability. Additionally, it produces attention maps that are better aligned with human expertise.

Clutch Control: An Attention-based Combinatorial Bandit for Efficient Mutation in JavaScript Engine Fuzzing

JavaScript engines are widely used in web browsers, PDF readers, and server-side applications. The rise in concern over their security has led to the development of several targeted fuzzing techniques. However, existing approaches use random selection to determine where to perform mutations in JavaScript code. We postulate that the problem of selecting better mutation targets is suitable for combinatorial bandits with a volatile number of arms. Thus, we propose CLUTCH, a novel deep combinatorial bandit that can observe variable length JavaScript test case representations, using an attention mechanism from deep learning. Furthermore, using Concrete Dropout, CLUTCH can dynamically adapt its exploration. We show that CLUTCH increases efficiency in JavaScript fuzzing compared to three state-of-the-art solutions by increasing the number of valid test cases and coverage-per-testcase by, respectively, 20.3% and 8.9% on average. In volatile and combinatorial settings we show that CLUTCH outperforms state-of-the-art bandits, achieving at least 78.1% and 4.1% less regret in volatile and combinatorial settings, respectively.

Zero-Shot CFC: Fast Real-World Image Denoising based on Cross-Frequency Consistency

Zero-shot denoisers address the dataset dependency of deep-learning-based denoisers, enabling the denoising of unseen single images. Nonetheless, existing zero-shot methods suffer from long training times and rely on the assumption of noise independence and a zero-mean property, limiting their effectiveness in real-world denoising scenarios where noise characteristics are more complicated. This paper proposes an efficient and effective method for real-world denoising, the Zero-Shot denoiser based on Cross-Frequency Consistency (ZSCFC), which enables training and denoising with a single noisy image and does not rely on assumptions about noise distribution. Specifically, image textures exhibit position similarity and content consistency across different frequency bands, while noise does not. Based on this property, we developed cross-frequency consistency loss and an ultralight network to realize image denoising. Experiments on various real-world image datasets demonstrate that our ZSCFC outperforms other state-of-the-art zero-shot methods in terms of computational efficiency and denoising performance.

Deep Attention-guided Adaptive Subsampling

Although deep neural networks have provided impressive gains in performance, these improvements often come at the cost of increased computational complexity and expense. In many cases, such as 3D volume or video classification tasks, not all slices or frames are necessary due to inherent redundancies. To address this issue, we propose a novel learnable subsampling framework that can be integrated into any neural network architecture. Subsampling, being a nondifferentiable operation, poses significant challenges for direct adaptation into deep learning models. While some works, have proposed solutions using the Gumbel-max trick to overcome the problem of non-differentiability, they fall short in a crucial aspect: they are only task-adaptive and not inputadaptive. Once the sampling mechanism is learned, it remains static and does not adjust to different inputs, making it unsuitable for real-world applications. To this end, we propose an attention-guided sampling module that adapts to inputs even during inference. This dynamic adaptation results in performance gains and reduces complexity in deep neural network models. We demonstrate the effectiveness of our method on 3D medical imaging datasets from MedMNIST3D as well as two ultrasound video datasets for classification tasks, one of them being a challenging in-house dataset collected under real-world clinical conditions.

Low-Field Magnetic Resonance Image Quality Enhancement using a Conditional Flow Matching Model

This paper introduces a novel framework for image quality transfer based on conditional flow matching (CFM). Unlike conventional generative models that rely on iterative sampling or adversarial objectives, CFM learns a continuous flow between a noise distribution and target data distributions through the direct regression of an optimal velocity field. We evaluate this approach in the context of low-field magnetic resonance imaging (LF-MRI), a rapidly emerging modality that offers affordable and portable scanning but suffers from inherently low signal-to-noise ratio and reduced diagnostic quality. Our framework is designed to reconstruct high-field-like MR images from their corresponding low-field inputs, thereby bridging the quality gap without requiring expensive infrastructure. Experiments demonstrate that CFM not only achieves state-of-the-art performance, but also generalizes robustly to both in-distribution and out-of-distribution data. Importantly, it does so while utilizing significantly fewer parameters than competing deep learning methods. These results underline the potential of CFM as a powerful and scalable tool for MRI reconstruction, particularly in resource-limited clinical environments.

Multitask finetuning and acceleration of chemical pretrained models for small molecule drug property prediction

Chemical pretrained models, sometimes referred to as foundation models, are receiving considerable interest for drug discovery applications. The general chemical knowledge extracted from self-supervised training has the potential to improve predictions for critical drug discovery endpoints, including on-target potency and ADMET properties. Multi-task learning has previously been successfully leveraged to improve predictive models. Here, we show that enabling multitasking in finetuning of chemical pretrained graph neural network models such as Kinetic GROVER Multi-Task (KERMT), an enhanced version of the GROVER model, and Knowledge-guided Pre-training of Graph Transformer (KGPT) significantly improves performance over non-pretrained graph neural network models. Surprisingly, we find that the performance improvement from finetuning KERMT in a multitask manner is most significant at larger data sizes. Additionally, we publish two multitask ADMET data splits to enable more accurate benchmarking of multitask deep learning methods for drug property prediction. Finally, we provide an accelerated implementation of the KERMT model on GitHub, unlocking large-scale pretraining, finetuning, and inference in industrial drug discovery workflows.