Ziwen Liu

Yanfeng Zhou, Lingrui Li, Zichen Wang et al.

XNet introduces a wavelet-based X-shaped unified architecture for fully- and semi-supervised biomedical segmentation. So far, however, XNet still faces the limitations, including performance degradation when images lack high-frequency (HF) information, underutilization of raw images and insufficient fusion. To address these issues, we propose XNet v2, a low- and high-frequency complementary model. XNet v2 performs wavelet-based image-level complementary fusion, using fusion results along with raw images inputs three different sub-networks to construct consistency loss. Furthermore, we introduce a feature-level fusion module to enhance the transfer of low-frequency (LF) information and HF information. XNet v2 achieves state-of-the-art in semi-supervised segmentation while maintaining competitve results in fully-supervised learning. More importantly, XNet v2 excels in scenarios where XNet fails. Compared to XNet, XNet v2 exhibits fewer limitations, better results and greater universality. Extensive experiments on three 2D and two 3D datasets demonstrate the effectiveness of XNet v2. Code is available at https://github.com/Yanfeng-Zhou/XNetv2 .

Ziwen Liu, Bonan Li, Congying Han et al.

Contrastive learning (CL) has shown great power in self-supervised learning due to its ability to capture insight correlations among large-scale data. Current CL models are biased to learn only the ability to discriminate positive and negative pairs due to the discriminative task setting. However, this bias would lead to ignoring its sufficiency for other downstream tasks, which we call the discriminative information overfitting problem. In this paper, we propose to tackle the above problems from the aspect of the Information Bottleneck (IB) principle, further pushing forward the frontier of CL. Specifically, we present a new perspective that CL is an instantiation of the IB principle, including information compression and expression. We theoretically analyze the optimal information situation and demonstrate that minimum sufficient augmentation and information-generalized representation are the optimal requirements for achieving maximum compression and generalizability to downstream tasks. Therefore, we propose the Masked Reconstruction Contrastive Learning~(MRCL) model to improve CL models. For implementation in practice, MRCL utilizes the masking operation for stronger augmentation, further eliminating redundant and noisy information. In order to alleviate the discriminative information overfitting problem effectively, we employ the reconstruction task to regularize the discriminative task. We conduct comprehensive experiments and show the superiority of the proposed model on multiple tasks, including image classification, semantic segmentation and objective detection.

Ziwen Liu, Meng Li

Discrete probability laws underpin statistical modeling, yet the catalog of interpretable distributions has expanded only gradually through centuries of case-by-case mathematical derivations. We introduce symbolic density estimation (SDE), an unsupervised framework that automatically recovers closed-form probability mass functions by composing elementary analytic operations within a structured search space. Our method integrates domain-specific structural priors with evolutionary search and a validity-aware inference stage, and it extends to richer distribution families such as zero inflation and finite mixtures. To support systematic evaluation and future research, we contribute a benchmark dataset spanning a broad collection of commonly used discrete distributions. The proposed algorithm recovers all benchmark families with accurate parameter estimates. A real data application shows that it identifies concise and interpretable mixture models that improve goodness-of-fit over standard models.

Ziwen Liu, Josep Grau-Bove, Scott Allan Orr

Multi-label Text Classification (MLTC) is the task of categorizing documents into one or more topics. Considering the large volumes of data and varying domains of such tasks, fully supervised learning requires manually fully annotated datasets which is costly and time-consuming. In this paper, we propose BERT-Flow-VAE (BFV), a Weakly-Supervised Multi-Label Text Classification (WSMLTC) model that reduces the need for full supervision. This new model (1) produces BERT sentence embeddings and calibrates them using a flow model, (2) generates an initial topic-document matrix by averaging results of a seeded sparse topic model and a textual entailment model which only require surface name of topics and 4-6 seed words per topic, and (3) adopts a VAE framework to reconstruct the embeddings under the guidance of the topic-document matrix. Finally, (4) it uses the means produced by the encoder model in the VAE architecture as predictions for MLTC. Experimental results on 6 multi-label datasets show that BFV can substantially outperform other baseline WSMLTC models in key metrics and achieve approximately 84% performance of a fully-supervised model.

Ziwen Liu, Huawei Lin, Yide Ran et al.

Large language models (LLMs) sometimes memorize undesirable knowledge, which must be removed after deployment. Prior work on machine unlearning has focused largely on optimization methods that adjust parameters to enforce forgetting while preserving retention. However, these approaches assume that the forget and retain sets are readily available, which rarely holds in practice. Unlearning is typically triggered by an undesired generation at inference time, making the retrieval of relevant data the central challenge. We introduce the notion of data Pareto improvement for LLM unlearning, which formalizes how retrieval can expand the achievable trade-off frontier between forgetting and retention. To realize this principle, we propose Randomized Antipodal Search on Linearized Influence Kernel (RASLIK), a retrieval algorithm that combines permutation-projection hashing with randomized antipodal search. RASLIK reduces selection variance, achieves sublinear complexity, and yields a double gain in both quality and efficiency. Across multiple models, datasets, and unlearning algorithms, RASLIK consistently outperforms deterministic baselines and even oracle sampling, establishing randomized search as a principled and scalable solution for data-centric unlearning.

Talon Chandler, Eduardo Hirata-Miyasaki, Ivan E. Ivanov et al.

Correlative computational microscopy is accelerating the mapping of dynamic biological systems by integrating morphological and molecular measurements across spatial scales, from organelles to entire organisms. Visualization, measurement, and prediction of interactions among the components of biological systems can be accelerated by generalist computational imaging frameworks that relax the trade-offs imposed by multiplex dynamic imaging. This work reports a generalist framework for wave optical imaging of the architectural order (waveOrder) among biomolecules for encoding and decoding multiple specimen properties from a minimal set of acquired channels, with or without fluorescent labels. waveOrder expresses material properties in terms of elegant physically motivated basis vectors directly interpretable as phase, absorption, birefringence, diattenuation, and fluorophore density; and it expresses image data in terms of directly measurable Stokes parameters. We report a corresponding multi-channel reconstruction algorithm to recover specimen properties in multiple contrast modes. With this framework, we implement multiple 3D computational microscopy methods, including quantitative phase imaging, quantitative label-free imaging with phase and polarization, and fluorescence deconvolution imaging, across scales ranging from organelles to whole zebrafish. These advances are available via an extensible open-source computational imaging library, waveOrder, and a napari plugin, recOrder.

Eduardo Hirata-Miyasaki, Soorya Pradeep, Ziwen Liu et al.

We report DynaCLR, a self-supervised method for embedding cell and organelle Dynamics via Contrastive Learning of Representations of time-lapse images. DynaCLR integrates single-cell tracking and time-aware contrastive sampling to learn robust, temporally regularized representations of cell dynamics. DynaCLR embeddings generalize effectively to in-distribution and out-of-distribution datasets, and can be used for several downstream tasks with sparse human annotations. We demonstrate efficient annotations of cell states with a human-in-the-loop using fluorescence and label-free imaging channels. DynaCLR method enables diverse downstream biological analyses: classification of cell division and infection, clustering heterogeneous cell migration patterns, cross-modal distillation of cell states from fluorescence to label-free channel, alignment of asynchronous cellular responses and broken cell tracks, and discovering organelle response due to infection. DynaCLR is a flexible method for comparative analyses of dynamic cellular responses to pharmacological, microbial, and genetic perturbations. We provide PyTorch-based implementations of the model training and inference pipeline (https://github.com/mehta-lab/viscy) and a GUI (https://github.com/czbiohub-sf/napari-iohub) for the visualization and annotation of trajectories of cells in the real space and the embedding space.

Zicheng Zhang, Ruobing Zheng, Ziwen Liu et al.

Recent works in implicit representations, such as Neural Radiance Fields (NeRF), have advanced the generation of realistic and animatable head avatars from video sequences. These implicit methods are still confronted by visual artifacts and jitters, since the lack of explicit geometric constraints poses a fundamental challenge in accurately modeling complex facial deformations. In this paper, we introduce Dynamic Tetrahedra (DynTet), a novel hybrid representation that encodes explicit dynamic meshes by neural networks to ensure geometric consistency across various motions and viewpoints. DynTet is parameterized by the coordinate-based networks which learn signed distance, deformation, and material texture, anchoring the training data into a predefined tetrahedra grid. Leveraging Marching Tetrahedra, DynTet efficiently decodes textured meshes with a consistent topology, enabling fast rendering through a differentiable rasterizer and supervision via a pixel loss. To enhance training efficiency, we incorporate classical 3D Morphable Models to facilitate geometry learning and define a canonical space for simplifying texture learning. These advantages are readily achievable owing to the effective geometric representation employed in DynTet. Compared with prior works, DynTet demonstrates significant improvements in fidelity, lip synchronization, and real-time performance according to various metrics. Beyond producing stable and visually appealing synthesis videos, our method also outputs the dynamic meshes which is promising to enable many emerging applications.

Jia He, Bonan Li, Ge Yang et al.

Solving 3D medical inverse problems such as image restoration and reconstruction is crucial in modern medical field. However, the curse of dimensionality in 3D medical data leads mainstream volume-wise methods to suffer from high resource consumption and challenges models to successfully capture the natural distribution, resulting in inevitable volume inconsistency and artifacts. Some recent works attempt to simplify generation in the latent space but lack the capability to efficiently model intricate image details. To address these limitations, we present Blaze3DM, a novel approach that enables fast and high-fidelity generation by integrating compact triplane neural field and powerful diffusion model. In technique, Blaze3DM begins by optimizing data-dependent triplane embeddings and a shared decoder simultaneously, reconstructing each triplane back to the corresponding 3D volume. To further enhance 3D consistency, we introduce a lightweight 3D aware module to model the correlation of three vertical planes. Then, diffusion model is trained on latent triplane embeddings and achieves both unconditional and conditional triplane generation, which is finally decoded to arbitrary size volume. Extensive experiments on zero-shot 3D medical inverse problem solving, including sparse-view CT, limited-angle CT, compressed-sensing MRI, and MRI isotropic super-resolution, demonstrate that Blaze3DM not only achieves state-of-the-art performance but also markedly improves computational efficiency over existing methods (22~40x faster than previous work).

Chenguang Wang, Ziwen Liu

In this paper, we introduce a self-supervised learning method to enhance the graph-level representations with the help of a set of subgraphs. For this purpose, we propose a universal framework to generate subgraphs in an auto-regressive way and then using these subgraphs to guide the learning of graph representation by Graph Neural Networks. Under this framework, we can get a comprehensive understanding of the graph structure in a learnable way. And to fully capture enough information of original graphs, we design three information aggregators: \textbf{attribute-conv}, \textbf{layer-conv} and \textbf{subgraph-conv} to gather information from different aspects. And to achieve efficient and effective contrastive learning, a Head-Tail contrastive construction is proposed to provide abundant negative samples. Under all proposed components which can be generalized to any Graph Neural Networks, in the unsupervised case, we achieve new state-of-the-art results in several benchmarks. We also evaluate our model on semi-supervised learning tasks and make a fair comparison to state-of-the-art semi-supervised methods.

Ziwen Liu, Mingqiang Li, Congying Han

We propose a novel and theoretical model, blocked and hierarchical variational autoencoder (BHiVAE), to get better-disentangled representation. It is well known that information theory has an excellent explanatory meaning for the network, so we start to solve the disentanglement problem from the perspective of information theory. BHiVAE mainly comes from the information bottleneck theory and information maximization principle. Our main idea is that (1) Neurons block not only one neuron node is used to represent attribute, which can contain enough information; (2) Create a hierarchical structure with different attributes on different layers, so that we can segment the information within each layer to ensure that the final representation is disentangled. Furthermore, we present supervised and unsupervised BHiVAE, respectively, where the difference is mainly reflected in the separation of information between different blocks. In supervised BHiVAE, we utilize the label information as the standard to separate blocks. In unsupervised BHiVAE, without extra information, we use the Total Correlation (TC) measure to achieve independence, and we design a new prior distribution of the latent space to guide the representation learning. It also exhibits excellent disentanglement results in experiments and superior classification accuracy in representation learning.