Lei Du

Yaonai Wei, Tuo Zhang, Han Zhang et al.

Over decades, neuroscience has accumulated a wealth of research results in the text modality that can be used to explore cognitive processes. Meta-analysis is a typical method that successfully establishes a link from text queries to brain activation maps using these research results, but it still relies on an ideal query environment. In practical applications, text queries used for meta-analyses may encounter issues such as semantic redundancy and ambiguity, resulting in an inaccurate mapping to brain images. On the other hand, large language models (LLMs) like ChatGPT have shown great potential in tasks such as context understanding and reasoning, displaying a high degree of consistency with human natural language. Hence, LLMs could improve the connection between text modality and neuroscience, resolving existing challenges of meta-analyses. In this study, we propose a method called Chat2Brain that combines LLMs to basic text-2-image model, known as Text2Brain, to map open-ended semantic queries to brain activation maps in data-scarce and complex query environments. By utilizing the understanding and reasoning capabilities of LLMs, the performance of the mapping model is optimized by transferring text queries to semantic queries. We demonstrate that Chat2Brain can synthesize anatomically plausible neural activation patterns for more complex tasks of text queries.

Akira Imakura, Lei Du, Tetsuya Sakurai

Recently, contour integral-based methods have been actively studied for solving interior eigenvalue problems that find all eigenvalues located in a certain region and their corresponding eigenvectors. In this paper, we reconsider the algorithms of the five typical contour integral-based eigensolvers from the viewpoint of projection methods, and then map the relationships among these methods. From the analysis, we conclude that all contour integral-based eigensolvers can be regarded as projection methods and can be categorized based on their subspace used, the type of projection and the problem to which they are applied implicitly.

Hongjia Chen, Chun-Hua Zhang, Zhongming Teng et al.

This paper considers the numerical solution of generalized Sylvester matrix equations, which arise in many scientific and engineering applications but remain challenging to solve efficiently, particularly when the coefficient matrices are general and the spectral radius of the associated operator is large but not greater than $1$. We propose a new iterative method, termed preconditioned-alternating Anderson acceleration (P-aAA), which combines a matrix-oriented variant of Anderson acceleration (AA) with a novel preconditioning strategy. The method alternates between preconditioned fixed-point iterations and Anderson acceleration updates, thereby reducing both computational cost and iteration count. A key contribution is the development of an efficient preconditioning operator based on a first-order Neumann series approximation, which avoids expensive operator inversions while enhancing convergence. We theoretically prove that the proposed preconditioning operator accelerates the convergence rate without increasing the overall computational complexity. Extensive numerical experiments further demonstrate that the proposed approach consistently outperforms existing state-of-the-art methods for both medium- and large-scale problems, achieving substantial reductions in computation time and iteration number.

Lei Du, Shengqi Zhang

As a cornerstone of reduced-order modeling, the POD-Galerkin framework has garnered widespread attention and remains one of the most widely adopted approaches. Constructing POD-Galerkin PROMs involves integrating this framework with advanced interpolation techniques to obtain POD modes at target (unseen) parameters. While Grassmann manifold interpolation (GMI) serves as an accurate baseline, mode-realigned pointwise interpolation (MRPWI) is proposed to develop highly efficient PROMs that maintain comparable accuracy. Notably, the MRPWI employs a two-step mode realignment procedure, consisting of sign alignment and rotation alignment, to effectively synchronize the POD modes. Demonstration and evaluation of the constructed POD-Galerkin PROMs are conducted by examining flow over a cylinder. These models exhibit high fidelity in comparison to direct numerical simulation and standard POD-Galerkin ROMs. PROMs constructed via MRPWI achieve accuracy comparable to those using GMI, while providing significantly higher computational efficiency.

Hai-Feng Zhang, Zhao-Yun Chen, Peng Wang et al.

Quantum machine learning (QML) models, like their classical counterparts, are vulnerable to adversarial attacks, hindering their secure deployment. Here, we report the first systematic experimental robustness benchmark for 20-qubit quantum neural network (QNN) classifiers executed on a superconducting processor. Our benchmarking framework features an efficient adversarial attack algorithm designed for QNNs, enabling quantitative characterization of adversarial robustness and robustness bounds. From our analysis, we verify that adversarial training reduces sensitivity to targeted perturbations by regularizing input gradients, significantly enhancing QNN's robustness. Additionally, our analysis reveals that QNNs exhibit superior adversarial robustness compared to classical neural networks, an advantage attributed to inherent quantum noise. Furthermore, the empirical upper bound extracted from our attack experiments shows a minimal deviation ($3 \times 10^{-3}$) from the theoretical lower bound, providing strong experimental confirmation of the attack's effectiveness and the tightness of fidelity-based robustness bounds. This work establishes a critical experimental framework for assessing and improving quantum adversarial robustness, paving the way for secure and reliable QML applications.

Huiwei Zhou, Zhuang Liu1, Shixian Ning et al.

Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. However, many of the current PPI extraction methods need extensive feature engineering and cannot make full use of the prior knowledge in knowledge bases (KB). KBs contain huge amounts of structured information about entities and relationships, therefore plays a pivotal role in PPI extraction. This paper proposes a knowledge-aware attention network (KAN) to fuse prior knowledge about protein-protein pairs and context information for PPI extraction. The proposed model first adopts a diagonal-disabled multi-head attention mechanism to encode context sequence along with knowledge representations learned from KB. Then a novel multi-dimensional attention mechanism is used to select the features that can best describe the encoded context. Experiment results on the BioCreative VI PPI dataset show that the proposed approach could acquire knowledge-aware dependencies between different words in a sequence and lead to a new state-of-the-art performance.

Huiwei Zhou, Chengkun Lang, Zhuang Liu et al.

Background: Automatic extraction of chemical-disease relations (CDR) from unstructured text is of essential importance for disease treatment and drug development. Meanwhile, biomedical experts have built many highly-structured knowledge bases (KBs), which contain prior knowledge about chemicals and diseases. Prior knowledge provides strong support for CDR extraction. How to make full use of it is worth studying. Results: This paper proposes a novel model called "Knowledge-guided Convolutional Networks (KCN)" to leverage prior knowledge for CDR extraction. The proposed model first learns knowledge representations including entity embeddings and relation embeddings from KBs. Then, entity embeddings are used to control the propagation of context features towards a chemical-disease pair with gated convolutions. After that, relation embeddings are employed to further capture the weighted context features by a shared attention pooling. Finally, the weighted context features containing additional knowledge information are used for CDR extraction. Experiments on the BioCreative V CDR dataset show that the proposed KCN achieves 71.28% F1-score, which outperforms most of the state-of-the-art systems. Conclusions: This paper proposes a novel CDR extraction model KCN to make full use of prior knowledge. Experimental results demonstrate that KCN could effectively integrate prior knowledge and contexts for the performance improvement.

Huiwei Zhou, Xuefei Li, Weihong Yao et al.

Protein-protein interaction (PPI) extraction from published scientific literature provides additional support for precision medicine efforts. Meanwhile, knowledge bases (KBs) contain huge amounts of structured information of protein entities and their relations, which can be encoded in entity and relation embeddings to help PPI extraction. However, the prior knowledge of protein-protein pairs must be selectively used so that it is suitable for different contexts. This paper proposes a Knowledge Selection Model (KSM) to fuse the selected prior knowledge and context information for PPI extraction. Firstly, two Transformers encode the context sequence of a protein pair according to each protein embedding, respectively. Then, the two outputs are fed to a mutual attention to capture the important context features towards the protein pair. Next, the context features are used to distill the relation embedding by a knowledge selector. Finally, the selected relation embedding and the context features are concatenated for PPI extraction. Experiments on the BioCreative VI PPI dataset show that KSM achieves a new state-of-the-art performance (38.08% F1-score) by adding knowledge selection.

Xian-Ming Gu, Ting-Zhu Huang, Guojian Yin et al.

It is known that the restarted full orthogonalization method (FOM) outperforms the restarted generalized minimum residual (GMRES) method in several circumstances for solving shifted linear systems when the shifts are handled simultaneously. Many variants of them have been proposed to enhance their performance. We show that another restarted method, the restarted Hessenberg method [M. Heyouni, Méthode de Hessenberg Généralisée et Applications, Ph.D. Thesis, Université des Sciences et Technologies de Lille, France, 1996] based on Hessenberg procedure, can effectively be employed, which can provide accelerating convergence rate with respect to the number of restarts. Theoretical analysis shows that the new residual of shifted restarted Hessenberg method is still collinear with each other. In these cases where the proposed algorithm needs less enough CPU time elapsed to converge than the earlier established restarted shifted FOM, weighted restarted shifted FOM, and some other popular shifted iterative solvers based on the short-term vector recurrence, as shown via extensive numerical experiments involving the recent popular applications of handling the time fractional differential equations.