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Ge Wang

Publications and source records attributed to Ge Wang.

At least 109 records · Page 6Linked to original sources

LLM-based MOFs Synthesis Condition Extraction using Few-Shot Demonstrations

The extraction of Metal-Organic Frameworks (MOFs) synthesis route from literature has been crucial for the logical MOFs design with desirable functionality. The recent advent of large language models (LLMs) provides disruptively new solution to this long-standing problem. While the latest researches mostly stick to primitive zero-shot LLMs lacking specialized material knowledge, we introduce in this work the few-shot LLM in-context learning paradigm. First, a human-AI interactive data curation approach is proposed to secure high-quality demonstrations. Second, an information retrieval algorithm is applied to pick and quantify few-shot demonstrations for each extraction. Over three datasets randomly sampled from nearly 90,000 well-defined MOFs, we conduct triple evaluations to validate our method. The synthesis extraction, structure inference, and material design performance of the proposed few-shot LLMs all significantly outplay zero-shot LLM and baseline methods. The lab-synthesized material guided by LLM surpasses 91.1% high-quality MOFs of the same class reported in the literature, on the key physical property of specific surface area.

cs.CL↗

PFCM: Poisson flow consistency models for low-dose CT image denoising

X-ray computed tomography (CT) is widely used for medical diagnosis and treatment planning; however, concerns about ionizing radiation exposure drive efforts to optimize image quality at lower doses. This study introduces Poisson Flow Consistency Models (PFCM), a novel family of deep generative models that combines the robustness of PFGM++ with the efficient single-step sampling of consistency models. PFCM are derived by generalizing consistency distillation to PFGM++ through a change-of-variables and an updated noise distribution. As a distilled version of PFGM++, PFCM inherit the ability to trade off robustness for rigidity via the hyperparameter $D \in (0,\infty)$. A fact that we exploit to adapt this novel generative model for the task of low-dose CT image denoising, via a ``task-specific'' sampler that ``hijacks'' the generative process by replacing an intermediate state with the low-dose CT image. While this ``hijacking'' introduces a severe mismatch -- the noise characteristics of low-dose CT images are different from that of intermediate states in the Poisson flow process -- we show that the inherent robustness of PFCM at small $D$ effectively mitigates this issue. The resulting sampler achieves excellent performance in terms of LPIPS, SSIM, and PSNR on the Mayo low-dose CT dataset. By contrast, an analogous sampler based on standard consistency models is found to be significantly less robust under the same conditions, highlighting the importance of a tunable $D$ afforded by our novel framework. To highlight generalizability, we show effective denoising of clinical images from a prototype photon-counting system reconstructed using a sharper kernel and at a range of energy levels.

eess.IV↗

Accelerated X-Ray Fluorescence Computed Tomography via Multi-Pencil-Beam Excitation

X-ray fluorescence computed tomography (XFCT), a form of X-ray molecular imaging, offers detailed quantitative imaging capabilities for high-Z metal nanoparticles (MNPs), which are widely studied for their applications in multifunctional theranostics. Due to its affordability and accessibility, the benchtop XFCT prototype typically employs a single-pixel detector (SPD) with single-pencil-beam (SPB) X-ray excitation. While this design (resembling the first-generation CT geometry) achieves reliable detection sensitivity, it is hindered by long imaging times. The use of simultaneous multiple-pencil-beam (MPB) excitation presents a promising solution to significantly reduce imaging times. In this study, we developed a repeatable workflow that combines Monte Carlo (MC) simulations and 3D printing to design Nbeam-MPB collimator, where Nbeam is the number of beams generated by the collimator. As an initial test, we fabricated a 2-MPB collimator and evaluated the performance of 2-MPB-based XFCT imaging on a physical phantom and small animals surgically implanted with agarose pellets containing gold chloride (H[AuCl4]). The results demonstrated a 2x acceleration in image acquisition without compromising the contrast-to-noise ratio (CNR). We further investigated the concept of Nbeam-MPB acceleration on the MC computational XFCT system, which confirmed the feasibility of achieving at least 4x acceleration with 4-MPB excitation. Combined with additional system optimization, such as X-ray beam flux optimization, XFCT imaging could be further accelerated, reducing acquisition time from hours to minutes and meeting the requirements for routine MNP imaging.

physics.med-ph↗

Poisson Flow Joint Model for Multiphase contrast-enhanced CT

In clinical practice, multiphase contrast-enhanced CT (MCCT) is important for physiological and pathological imaging with contrast injection, which undergoes non-contrast, venous, and delayed phases. Inevitably, the accumulated radiation dose to a patient is higher for multiphase scans than for a plain CT scan. Low-dose CECT is thus highly desirable, but it often leads to suboptimal image quality due to reduced radiation dose. Recently, a generalized Poisson flow generative model (PFGM++) was proposed to unify the diffusion model and the Poisson flow generative models (PFGM), and outperform either of them with an optimized dimensionality of the augmentation data space, holding a significant promise for generic or conditional image generation. In this paper, we propose a Poisson flow joint model (PFJM) for low-dose MCCT to suppress image noise and preserve clinical features. Our model is built on the PFGM++ architecture to transform the multiphase imaging problem into learning the joint distribution of routine-dose MCCT images by optimizing a task-specific generation path with respect to the dimensionality D of the augmented data space. Then, our PFJM model takes the joint low-dose MCCT images as the condition and robustly drives the generative trajectory towards the solution in the routine-dose MCCT domain. Extensive experiments demonstrate that our model is favorably compared with competing models, with MAE of 8.99 HU, SSIM of 98.75% and PSNR of 48.24db, as averaged over all the phases.

eess.IV↗

Information-Maximized Soft Variable Discretization for Self-Supervised Image Representation Learning

Self-supervised learning (SSL) has emerged as a crucial technique in image processing, encoding, and understanding, especially for developing today's vision foundation models that utilize large-scale datasets without annotations to enhance various downstream tasks. This study introduces a novel SSL approach, Information-Maximized Soft Variable Discretization (IMSVD), for image representation learning. Specifically, IMSVD softly discretizes each variable in the latent space, enabling the estimation of their probability distributions over training batches and allowing the learning process to be directly guided by information measures. Motivated by the MultiView assumption, we propose an information-theoretic objective function to learn transform-invariant, non-travail, and redundancy-minimized representation features. We then derive a joint-cross entropy loss function for self-supervised image representation learning, which theoretically enjoys superiority over the existing methods in reducing feature redundancy. Notably, our non-contrastive IMSVD method statistically performs contrastive learning. Extensive experimental results demonstrate the effectiveness of IMSVD on various downstream tasks in terms of both accuracy and efficiency. Thanks to our variable discretization, the embedding features optimized by IMSVD offer unique explainability at the variable level. IMSVD has the potential to be adapted to other learning paradigms. Our code is publicly available at https://github.com/niuchuangnn/IMSVD.

cs.CV↗

A Generalizable 3D Diffusion Framework for Low-Dose and Few-View Cardiac SPECT

Myocardial perfusion imaging using SPECT is widely utilized to diagnose coronary artery diseases, but image quality can be negatively affected in low-dose and few-view acquisition settings. Although various deep learning methods have been introduced to improve image quality from low-dose or few-view SPECT data, previous approaches often fail to generalize across different acquisition settings, limiting their applicability in reality. This work introduced DiffSPECT-3D, a diffusion framework for 3D cardiac SPECT imaging that effectively adapts to different acquisition settings without requiring further network re-training or fine-tuning. Using both image and projection data, a consistency strategy is proposed to ensure that diffusion sampling at each step aligns with the low-dose/few-view projection measurements, the image data, and the scanner geometry, thus enabling generalization to different low-dose/few-view settings. Incorporating anatomical spatial information from CT and total variation constraint, we proposed a 2.5D conditional strategy to allow the DiffSPECT-3D to observe 3D contextual information from the entire image volume, addressing the 3D memory issues in diffusion model. We extensively evaluated the proposed method on 1,325 clinical 99mTc tetrofosmin stress/rest studies from 795 patients. Each study was reconstructed into 5 different low-count and 5 different few-view levels for model evaluations, ranging from 1% to 50% and from 1 view to 9 view, respectively. Validated against cardiac catheterization results and diagnostic comments from nuclear cardiologists, the presented results show the potential to achieve low-dose and few-view SPECT imaging without compromising clinical performance. Additionally, DiffSPECT-3D could be directly applied to full-dose SPECT images to further improve image quality, especially in a low-dose stress-first cardiac SPECT imaging protocol.

eess.IV↗

Starting a Synthetic Biological Intelligence Lab from Scratch

With the recent advancements in artificial intelligence, researchers and industries are deploying gigantic models trained on billions of samples. While training these models consumes a huge amount of energy, human brains produce similar outputs (along with other capabilities) with massively lower data and energy requirements. For this reason, more researchers are increasingly considering alternatives. One of these alternatives is known as synthetic biological intelligence, which involves training \textit{in vitro} neurons for goal-directed tasks. This multidisciplinary field requires knowledge of tissue engineering, bio-materials, digital signal processing, computer programming, neuroscience, and even artificial intelligence. The multidisciplinary requirements make starting synthetic biological intelligence research highly non-trivial and time-consuming. Generally, most labs either specialize in the biological aspects or the computational ones. Here, we propose how a lab focusing on computational aspects, including machine learning and device interfacing, can start working on synthetic biological intelligence, including organoid intelligence. We will also discuss computational aspects, which can be helpful for labs that focus on biological research. To facilitate synthetic biological intelligence research, we will describe such a general process step by step, including risks and precautions that could lead to substantial delay or additional cost.

q-bio.NC↗

Can Large Language Models Effectively Process and Execute Financial Trading Instructions?

The development of Large Language Models (LLMs) has created transformative opportunities for the financial industry, especially in the area of financial trading. However, how to integrate LLMs with trading systems has become a challenge. To address this problem, we propose an intelligent trade order recognition pipeline that enables the conversion of trade orders into a standard format in trade execution. The system improves the ability of human traders to interact with trading platforms while addressing the problem of misinformation acquisition in trade execution. In addition, we have created a trade order dataset of 500 pieces of data to simulate real-world trading scenarios. Moreover, we designed several metrics to provide a comprehensive assessment of dataset reliability and the generative power of big models in finance by experimenting with five state-of-the-art LLMs on our dataset. The results indicate that while LLMs demonstrate high generation rates (87.50% to 98.33%) and perfect follow-up rates, they face significant challenges in accuracy (5% to 10%) and completeness, with high missing rates (14.29% to 67.29%). In addition, LLMs tend to over-interrogate, suggesting that large models tend to collect more information, carrying certain challenges for information security.

cs.CE↗

ECG-SleepNet: Deep Learning-Based Comprehensive Sleep Stage Classification Using ECG Signals

Accurate sleep stage classification is essential for understanding sleep disorders and improving overall health. This study proposes a novel three-stage approach for sleep stage classification using ECG signals, offering a more accessible alternative to traditional methods that often rely on complex modalities like EEG. In Stages 1 and 2, we initialize the weights of two networks, which are then integrated in Stage 3 for comprehensive classification. In the first phase, we estimate key features using Feature Imitating Networks (FINs) to achieve higher accuracy and faster convergence. The second phase focuses on identifying the N1 sleep stage through the time-frequency representation of ECG signals. Finally, the third phase integrates models from the previous stages and employs a Kolmogorov-Arnold Network (KAN) to classify five distinct sleep stages. Additionally, data augmentation techniques, particularly SMOTE, are used in enhancing classification capabilities for underrepresented stages like N1. Our results demonstrate significant improvements in the classification performance, with an overall accuracy of 80.79% an overall kappa of 0.73. The model achieves specific accuracies of 86.70% for Wake, 60.36% for N1, 83.89% for N2, 84.85% for N3, and 87.16% for REM. This study emphasizes the importance of weight initialization and data augmentation in optimizing sleep stage classification with ECG signals.

cs.AI↗

Pan-protein Design Learning Enables Task-adaptive Generalization for Low-resource Enzyme Design

Computational protein design (CPD) offers transformative potential for bioengineering, but current deep CPD models, focused on universal domains, struggle with function-specific designs. This work introduces a novel CPD paradigm tailored for functional design tasks, particularly for enzymes-a key protein class often lacking specific application efficiency. To address structural data scarcity, we present CrossDesign, a domain-adaptive framework that leverages pretrained protein language models (PPLMs). By aligning protein structures with sequences, CrossDesign transfers pretrained knowledge to structure models, overcoming the limitations of limited structural data. The framework combines autoregressive (AR) and non-autoregressive (NAR) states in its encoder-decoder architecture, applying it to enzyme datasets and pan-proteins. Experimental results highlight CrossDesign's superior performance and robustness, especially with out-of-domain enzymes. Additionally, the model excels in fitness prediction when tested on large-scale mutation data, showcasing its stability.

q-bio.QM↗

Enhancing Low Dose Computed Tomography Images Using Consistency Training Techniques

Diffusion models have significant impact on wide range of generative tasks, especially on image inpainting and restoration. Although the improvements on aiming for decreasing number of function evaluations (NFE), the iterative results are still computationally expensive. Consistency models are as a new family of generative models, enable single-step sampling of high quality data without the need for adversarial training. In this paper, we introduce the beta noise distribution, which provides flexibility in adjusting noise levels. This is combined with a sinusoidal curriculum that enhances the learning of the trajectory between the noise distribution and the posterior distribution of interest, allowing High Noise Improved Consistency Training (HN-iCT) to be trained in a supervised fashion. Additionally, High Noise Improved Consistency Training with Image Condition (HN-iCT-CN) architecture is introduced, enables to take Low Dose images as a condition for extracting significant features by Weighted Attention Gates (WAG).Our results indicate that unconditional image generation using HN-iCT significantly outperforms basic CT and iCT training techniques with NFE=1 on the CIFAR10 and CelebA datasets. Moreover, our image-conditioned model demonstrates exceptional performance in enhancing low-dose (LD) CT scans.

eess.IV↗

Algorithmic Autonomy in Data-Driven AI

In societies increasingly entangled with algorithms, our choices are constantly influenced and shaped by automated systems. This convergence highlights significant concerns for individual autonomy in the age of data-driven AI. It leads to pressing issues such as data-driven segregation, gaps in accountability for algorithmic decisions, and the infringement on essential human rights and values. Through this article, we introduce and explore the concept of algorithmic autonomy, examining what it means for individuals to have autonomy in the face of the pervasive impact of algorithms on our societies. We begin by outlining the data-driven characteristics of AI and its role in diminishing personal autonomy. We then explore the notion of algorithmic autonomy, drawing on existing research. Finally, we address important considerations, highlighting current challenges and directions for future research.

cs.HC↗

Data and Physics driven Deep Learning Models for Fast MRI Reconstruction: Fundamentals and Methodologies

Magnetic Resonance Imaging (MRI) is a pivotal clinical diagnostic tool, yet its extended scanning times often compromise patient comfort and image quality, especially in volumetric, temporal and quantitative scans. This review elucidates recent advances in MRI acceleration via data and physics-driven models, leveraging techniques from algorithm unrolling models, enhancement-based methods, and plug-and-play models to the emerging full spectrum of generative model-based methods. We also explore the synergistic integration of data models with physics-based insights, encompassing the advancements in multi-coil hardware accelerations like parallel imaging and simultaneous multi-slice imaging, and the optimization of sampling patterns. We then focus on domain-specific challenges and opportunities, including image redundancy exploitation, image integrity, evaluation metrics, data heterogeneity, and model generalization. This work also discusses potential solutions and future research directions, with an emphasis on the role of data harmonization and federated learning for further improving the general applicability and performance of these methods in MRI reconstruction.

eess.SP↗

A 3D-Printed Table for Hybrid X-ray CT and Optical Imaging of a Live Mouse

Multimodal imaging has shown great potential in cancer research by concurrently providing anatomical, functional, and molecular information in live, intact animals. During preclinical imaging of small animals like mice, anesthesia is required to prevent movement and improve image quality. However, their high surface area-to-body weight ratio predisposes mice, particularly nude mice, to hypothermia under anesthesia. To address this, we developed a detachable mouse scanning table with heating function for hybrid x-ray and optical imaging modalities, without introducing metal artifacts. Specifically, we employed Polylactic Acid (PLA) 3D printing technology to fabricate a customized scanning table, compatible with both CT and optical imaging systems. This innovation enables seamless transportation of the table between different imaging setups, while its detachable design facilitates maintaining a clutter-free operational environment within the imaging systems. This is crucial for accommodating various projects within the same scanner. The table features positioned fixation points to secure mice, ensuring positional consistency across imaging modalities. Additionally, we integrated a carbon nanotube-based heating pad into the table to regulate the body temperature of mice during examinations, providing an ethical and effective temperature maintenance solution. Our evaluations confirmed the table's ability to maintain a 30g water bag at approximately 40$^\circ$C, effectively regulating mouse body temperature to an optimal 36$^\circ$C during preclinical imaging sessions. This scanning table serves as a useful tool in preclinical cancer research, offering a versatile tool that upholds animal welfare standards.

physics.med-ph↗

Switch EMA: A Free Lunch for Better Flatness and Sharpness

Exponential Moving Average (EMA) is a widely used weight averaging (WA) regularization to learn flat optima for better generalizations without extra cost in deep neural network (DNN) optimization. Despite achieving better flatness, existing WA methods might fall into worse final performances or require extra test-time computations. This work unveils the full potential of EMA with a single line of modification, i.e., switching the EMA parameters to the original model after each epoch, dubbed as Switch EMA (SEMA). From both theoretical and empirical aspects, we demonstrate that SEMA can help DNNs to reach generalization optima that better trade-off between flatness and sharpness. To verify the effectiveness of SEMA, we conduct comparison experiments with discriminative, generative, and regression tasks on vision and language datasets, including image classification, self-supervised learning, object detection and segmentation, image generation, video prediction, attribute regression, and language modeling. Comprehensive results with popular optimizers and networks show that SEMA is a free lunch for DNN training by improving performances and boosting convergence speeds.

cs.LG↗

Noise-aware Dynamic Image Denoising and Positron Range Correction for Rubidium-82 Cardiac PET Imaging via Self-supervision

Rb-82 is a radioactive isotope widely used for cardiac PET imaging. Despite numerous benefits of 82-Rb, there are several factors that limits its image quality and quantitative accuracy. First, the short half-life of 82-Rb results in noisy dynamic frames. Low signal-to-noise ratio would result in inaccurate and biased image quantification. Noisy dynamic frames also lead to highly noisy parametric images. The noise levels also vary substantially in different dynamic frames due to radiotracer decay and short half-life. Existing denoising methods are not applicable for this task due to the lack of paired training inputs/labels and inability to generalize across varying noise levels. Second, 82-Rb emits high-energy positrons. Compared with other tracers such as 18-F, 82-Rb travels a longer distance before annihilation, which negatively affect image spatial resolution. Here, the goal of this study is to propose a self-supervised method for simultaneous (1) noise-aware dynamic image denoising and (2) positron range correction for 82-Rb cardiac PET imaging. Tested on a series of PET scans from a cohort of normal volunteers, the proposed method produced images with superior visual quality. To demonstrate the improvement in image quantification, we compared image-derived input functions (IDIFs) with arterial input functions (AIFs) from continuous arterial blood samples. The IDIF derived from the proposed method led to lower AUC differences, decreasing from 11.09% to 7.58% on average, compared to the original dynamic frames. The proposed method also improved the quantification of myocardium blood flow (MBF), as validated against 15-O-water scans, with mean MBF differences decreased from 0.43 to 0.09, compared to the original dynamic frames. We also conducted a generalizability experiment on 37 patient scans obtained from a different country using a different scanner.

eess.IV↗

Multi-Conditioned Denoising Diffusion Probabilistic Model (mDDPM) for Medical Image Synthesis

Medical imaging applications are highly specialized in terms of human anatomy, pathology, and imaging domains. Therefore, annotated training datasets for training deep learning applications in medical imaging not only need to be highly accurate but also diverse and large enough to encompass almost all plausible examples with respect to those specifications. We argue that achieving this goal can be facilitated through a controlled generation framework for synthetic images with annotations, requiring multiple conditional specifications as input to provide control. We employ a Denoising Diffusion Probabilistic Model (DDPM) to train a large-scale generative model in the lung CT domain and expand upon a classifier-free sampling strategy to showcase one such generation framework. We show that our approach can produce annotated lung CT images that can faithfully represent anatomy, convincingly fooling experts into perceiving them as real. Our experiments demonstrate that controlled generative frameworks of this nature can surpass nearly every state-of-the-art image generative model in achieving anatomical consistency in generated medical images when trained on comparable large medical datasets.

cs.CV↗

Physics-Inspired Generative Models in Medical Imaging: A Review

Physics-inspired Generative Models (GMs), in particular Diffusion Models (DMs) and Poisson Flow Models (PFMs), enhance Bayesian methods and promise great utility in medical imaging. This review examines the transformative role of such generative methods. First, a variety of physics-inspired GMs, including Denoising Diffusion Probabilistic Models (DDPMs), Score-based Diffusion Models (SDMs), and Poisson Flow Generative Models (PFGMs and PFGM++), are revisited, with an emphasis on their accuracy, robustness as well as acceleration. Then, major applications of physics-inspired GMs in medical imaging are presented, comprising image reconstruction, image generation, and image analysis. Finally, future research directions are brainstormed, including unification of physics-inspired GMs, integration with Vision-Language Models (VLMs), and potential novel applications of GMs. Since the development of generative methods has been rapid, this review will hopefully give peers and learners a timely snapshot of this new family of physics-driven generative models and help capitalize their enormous potential for medical imaging.

eess.IV↗