Tianzi Jiang

Hui Xiong, Congying Chu, Lingzhong Fan et al.

In recent years, advances in neuroscience and artificial intelligence have paved the way for unprecedented opportunities for understanding the complexity of the brain and its emulation by computational systems. Cutting-edge advancements in neuroscience research have revealed the intricate relationship between brain structure and function, while the success of artificial neural networks highlights the importance of network architecture. Now is the time to bring them together to better unravel how intelligence emerges from the brain's multiscale repositories. In this review, we propose the Digital Twin Brain (DTB) as a transformative platform that bridges the gap between biological and artificial intelligence. It consists of three core elements: the brain structure that is fundamental to the twinning process, bottom-layer models to generate brain functions, and its wide spectrum of applications. Crucially, brain atlases provide a vital constraint, preserving the brain's network organization within the DTB. Furthermore, we highlight open questions that invite joint efforts from interdisciplinary fields and emphasize the far-reaching implications of the DTB. The DTB can offer unprecedented insights into the emergence of intelligence and neurological disorders, which holds tremendous promise for advancing our understanding of both biological and artificial intelligence, and ultimately propelling the development of artificial general intelligence and facilitating precision mental healthcare.

Bokai Zhao, Yiyang Zhang, Yuanchi Zhu et al.

Pathology foundation models (PFMs) have emerged as a core approach for learning transferable representations from whole slide images (WSIs), and they are typically benchmarked through downstream clinical endpoints. While such task level evaluations are indispensable, they offer limited insight into what the representations themselves encode, particularly whether PFM embeddings can distinguish meaningful tissue regions and capture their spatial relationships. We present SpaPath-Bench, a representation level benchmark designed to diagnose spatial representation capability in PFMs. SpaPath-Bench formulates spatial domain identification (SDI) on paired whole slide image and spatial transcriptomics (ST) data as a diagnostic task. It curates 42 public paired WSI and ST slides, enables large scale evaluation across 19 encoders and seven SDI methods, and measures partition quality using three complementary criteria: unsupervised spatial coherence, transcriptomics referenced agreement, and expert referenced agreement. Across 83K runs, SpaPath-Bench reveals that different pretraining paradigms capture distinct aspects of tissue spatial architecture, and it provides practical guidance for building the next generation of spatially aware computational pathology models. Code and data pipelines are publicly available at https://bokai-zhao.github.io/SpaPath-benchboard/.

Bokai Zhao, Weiyang Shi, Hanqing Chao et al.

Spatial proteomics maps protein distributions in tissues, providing transformative insights for life sciences. However, current sequencing-based technologies suffer from low spatial resolution, and substantial inter-tissue variability in protein expression further compromises the performance of existing molecular data prediction methods. In this work, we introduce the novel task of spatial super-resolution for sequencing-based spatial proteomics (seq-SP) and, to the best of our knowledge, propose the first deep learning model for this task--Neural Proteomics Fields (NPF). NPF formulates seq-SP as a protein reconstruction problem in continuous space by training a dedicated network for each tissue. The model comprises a Spatial Modeling Module, which learns tissue-specific protein spatial distributions, and a Morphology Modeling Module, which extracts tissue-specific morphological features. Furthermore, to facilitate rigorous evaluation, we establish an open-source benchmark dataset, Pseudo-Visium SP, for this task. Experimental results demonstrate that NPF achieves state-of-the-art performance with fewer learnable parameters, underscoring its potential for advancing spatial proteomics research. Our code and dataset are publicly available at https://github.com/Bokai-Zhao/NPF.

Jian Cui, Liqiang Yuan, Zhaoxiang Wang et al.

As deep learning has achieved state-of-the-art performance for many tasks of EEG-based BCI, many efforts have been made in recent years trying to understand what have been learned by the models. This is commonly done by generating a heatmap indicating to which extent each pixel of the input contributes to the final classification for a trained model. Despite the wide use, it is not yet understood to which extent the obtained interpretation results can be trusted and how accurate they can reflect the model decisions. In order to fill this research gap, we conduct a study to evaluate different deep interpretation techniques quantitatively on EEG datasets. The results reveal the importance of selecting a proper interpretation technique as the initial step. In addition, we also find that the quality of the interpretation results is inconsistent for individual samples despite when a method with an overall good performance is used. Many factors, including model structure and dataset types, could potentially affect the quality of the interpretation results. Based on the observations, we propose a set of procedures that allow the interpretation results to be presented in an understandable and trusted way. We illustrate the usefulness of our method for EEG-based BCI with instances selected from different scenarios.

Xin Li, Yaohua Hu, Chong Li et al.

In this paper, we discuss the statistical properties of the $\ell_q$ optimization methods $(0<q\leq 1)$, including the $\ell_q$ minimization method and the $\ell_q$ regularization method, for estimating a sparse parameter from noisy observations in high-dimensional linear regression with either a deterministic or random design. For this purpose, we introduce a general $q$-restricted eigenvalue condition (REC) and provide its sufficient conditions in terms of several widely-used regularity conditions such as sparse eigenvalue condition, restricted isometry property, and mutual incoherence property. By virtue of the $q$-REC, we exhibit the stable recovery property of the $\ell_q$ optimization methods for either deterministic or random designs by showing that the $\ell_2$ recovery bound $O(ε^2)$ for the $\ell_q$ minimization method and the oracle inequality and $\ell_2$ recovery bound $O(λ^{\frac{2}{2-q}}s)$ for the $\ell_q$ regularization method hold respectively with high probability. The results in this paper are nonasymptotic and only assume the weak $q$-REC. The preliminary numerical results verify the established statistical property and demonstrate the advantages of the $\ell_q$ regularization method over some existing sparse optimization methods.

Jian Cheng, Tianzi Jiang, Rachid Deriche et al.

Compressed Sensing (CS) takes advantage of signal sparsity or compressibility and allows superb signal reconstruction from relatively few measurements. Based on CS theory, a suitable dictionary for sparse representation of the signal is required. In diffusion MRI (dMRI), CS methods were proposed to reconstruct diffusion-weighted signal and the Ensemble Average Propagator (EAP), and there are two kinds of Dictionary Learning (DL) methods: 1) Discrete Representation DL (DR-DL), and 2) Continuous Representation DL (CR-DL). DR-DL is susceptible to numerical inaccuracy owing to interpolation and regridding errors in a discretized q-space. In this paper, we propose a novel CR-DL approach, called Dictionary Learning - Spherical Polar Fourier Imaging (DL-SPFI) for effective compressed-sensing reconstruction of the q-space diffusion-weighted signal and the EAP. In DL-SPFI, an dictionary that sparsifies the signal is learned from the space of continuous Gaussian diffusion signals. The learned dictionary is then adaptively applied to different voxels using a weighted LASSO framework for robust signal reconstruction. The adaptive dictionary is proved to be optimal. Compared with the start-of-the-art CR-DL and DR-DL methods proposed by Merlet et al. and Bilgic et al., espectively, our work offers the following advantages. First, the learned dictionary is proved to be optimal for Gaussian diffusion signals. Second, to our knowledge, this is the first work to learn a voxel-adaptive dictionary. The importance of the adaptive dictionary in EAP reconstruction will be demonstrated theoretically and empirically. Third, optimization in DL-SPFI is only performed in a small subspace resided by the SPF coefficients, as opposed to the q-space approach utilized by Merlet et al. The experiment results demonstrate the advantages of DL-SPFI over the original SPF basis and Bilgic et al.'s method.