Advances in Photoacoustic Imaging Reconstruction and Quantitative Analysis for Biomedical Applications

Photoacoustic imaging (PAI) represents an innovative biomedical imaging modality that harnesses the advantages of optical resolution and acoustic penetration depth while ensuring enhanced safety. Despite its promising potential across a diverse array of preclinical and clinical applications, the clinical implementation of PAI faces significant challenges, including the trade-off between penetration depth and spatial resolution, as well as the demand for faster imaging speeds. This paper explores the fundamental principles underlying PAI, with a particular emphasis on three primary implementations: photoacoustic computed tomography (PACT), photoacoustic microscopy (PAM), and photoacoustic endoscopy (PAE). We undertake a critical assessment of their respective strengths and practical limitations. Furthermore, recent developments in utilizing conventional or deep learning (DL) methodologies for image reconstruction and artefact mitigation across PACT, PAM, and PAE are outlined, demonstrating considerable potential to enhance image quality and accelerate imaging processes. Furthermore, this paper examines the recent developments in quantitative analysis within PAI, including the quantification of haemoglobin concentration, oxygen saturation, and other physiological parameters within tissues. Finally, our discussion encompasses current trends and future directions in PAI research while emphasizing the transformative impact of deep learning on advancing PAI.

EMOCPD: Efficient Attention-based Models for Computational Protein Design Using Amino Acid Microenvironment

Computational protein design (CPD) refers to the use of computational methods to design proteins. Traditional methods relying on energy functions and heuristic algorithms for sequence design are inefficient and do not meet the demands of the big data era in biomolecules, with their accuracy limited by the energy functions and search algorithms. Existing deep learning methods are constrained by the learning capabilities of the networks, failing to extract effective information from sparse protein structures, which limits the accuracy of protein design. To address these shortcomings, we developed an Efficient attention-based Models for Computational Protein Design using amino acid microenvironment (EMOCPD). It aims to predict the category of each amino acid in a protein by analyzing the three-dimensional atomic environment surrounding the amino acids, and optimize the protein based on the predicted high-probability potential amino acid categories. EMOCPD employs a multi-head attention mechanism to focus on important features in the sparse protein microenvironment and utilizes an inverse residual structure to optimize the network architecture. The proposed EMOCPD achieves over 80% accuracy on the training set and 68.33% and 62.32% accuracy on two independent test sets, respectively, surpassing the best comparative methods by over 10%. In protein design, the thermal stability and protein expression of the predicted mutants from EMOCPD show significant improvements compared to the wild type, effectively validating EMOCPD's potential in designing superior proteins. Furthermore, the predictions of EMOCPD are influenced positively, negatively, or have minimal impact based on the content of the 20 amino acids, categorizing amino acids as positive, negative, or neutral. Research findings indicate that EMOCPD is more suitable for designing proteins with lower contents of negative amino acids.

Hierarchical Multiple Kernel K-Means Algorithm Based on Sparse Connectivity

Multiple kernel learning (MKL) aims to find an optimal, consistent kernel function. In the hierarchical multiple kernel clustering (HMKC) algorithm, sample features are extracted layer by layer from a high-dimensional space to maximize the retention of effective information. However, information interaction between layers is often ignored. In this model, only corresponding nodes in adjacent layers exchange information; other nodes remain isolated, and if full connectivity is adopted, the diversity of the final consistency matrix is reduced. Therefore, this paper proposes a hierarchical multiple kernel K-Means (SCHMKKM) algorithm based on sparse connectivity, which controls the assignment matrix to achieve sparse connections through a sparsity rate, thereby locally fusing the features obtained by distilling information between layers. Finally, we conduct cluster analysis on multiple datasets and compare it with the fully connected hierarchical multiple kernel K-Means (FCHMKKM) algorithm in experiments. It is shown that more discriminative information fusion is beneficial for learning a better consistent partition matrix, and the fusion strategy based on sparse connection outperforms the full connection strategy.

Symmetry Nonnegative Matrix Factorization Algorithm Based on Self-paced Learning

A symmetric nonnegative matrix factorization algorithm based on self-paced learning was proposed to improve the clustering performance of the model. It could make the model better distinguish normal samples from abnormal samples in an error-driven way. A weight variable that could measure the degree of difficulty to all samples was assigned in this method, and the variable was constrained by adopting both hard-weighting and soft-weighting strategies to ensure the rationality of the model. Cluster analysis was carried out on multiple data sets such as images and texts, and the experimental results showed the effectiveness of the proposed algorithm.

ChartifyText: Automated Chart Generation from Data-Involved Texts via LLM

Text documents with numerical values involved are widely used in various applications such as scientific research, economy, public health and journalism. However, it is difficult for readers to quickly interpret such data-involved texts and gain deep insights. To fill this research gap, this work aims to automatically generate charts to accurately convey the underlying data and ideas to readers, which is essentially a challenging task. The challenges originate from text ambiguities, intrinsic sparsity and uncertainty of data in text documents, and subjective sentiment differences. Specifically, we propose ChartifyText, a novel fully-automated approach that leverages Large Language Models (LLMs) to convert complex data-involved texts to expressive charts. It consists of two major modules: tabular data inference and expressive chart generation. The tabular data inference module employs systematic prompt engineering to guide the LLM (e.g., GPT-4) to infer table data, where data ranges, uncertainties, missing data values and corresponding subjective sentiments are explicitly considered. The expressive chart generation module augments standard charts with intuitive visual encodings and concise texts to accurately convey the underlying data and insights. We extensively evaluate the effectiveness of ChartifyText on real-world data-involved text documents through case studies, in-depth interviews with three visualization experts, and a carefully-designed user study with 15 participants. The results demonstrate the usefulness and effectiveness of ChartifyText in helping readers efficiently and effectively make sense of data-involved texts.

MathHay: An Automated Benchmark for Long-Context Mathematical Reasoning in LLMs

Recent large language models (LLMs) have demonstrated versatile capabilities in long-context scenarios. Although some recent benchmarks have been developed to evaluate the long-context capabilities of LLMs, there is a lack of benchmarks evaluating the mathematical reasoning abilities of LLMs over long contexts, which is crucial for LLMs' application in real-world scenarios. In this paper, we introduce MathHay, an automated benchmark designed to assess the long-context mathematical reasoning capabilities of LLMs. Unlike previous benchmarks like Needle in a Haystack, which focus primarily on information retrieval within long texts, MathHay demands models with both information-seeking and complex mathematical reasoning abilities. We conduct extensive experiments on MathHay to assess the long-context mathematical reasoning abilities of eight top-performing LLMs. Even the best-performing model, Gemini-1.5-Pro-002, still struggles with mathematical reasoning over long contexts, achieving only 51.26% accuracy at 128K tokens. This highlights the significant room for improvement on the MathHay benchmark.

GenSim: A General Social Simulation Platform with Large Language Model based Agents

With the rapid advancement of large language models (LLMs), recent years have witnessed many promising studies on leveraging LLM-based agents to simulate human social behavior. While prior work has demonstrated significant potential across various domains, much of it has focused on specific scenarios involving a limited number of agents and has lacked the ability to adapt when errors occur during simulation. To overcome these limitations, we propose a novel LLM-agent-based simulation platform called \textit{GenSim}, which: (1) \textbf{Abstracts a set of general functions} to simplify the simulation of customized social scenarios; (2) \textbf{Supports one hundred thousand agents} to better simulate large-scale populations in real-world contexts; (3) \textbf{Incorporates error-correction mechanisms} to ensure more reliable and long-term simulations. To evaluate our platform, we assess both the efficiency of large-scale agent simulations and the effectiveness of the error-correction mechanisms. To our knowledge, GenSim represents an initial step toward a general, large-scale, and correctable social simulation platform based on LLM agents, promising to further advance the field of social science.

LEGO: Learnable Expansion of Graph Operators for Multi-Modal Feature Fusion

In computer vision tasks, features often come from diverse representations, domains, and modalities, such as text, images, and videos. Effectively fusing these features is essential for robust performance, especially with the availability of powerful pre-trained models like vision-language models. However, common fusion methods, such as concatenation, element-wise operations, and non-linear techniques, often fail to capture structural relationships, deep feature interactions, and suffer from inefficiency or misalignment of features across domains. In this paper, we shift from high-dimensional feature space to a lower-dimensional, interpretable graph space by constructing similarity graphs that encode feature relationships at different levels, e.g., clip, frame, patch, token, etc. To capture deeper interactions, we use graph power expansions and introduce a learnable graph fusion operator to combine these graph powers for more effective fusion. Our approach is relationship-centric, operates in a homogeneous space, and is mathematically principled, resembling element-wise similarity score aggregation via multilinear polynomials. We demonstrate the effectiveness of our graph-based fusion method on video anomaly detection, showing strong performance across multi-representational, multi-modal, and multi-domain feature fusion tasks.

A novel brain registration model combining structural and functional MRI information

Although developed functional magnetic resonance imaging (fMRI) registration algorithms based on deep learning have achieved a certain degree of alignment of functional area, they underutilized fine structural information. In this paper, we propose a semi-supervised convolutional neural network (CNN) registration model that integrates both structural and functional MRI information. The model first learns to generate deformation fields by inputting structural MRI (T1w-MRI) into the CNN to capture fine structural information. Then, we construct a local functional connectivity pattern to describe the local fMRI information, and use the Bhattacharyya coefficient to measure the similarity between two fMRI images, which is used as a loss function to facilitate the alignment of functional areas. In the inter-subject registration experiment, our model achieved an average number of voxels exceeding the threshold of 4.24 is 2248 in the group-level t-test maps for the four functional brain networks (default mode network, visual network, central executive network, and sensorimotor network). Additionally, the atlas-based registration experiment results show that the average number of voxels exceeding this threshold is 3620. The results are the largest among all methods. Our model achieves an excellent registration performance in fMRI and improves the consistency of functional regions. The proposed model has the potential to optimize fMRI image processing and analysis, facilitating the development of fMRI applications.

Fast Extrinsic Calibration for Multiple Inertial Measurement Units in Visual-Inertial System

In this paper, we propose a fast extrinsic calibration method for fusing multiple inertial measurement units (MIMU) to improve visual-inertial odometry (VIO) localization accuracy. Currently, data fusion algorithms for MIMU highly depend on the number of inertial sensors. Based on the assumption that extrinsic parameters between inertial sensors are perfectly calibrated, the fusion algorithm provides better localization accuracy with more IMUs, while neglecting the effect of extrinsic calibration error. Our method builds two non-linear least-squares problems to estimate the MIMU relative position and orientation separately, independent of external sensors and inertial noises online estimation. Then we give the general form of the virtual IMU (VIMU) method and propose its propagation on manifold. We perform our method on datasets, our self-made sensor board, and board with different IMUs, validating the superiority of our method over competing methods concerning speed, accuracy, and robustness. In the simulation experiment, we show that only fusing two IMUs with our calibration method to predict motion can rival nine IMUs. Real-world experiments demonstrate better localization accuracy of the VIO integrated with our calibration method and VIMU propagation on manifold.