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Aug 6

ISLES 2022: A multi-center magnetic resonance imaging stroke lesion segmentation dataset

Magnetic resonance imaging (MRI) is a central modality for stroke imaging. It is used upon patient admission to make treatment decisions such as selecting patients for intravenous thrombolysis or endovascular therapy. MRI is later used in the duration of hospital stay to predict outcome by visualizing infarct core size and location. Furthermore, it may be used to characterize stroke etiology, e.g. differentiation between (cardio)-embolic and non-embolic stroke. Computer based automated medical image processing is increasingly finding its way into clinical routine. Previous iterations of the Ischemic Stroke Lesion Segmentation (ISLES) challenge have aided in the generation of identifying benchmark methods for acute and sub-acute ischemic stroke lesion segmentation. Here we introduce an expert-annotated, multicenter MRI dataset for segmentation of acute to subacute stroke lesions. This dataset comprises 400 multi-vendor MRI cases with high variability in stroke lesion size, quantity and location. It is split into a training dataset of n=250 and a test dataset of n=150. All training data will be made publicly available. The test dataset will be used for model validation only and will not be released to the public. This dataset serves as the foundation of the ISLES 2022 challenge with the goal of finding algorithmic methods to enable the development and benchmarking of robust and accurate segmentation algorithms for ischemic stroke.

  • 25 authors
·
Jun 14, 2022

BAAI Cardiac Agent: An intelligent multimodal agent for automated reasoning and diagnosis of cardiovascular diseases from cardiac magnetic resonance imaging

Cardiac magnetic resonance (CMR) is a cornerstone for diagnosing cardiovascular disease. However, it remains underutilized due to complex, time-consuming interpretation across multi-sequences, phases, quantitative measures that heavily reliant on specialized expertise. Here, we present BAAI Cardiac Agent, a multimodal intelligent system designed for end-to-end CMR interpretation. The agent integrates specialized cardiac expert models to perform automated segmentation of cardiac structures, functional quantification, tissue characterization and disease diagnosis, and generates structured clinical reports within a unified workflow. Evaluated on CMR datasets from two hospitals (2413 patients) spanning 7-types of major cardiovascular diseases, the agent achieved an area under the receiver-operating-characteristic curve exceeding 0.93 internally and 0.81 externally. In the task of estimating left ventricular function indices, the results generated by this system for core parameters such as ejection fraction, stroke volume, and left ventricular mass are highly consistent with clinical reports, with Pearson correlation coefficients all exceeding 0.90. The agent outperformed state-of-the-art models in segmentation and diagnostic tasks, and generated clinical reports showing high concordance with expert radiologists (six readers across three experience levels). By dynamically orchestrating expert models for coordinated multimodal analysis, this agent framework enables accurate, efficient CMR interpretation and highlights its potentials for complex clinical imaging workflows. Code is available at https://github.com/plantain-herb/Cardiac-Agent.

  • 21 authors
·
Apr 4

NMRGym: A Comprehensive Benchmark for Nuclear Magnetic Resonance Based Molecular Structure Elucidation

Nuclear Magnetic Resonance (NMR) spectroscopy is the cornerstone of small-molecule structure elucidation. While deep learning has demonstrated significant potential in automating structure elucidation and spectral simulation, current progress is severely impeded by the reliance on synthetic datasets, which introduces significant domain shifts when applied to real-world experimental spectra. Furthermore, the lack of standardized evaluation protocols and rigorous data splitting strategies frequently leads to unfair comparisons and data leakage. To address these challenges, we introduce NMRGym, the largest and most comprehensive standardized dataset and benchmark derived from high-quality experimental NMR data to date. Comprising 269,999 unique molecules paired with high-fidelity ^1H and ^{13}C spectra, NMRGym bridges the critical gap between synthetic approximations and real-world diversity. We implement a strict quality control pipeline and unify data formats to ensure fair comparison. To strictly prevent data leakage, we enforce a scaffold-based split. Additionally, we provide fine-grained peak-atom level annotations to support future usage. Leveraging this resource, we establish a comprehensive evaluation suite covering diverse downstream tasks, including structure elucidation, functional group prediction from NMR, toxicity prediction from NMR, and spectral simulation, benchmarking representative state-of-the-art methodologies. Finally, we release an open-source leadboard with an automated leaderboard to foster community collaboration and standardize future research. The dataset, benchmark and leaderboard are publicly available at blue{https://AIMS-Lab-HKUSTGZ.github.io/NMRGym/}.

  • 8 authors
·
Jan 22

Quantum simulations of nuclear resonances with variational methods

The many-body nature of nuclear physics problems poses significant computational challenges. These challenges become even more pronounced when studying the resonance states of nuclear systems, which are governed by the non-Hermitian Hamiltonian. Quantum computing, particularly for quantum many-body systems, offers a promising alternative, especially within the constraints of current noisy intermediate-scale quantum (NISQ) devices. This work aims to simulate nuclear resonances using quantum algorithms by developing a variational framework compatible with non-Hermitian Hamiltonians and implementing it fully on a quantum simulator. We employ the complex scaling technique to extract resonance positions classically and adapt it for quantum simulations using a two-step algorithm. First, we transform the non-Hermitian Hamiltonian into a Hermitian form by using the energy variance as a cost function within a variational framework. Second, we perform theta-trajectory calculations to determine optimal resonance positions in the complex energy plane. To address resource constraints on NISQ devices, we utilize Gray Code (GC) encoding to reduce qubit requirements. We first validate our approach using a schematic potential model that mimics a nuclear potential, successfully reproducing known resonance energies with high fidelity. We then extend the method to a more realistic alpha-alpha nuclear potential and compute the resonance energies with a basis size of 16, using only four qubits. This study demonstrates, for the first time, that the complete theta-trajectory method can be implemented on a quantum computer without relying on any classical input beyond the Hamiltonian. The results establish a scalable and efficient quantum framework for simulating resonance phenomena in nuclear systems. This work represents a significant step toward quantum simulations of open quantum systems.

  • 3 authors
·
Apr 15, 2025

Memory as Resonance: A Biomimetic Architecture for Infinite Context Memory on Ergodic Phonetic Manifolds

The memory of contemporary Large Language Models is bound by a physical paradox: as they learn, they fill up. The linear accumulation (O(N)) of Key-Value states treats context as a warehouse of static artifacts, eventually forcing a destructive choice between amnesia and latency. We challenge this discrete orthodoxy, proposing that long-term memory is not the storage of items, but the persistence of a trajectory. We introduce Phonetic Trajectory Memory (PTM), a neuro-symbolic architecture that encodes language not as a sequence of tensors, but as a continuous path on an ergodic manifold governed by irrational rotation matrices. By decoupling the navigation (an invariant O(1) geometric signal) from the reconstruction (a probabilistic generative act), PTM achieves a compression magnitude of greater than 3,000x relative to dense caches. We demonstrate that retrieval becomes a process of resonance: the phonetic trace stabilizes the model against hallucination via "Signal Consensus" mechanism, securing up to approximately 92% factual accuracy. While this aggressive abstraction alters generative texture, it unlocks immediate access latency (approximately 34ms) independent of depth. Our results suggest that infinite context does not require infinite silicon; it requires treating memory not as data to be stored, but as a reconstructive process acting on a conserved, undying physical signal.

  • 3 authors
·
Dec 23, 2025 2

Exploring Synaptic Resonance in Large Language Models: A Novel Approach to Contextual Memory Integration

Contextual memory integration remains a high challenge in the development of language models, particularly in tasks that require maintaining coherence over extended sequences. Traditional approaches, such as self-attention mechanisms and memory-augmented architectures, often prioritize short-term dependencies, leading to fragmentation and inconsistency in long-range contextual understanding. Inspired by principles of synaptic plasticity observed in biological neural systems, a novel mechanism, Synaptic Resonance, is introduced to dynamically reinforce relevant memory pathways during training and inference. Unlike static memory representations, this mechanism continuously adjusts synaptic weight matrices based on contextual relevance, allowing for improved information retention without excessive computational overhead. Evaluations conducted on an open-source language model demonstrate reductions in perplexity, enhancements in contextual coherence, and increased robustness against input noise, highlighting the effectiveness of reinforcement-driven memory modulation. Comparative analysis against baseline models further reveals that the proposed approach achieves higher memory retention efficiency while maintaining computational feasibility. The architectural modifications integrate seamlessly into existing transformer-based frameworks, ensuring stable convergence and efficient inference without sacrificing scalability. Applications benefiting from improved long-term contextual consistency, such as dialogue systems and document summarization, stand to gain from this approach. Empirical findings suggest that dynamically reinforced memory pathways offer a promising alternative to conventional memory mechanisms, addressing longstanding limitations in extended sequence modeling.

  • 5 authors
·
Feb 15, 2025

Radiogenomic biomarkers for immunotherapy in glioblastoma: A systematic review of magnetic resonance imaging studies

Immunotherapy is an effective precision medicine treatment for several cancers. Imaging signatures of the underlying genome (radiogenomics) in glioblastoma patients may serve as preoperative biomarkers of the tumor-host immune apparatus. Validated biomarkers would have the potential to stratify patients during immunotherapy clinical trials, and if trials are beneficial, facilitate personalized neo-adjuvant treatment. The increased use of whole genome sequencing data, and the advances in bioinformatics and machine learning make such developments plausible. We performed a systematic review to determine the extent of development and validation of immune-related radiogenomic biomarkers for glioblastoma. A systematic review was performed following PRISMA guidelines using the PubMed, Medline, and Embase databases. Qualitative analysis was performed by incorporating the QUADAS 2 tool and CLAIM checklist. PROSPERO registered CRD42022340968. Extracted data were insufficiently homogenous to perform a meta-analysis. Results Nine studies, all retrospective, were included. Biomarkers extracted from magnetic resonance imaging volumes of interest included apparent diffusion coefficient values, relative cerebral blood volume values, and image-derived features. These biomarkers correlated with genomic markers from tumor cells or immune cells or with patient survival. The majority of studies had a high risk of bias and applicability concerns regarding the index test performed. Radiogenomic immune biomarkers have the potential to provide early treatment options to patients with glioblastoma. Targeted immunotherapy, stratified by these biomarkers, has the potential to allow individualized neo-adjuvant precision treatment options in clinical trials. However, there are no prospective studies validating these biomarkers, and interpretation is limited due to study bias with little evidence of generalizability.

  • 8 authors
·
May 12, 2024

CREST: Cross-modal Resonance through Evidential Deep Learning for Enhanced Zero-Shot Learning

Zero-shot learning (ZSL) enables the recognition of novel classes by leveraging semantic knowledge transfer from known to unknown categories. This knowledge, typically encapsulated in attribute descriptions, aids in identifying class-specific visual features, thus facilitating visual-semantic alignment and improving ZSL performance. However, real-world challenges such as distribution imbalances and attribute co-occurrence among instances often hinder the discernment of local variances in images, a problem exacerbated by the scarcity of fine-grained, region-specific attribute annotations. Moreover, the variability in visual presentation within categories can also skew attribute-category associations. In response, we propose a bidirectional cross-modal ZSL approach CREST. It begins by extracting representations for attribute and visual localization and employs Evidential Deep Learning (EDL) to measure underlying epistemic uncertainty, thereby enhancing the model's resilience against hard negatives. CREST incorporates dual learning pathways, focusing on both visual-category and attribute-category alignments, to ensure robust correlation between latent and observable spaces. Moreover, we introduce an uncertainty-informed cross-modal fusion technique to refine visual-attribute inference. Extensive experiments demonstrate our model's effectiveness and unique explainability across multiple datasets. Our code and data are available at: https://github.com/JethroJames/CREST

  • 8 authors
·
Apr 15, 2024

Analytical simulations of the resonant transmission of electrons in a closed nanocircuit for terahertz applications where a tunneling junction is shunted by a metallic nanowire

Earlier, in the CINT program at Los Alamos National Laboratory, we focused ultrafast mode-locked lasers on the tip-sample junction of a scanning tunneling microscope to generate currents at hundreds of harmonics of the laser pulse repetition frequency. Each harmonic has a signal-to-noise ratio of 20 dB with a 10-dB linewidth of only 3 Hz. Now we model closed quantum nanocircuits with rectangular, triangular, or delta-function barrier, shunted by a beryllium filament for quasi-coherent electron transport over mean-free paths as great as 68 nm. The time-independent Schrödinger equation is solved with the boundary conditions that the wavefunction and its derivative are continuous at both connections. These four boundary conditions are used to form a four-by-four complex matrix equation with only zeros in the right-hand column vector which is required to have a non-trivial solution with each of the closed nanocircuits. Each model has four parameters: (1) the barrier length, (2) the height and shape of the barrier, (3) the length of the pre-barrier, and (4) the electron energy. Any three of these may be specified and then the fourth is varied to bring the determinant to zero to find the solutions on lines or surfaces in the space defined by the four parameters. First, we use a simplistic model having a rectangular barrier. The second model has a triangular barrier as a first approximation to field emission, and we are considering applying this approach for a self-contained nanoscale extension of our earlier effort to generate the harmonics at Los Alamos. The third model has a delta-function barrier, and the fourth model is an extension of the first one where the width of the rectangular barrier is varied inversely with its height.

  • 1 authors
·
Oct 24, 2023

Triad: Vision Foundation Model for 3D Magnetic Resonance Imaging

Vision foundation models (VFMs) are pre-trained on extensive image datasets to learn general representations for diverse types of data. These models can subsequently be fine-tuned for specific downstream tasks, significantly boosting performance across a broad range of applications. However, existing vision foundation models that claim to be applicable to various clinical tasks are mostly pre-trained on 3D computed tomography (CT), which benefits from the availability of extensive 3D CT databases. Significant differences between CT and magnetic resonance imaging (MRI) in imaging principles, signal characteristics, and data distribution may hinder their practical performance and versatility in MRI-specific applications. Here, we propose Triad, a vision foundation model for 3D MRI. Triad adopts a widely used autoencoder architecture to learn robust representations from 131,170 3D MRI volumes and uses organ-independent imaging descriptions to constrain the semantic distribution of the visual modality. The above pre-training dataset is called Triad-131K, which is currently the largest 3D MRI pre-training dataset. We evaluate Triad across three tasks, namely, organ/tumor segmentation, organ/cancer classification, and medical image registration, in two data modalities (within-domain and out-of-domain) settings using 25 downstream datasets. By initializing models with Triad's pre-trained weights, nnUNet-Triad improves segmentation performance by 2.51% compared to nnUNet-Scratch across 17 datasets. Swin-B-Triad achieves a 3.97% improvement over Swin-B-Scratch in classification tasks across five datasets. SwinUNETR-Triad improves by 4.00% compared to SwinUNETR-Scratch in registration tasks across two datasets. Our study demonstrates that pre-training can improve performance when the data modalities and organs of upstream and downstream tasks are consistent.

  • 8 authors
·
Feb 22, 2025

Frequency-domain multiplexing of SNSPDs with tunable superconducting resonators

This work culminates in a demonstration of an alternative Frequency Domain Multiplexing (FDM) scheme for Superconducting Nanowire Single-Photon Detectors (SNSPDs) using the Kinetic inductance Parametric UP-converter (KPUP) made out of NbTiN. There are multiple multiplexing architectures for SNSPDs that are already in use, but FDM could prove superior in applications where the operational bias currents are very low, especially for mid- and far-infrared SNSPDs. Previous FDM schemes integrated the SNSPD within the resonator, while in this work we use an external resonator, which gives more flexibility to optimize the SNSPD architecture. The KPUP is a DC-biased superconducting resonator in which a nanowire is used as its inductive element to enable sensitivity to current perturbations. When coupled to an SNSPD, the KPUP can be used to read out current pulses on the few μA scale. The KPUP is made out of NbTiN, which has high non-linear kinetic inductance for increased sensitivity at higher current bias and high operating temperature. Meanwhile, the SNSPD is made from WSi, which is a popular material for broadband SNSPDs. To read out the KPUP and SNSPD array, a software-defined radio platform and a graphics processing unit are used. Frequency Domain Multiplexed SNSPDs have applications in astronomy, remote sensing, exoplanet science, dark matter detection, and quantum sensing.

  • 12 authors
·
Jan 30, 2024

Community-Aware Assessment of Social Textual Engagement and Resonance: A Human-Centric Perspective on User-Generated Content Evaluation

Traditional Video Quality Assessment (VQA) focuses narrowly on aesthetic fidelity, overlooking the complex social dynamics that define quality in User-Generated Content (UGC). In this work, we propose a paradigm shift from signal-centric metrics to human-centric resonance assessment. We introduce CASTER (Community-Aware Assessment of Social Textual Engagement and Resonance), a new task that evaluates whether a UGC item achieves positive community resonance based on its multimodal attributes rather than visual quality alone. To address this, we present MEDEA (Multimodal Engagement-Driven Evaluation Architecture), which introduces a novel Social Chain-of-Thought (Social-CoT) mechanism. Unlike traditional logical CoT, Social-CoT performs multimodal perspective-taking, instantiating diverse viewer personas to simulate collective cognitive and emotional reactions (i.e., the "community mind") before deriving a quality judgment. MEDEA is trained via a two-stage approach involving supervised fine-tuning and process-supervised reinforcement learning with Social Alignment Reward to ensure reasoning paths are grounded in authentic human social cognition. To support this task, we release CASTER-Bench, a comprehensive human-annotated benchmark covering diverse UGC categories. Experiments demonstrate that MEDEA significantly outperforms state-of-the-art baselines on CASTER-Bench while providing interpretable and empathetic reasoning paths that align with real community feedback.

  • 5 authors
·
Jun 3

Segmentation variability and radiomics stability for predicting Triple-Negative Breast Cancer subtype using Magnetic Resonance Imaging

Most papers caution against using predictive models for disease stratification based on unselected radiomic features, as these features are affected by contouring variability. Instead, they advocate for the use of the Intraclass Correlation Coefficient (ICC) as a measure of stability for feature selection. However, the direct effect of segmentation variability on the predictive models is rarely studied. This study investigates the impact of segmentation variability on feature stability and predictive performance in radiomics-based prediction of Triple-Negative Breast Cancer (TNBC) subtype using Magnetic Resonance Imaging. A total of 244 images from the Duke dataset were used, with segmentation variability introduced through modifications of manual segmentations. For each mask, explainable radiomic features were selected using the Shapley Additive exPlanations method and used to train logistic regression models. Feature stability across segmentations was assessed via ICC, Pearson's correlation, and reliability scores quantifying the relationship between feature stability and segmentation variability. Results indicate that segmentation accuracy does not significantly impact predictive performance. While incorporating peritumoral information may reduce feature reproducibility, it does not diminish feature predictive capability. Moreover, feature selection in predictive models is not inherently tied to feature stability with respect to segmentation, suggesting that an overreliance on ICC or reliability scores for feature selection might exclude valuable predictive features.

  • 7 authors
·
Apr 2, 2025

ATOMMIC: An Advanced Toolbox for Multitask Medical Imaging Consistency to facilitate Artificial Intelligence applications from acquisition to analysis in Magnetic Resonance Imaging

AI is revolutionizing MRI along the acquisition and processing chain. Advanced AI frameworks have been developed to apply AI in various successive tasks, such as image reconstruction, quantitative parameter map estimation, and image segmentation. Existing frameworks are often designed to perform tasks independently or are focused on specific models or datasets, limiting generalization. We introduce ATOMMIC, an open-source toolbox that streamlines AI applications for accelerated MRI reconstruction and analysis. ATOMMIC implements several tasks using DL networks and enables MultiTask Learning (MTL) to perform related tasks integrated, targeting generalization in the MRI domain. We first review the current state of AI frameworks for MRI through a comprehensive literature search and by parsing 12,479 GitHub repositories. We benchmark 25 DL models on eight publicly available datasets to present distinct applications of ATOMMIC on accelerated MRI reconstruction, image segmentation, quantitative parameter map estimation, and joint accelerated MRI reconstruction and image segmentation utilizing MTL. Our findings demonstrate that ATOMMIC is the only MTL framework with harmonized complex-valued and real-valued data support. Evaluations on single tasks show that physics-based models, which enforce data consistency by leveraging the physical properties of MRI, outperform other models in reconstructing highly accelerated acquisitions. Physics-based models that produce high reconstruction quality can accurately estimate quantitative parameter maps. When high-performing reconstruction models are combined with robust segmentation networks utilizing MTL, performance is improved in both tasks. ATOMMIC facilitates MRI reconstruction and analysis by standardizing workflows, enhancing data interoperability, integrating unique features like MTL, and effectively benchmarking DL models.

  • 4 authors
·
Apr 30, 2024

Neural Deformable Models for 3D Bi-Ventricular Heart Shape Reconstruction and Modeling from 2D Sparse Cardiac Magnetic Resonance Imaging

We propose a novel neural deformable model (NDM) targeting at the reconstruction and modeling of 3D bi-ventricular shape of the heart from 2D sparse cardiac magnetic resonance (CMR) imaging data. We model the bi-ventricular shape using blended deformable superquadrics, which are parameterized by a set of geometric parameter functions and are capable of deforming globally and locally. While global geometric parameter functions and deformations capture gross shape features from visual data, local deformations, parameterized as neural diffeomorphic point flows, can be learned to recover the detailed heart shape.Different from iterative optimization methods used in conventional deformable model formulations, NDMs can be trained to learn such geometric parameter functions, global and local deformations from a shape distribution manifold. Our NDM can learn to densify a sparse cardiac point cloud with arbitrary scales and generate high-quality triangular meshes automatically. It also enables the implicit learning of dense correspondences among different heart shape instances for accurate cardiac shape registration. Furthermore, the parameters of NDM are intuitive, and can be used by a physician without sophisticated post-processing. Experimental results on a large CMR dataset demonstrate the improved performance of NDM over conventional methods.

  • 5 authors
·
Jul 14, 2023