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Computational Biology

Junxian Wu, Xinyi Ke, XIAOMING JIANG, Huanwen Wu, Youyong Kong, Lizhi Shao

Survival prediction is a significant challenge in cancer management. Tumor micro-environment is a highly sophisticated ecosystem consisting of cancer cells, immune cells, endothelial cells, fibroblasts, nerves and extracellular matrix. The intratumor heterogeneity and the interaction across multiple tissue types profoundly impacts the prognosis. However, current methods often neglect the fact that the contribution to prognosis differs with tissue types. In this paper, we propose ProtoSurv, a novel heterogeneous graph model for WSI survival prediction. The learning process of ProtoSurv is not only driven by data but also incorporates pathological domain knowledge, including the awareness of tissue heterogeneity, the emphasis on prior knowledge of prognostic-related tissues, and the depiction of spatial interaction across multiple tissues. We validate ProtoSurv across five different cancer types from TCGA (i.e., BRCA, LGG, LUAD, COAD and PAAD), and demonstrate the superiority of our method over the state-of-the-art methods.

Generative Models · Diffusion models

Kendong Liu, Zhiyu Zhu, Chuanhao Li, Hui LIU, Huanqiang Zeng, Junhui Hou

In this paper, we make the first attempt to align diffusion models for image inpainting with human aesthetic standards via a reinforcement learning framework, significantly improving the quality and visual appeal of inpainted images. Specifically, instead of directly measuring the divergence with paired images, we train a reward model with the dataset we construct, consisting of nearly 51,000 images annotated with human preferences. Then, we adopt a reinforcement learning process to fine-tune the distribution of a pre-trained diffusion model for image inpainting in the direction of higher reward. Moreover, we theoretically deduce the upper bound on the error of the reward model, which illustrates the potential confidence of reward estimation throughout the reinforcement alignment process, thereby facilitating accurate regularization.Extensive experiments on inpainting comparison and downstream tasks, such as image extension and 3D reconstruction, demonstrate the effectiveness of our approach, showing significant improvements in the alignment of inpainted images with human preference compared with state-of-the-art methods. This research not only advances the field of image inpainting but also provides a framework for incorporating human preference into the iterative refinement of generative models based on modeling reward accuracy, with broad implications for the design of visually driven AI applications. Our code and dataset are publicly available at \url{https://prefpaint.github.io}.

Computer Vision · Stereo

Desai Xie, Sai Bi, Zhixin Shu, Kai Zhang, Zexiang Xu, Yi Zhou, Soeren Pirk, Arie Kaufman, Xin Sun, Hao Tan

We present LRM-Zero, a Large Reconstruction Model (LRM) trained entirely on synthesized 3D data, achieving high-quality sparse-view 3D reconstruction. The core of LRM-Zero is our procedural 3D dataset, Zeroverse, which is automatically synthesized from simple primitive shapes with random texturing and augmentations (e.g., height fields, boolean differences, and wireframes). Unlike previous 3D datasets (e.g., Objaverse) which are often captured or crafted by humans to approximate real 3D data, Zeroverse completely ignores realistic global semantics but is rich in complex geometric and texture details that are locally similar to or even more intricate than real objects. We demonstrate that our LRM-Zero, trained with our fully synthesized Zeroverse, can achieve high visual quality in the reconstruction of real-world objects, competitive with models trained on Objaverse. We also analyze several critical design choices of Zeroverse that contribute to LRM-Zero's capability and training stability. Our work demonstrates that 3D reconstruction, one of the core tasks in 3D vision, can potentially be addressed without the semantics of real-world objects. The Zeroverse's procedural synthesis code and interactive visualization are available at: https://desaixie.github.io/lrm-zero/.

Learning Theory

Marc Wanner, Laura Lewis, Chiranjib Bhattacharyya, Devdatt Dubhashi, Alexandru Gheorghiu

A fundamental problem in quantum many-body physics is that of finding ground states of localHamiltonians. A number of recent works gave provably efficient machine learning (ML) algorithmsfor learning ground states. Specifically, [Huang et al. Science 2022], introduced an approach for learningproperties of the ground state of an $n$-qubit gapped local Hamiltonian $H$ from only $n^{\mathcal{O}(1)}$ datapoints sampled from Hamiltonians in the same phase of matter. This was subsequently improvedby [Lewis et al. Nature Communications 2024], to $\mathcal{O}(\log 𝑛)$ samples when the geometry of the $n$-qubit system is known.In this work, we introduce two approaches that achieve a constant sample complexity, independentof system size $n$, for learning ground state properties. Our first algorithm consists of a simplemodification of the ML model used by Lewis et al. and applies to a property of interest known beforehand. Our second algorithm, which applies even if a description ofthe property is not known, is a deep neural network model. While empirical results showing theperformance of neural networks have been demonstrated, to our knowledge, this is the first rigoroussample complexity bound on a neural network model for predicting ground state properties. We also perform numerical experiments that confirm the improved scaling of our approach compared to earlier results.

Neuroscience, Cognitive Science

Changze Lv, Dongqi Han, Yansen Wang, Xiaoqing Zheng, Xuanjing Huang, Dongsheng Li

Spiking neural networks (SNNs) represent a promising approach to developing artificial neural networks that are both energy-efficient and biologically plausible.However, applying SNNs to sequential tasks, such as text classification and time-series forecasting, has been hindered by the challenge of creating an effective and hardware-friendly spike-form positional encoding (PE) strategy.Drawing inspiration from the central pattern generators (CPGs) in the human brain, which produce rhythmic patterned outputs without requiring rhythmic inputs, we propose a novel PE technique for SNNs, termed CPG-PE.We demonstrate that the commonly used sinusoidal PE is mathematically a specific solution to the membrane potential dynamics of a particular CPG.Moreover, extensive experiments across various domains, including time-series forecasting, natural language processing, and image classification, show that SNNs with CPG-PE outperform their conventional counterparts.Additionally, we perform analysis experiments to elucidate the mechanism through which SNNs encode positional information and to explore the function of CPGs in the human brain.This investigation may offer valuable insights into the fundamental principles of neural computation.

Reinforcement Learning · Everything Else

Arko Banerjee, Kia Rahmani, Joydeep Biswas, Isil Dillig

Among approaches for provably safe reinforcement learning, Model Predictive Shielding (MPS) has proven effective at complex tasks in continuous, high-dimensional state spaces, by leveraging a *backup policy* to ensure safety when the learned policy attempts to take risky actions. However, while MPS can ensure safety both during and after training, it often hinders task progress due to the conservative and task-oblivious nature of backup policies.This paper introduces *Dynamic Model Predictive Shielding* (DMPS), which optimizes reinforcement learning objectives while maintaining provable safety. DMPS employs a local planner to dynamically select safe recovery actions that maximize both short-term progress as well as long-term rewards. Crucially, the planner and the neural policy play a synergistic role in DMPS. When planning recovery actions for ensuring safety, the planner utilizes the neural policy to estimate long-term rewards, allowing it to *observe* beyond its short-term planning horizon. Conversely, the neural policy under training learns from the recovery plans proposed by the planner, converging to policies that are both *high-performing* and *safe* in practice.This approach guarantees safety during and after training, with bounded recovery regret that decreases exponentially with planning horizon depth. Experimental results demonstrate that DMPS converges to policies that rarely require shield interventions after training and achieve higher rewards compared to several state-of-the-art baselines.

Physical Models · Physics

Zipeng Xiao, Siqi Kou, Hao Zhongkai, Bokai Lin, Zhijie Deng

Fourier Neural Operators (FNOs) have shown promise for solving partial differential equations (PDEs).Typically, FNOs employ separate parameters for different frequency modes to specify tunable kernel integrals in Fourier space, which, yet, results in an undesirably large number of parameters when solving high-dimensional PDEs. A workaround is to abandon the frequency modes exceeding a predefined threshold, but this limits the FNOs' ability to represent high-frequency details and poses non-trivial challenges for hyper-parameter specification. To address these, we propose AMortized Fourier Neural Operator (AM-FNO), where an amortized neural parameterization of the kernel function is deployed to accommodate arbitrarily many frequency modes using a fixed number of parameters. We introduce two implementations of AM-FNO, based on the recently developed, appealing Kolmogorov–Arnold Network (KAN) and Multi-Layer Perceptrons (MLPs) equipped with orthogonal embedding functions respectively. We extensively evaluate our method on diverse datasets from various domains and observe up to 31\% average improvement compared to competing neural operator baselines.

Computational Biology

Ruihan Guo, Rui Wang, Ruidong Wu, Zhizhou Ren, Jiahan Li, Shitong Luo, Zuofan Wu, Qiang Liu, Jian Peng, Jianzhu Ma

Predicting the effects of protein mutations is crucial for analyzing protein functions and understanding genetic diseases. However, existing models struggle to effectively extract mutation-related local structure motifs from protein databases, which hinders their predictive accuracy and robustness. To tackle this problem, we design a novel retrieval-augmented framework for incorporating similar structure information in known protein structures. We create a vector database consisting of local structure motif embeddings from a pre-trained protein structure encoder, which allows for efficient retrieval of similar local structure motifs during mutation effect prediction. Our findings demonstrate that leveraging this method results in the SOTA performance across multiple protein mutation prediction datasets, and offers a scalable solution for studying mutation effects.

Applications

Krishna Neupane, Ervine Zheng, Qi Yu

Sequential recommender systems are designed to capture users' evolving interests over time. Existing methods typically assume a uniform time interval among consecutive user interactions and may not capture users' continuously evolving behavior in the short and long term. In reality, the actual time intervals of user interactions vary dramatically. Consequently, as the time interval between interactions increases, so does the uncertainty in user behavior. Intuitively, it is beneficial to establish a correlation between the interaction time interval and the model uncertainty to provide effective recommendations. To this end, we formulate a novel Evidential Neural Stochastic Differential Equation (*E-NSDE*) to seamlessly integrate NSDE and evidential learning for effective time-aware sequential recommendations. The NSDE enables the model to learn users' fine-grained time-evolving behavior by capturing continuous user representation while evidential learning quantifies both aleatoric and epistemic uncertainties considering interaction time interval to provide model confidence during prediction. Furthermore, we derive a mathematical relationship between the interaction time interval and model uncertainty to guide the learning process. Experiments on real-world data demonstrate the effectiveness of the proposed method compared to the SOTA methods.

Deep Learning · Representation Learning

Stefanos Pertigkiozoglou, Evangelos Chatzipantazis, Shubhendu Trivedi, Kostas Daniilidis

Equivariant neural networks have been widely used in a variety of applications due to their ability to generalize well in tasks where the underlying data symmetries are known. Despite their successes, such networks can be difficult to optimize and require careful hyperparameter tuning to train successfully. In this work, we propose a novel framework for improving the optimization of such models by relaxing the hard equivariance constraint during training: We relax the equivariance constraint of the network's intermediate layers by introducing an additional non-equivariant term that we progressively constrain until we arrive at an equivariant solution. By controlling the magnitude of the activation of the additional relaxation term, we allow the model to optimize over a larger hypothesis space containing approximate equivariant networks and converge back to an equivariant solution at the end of training. We provide experimental results on different state-of-the-art network architectures, demonstrating how this training framework can result in equivariant models with improved generalization performance. Our code is available at https://github.com/StefanosPert/Equivariant_Optimization_CR

Generative Models · Diffusion models

Hanshu Yan, Xingchao Liu, Jiachun Pan, Jun Hao Liew, Qiang Liu, Jiashi Feng

We present Piecewise Rectified Flow (PeRFlow), a flow-based method for accelerating diffusion models. PeRFlow divides the sampling process of generative flows into several time windows and straightens the trajectories in each interval via the reflow operation, thereby approaching piecewise linear flows. PeRFlow achieves superior performance in a few-step generation. Moreover, through dedicated parameterizations, the PeRFlow models inherit knowledge from the pretrained diffusion models. Thus, the training converges fast and the obtained models show advantageous transfer ability, serving as universal plug-and-play accelerators that are compatible with various workflows based on the pre-trained diffusion models.

Generative Models · Diffusion models

Seyedmorteza Sadat, Jakob Buhmann, Derek Bradley, Otmar Hilliges, Romann M Weber

Advances in latent diffusion models (LDMs) have revolutionized high-resolution image generation, but the design space of the autoencoder that is central to these systems remains underexplored. In this paper, we introduce LiteVAE, a new autoencoder design for LDMs, which leverages the 2D discrete wavelet transform to enhance scalability and computational efficiency over standard variational autoencoders (VAEs) with no sacrifice in output quality. We investigate the training methodologies and the decoder architecture of LiteVAE and propose several enhancements that improve the training dynamics and reconstruction quality. Our base LiteVAE model matches the quality of the established VAEs in current LDMs with a six-fold reduction in encoder parameters, leading to faster training and lower GPU memory requirements, while our larger model outperforms VAEs of comparable complexity across all evaluated metrics (rFID, LPIPS, PSNR, and SSIM).

Applications

Yao Lai, Jinxin Liu, David Z. Pan, Ping Luo

Across a wide range of hardware scenarios, the computational efficiency and physical size of the arithmetic units significantly influence the speed and footprint of the overall hardware system. Nevertheless, the effectiveness of prior arithmetic design techniques proves inadequate, as they do not sufficiently optimize speed and area, resulting in increased latency and larger module size. To boost computing performance, this work focuses on the two most common and fundamental arithmetic modules, adders and multipliers. We cast the design tasks as single-player tree generation games, leveraging reinforcement learning techniques to optimize their arithmetic tree structures. This tree generation formulation allows us to efficiently navigate the vast search space and discover superior arithmetic designs that improve computational efficiency and hardware size within just a few hours. Our proposed method, **ArithTreeRL**, achieves significant improvements for both adders and multipliers. For adders, our approach discovers designs of 128-bit adders that achieve Pareto optimality in theoretical metrics. Compared with PrefixRL, it reduces delay and size by up to 26% and 30%, respectively. For multipliers, compared to RL-MUL, our method enhances speed and reduces size by as much as 49% and 45%. Additionally, ArithTreeRL's flexibility and scalability enable seamless integration into 7nm technology. We believe our work will offer valuable insights into hardware design, further accelerating speed and reducing size through the refined search space and our tree generation methodologies.

Robotics

Xixi Hu, Qiang Liu, Xingchao Liu, Bo Liu

Diffusion-based imitation learning improves Behavioral Cloning (BC) on multi-modal decision-making, but comes at the cost of significantly slower inference due to the recursion in the diffusion process. It urges us to design efficient policy generators while keeping the ability to generate diverse actions. To address this challenge, we propose AdaFlow, an imitation learning framework based on flow-based generative modeling. AdaFlow represents the policy with state-conditioned ordinary differential equations (ODEs), which are known as probability flows. We reveal an intriguing connection between the conditional variance of their training loss and the discretization error of the ODEs.With this insight, we propose a variance-adaptive ODE solver that can adjust its step size in the inference stage, makingAdaFlow an adaptive decision-maker, offering rapid inference without sacrificing diversity. Interestingly, it automatically reduces to a one-step generator when the action distribution is uni-modal. Our comprehensive empirical evaluation shows that AdaFlow achieves high performance with fast inference speed.

Physical Models · Physics

Baiyu Su, Qiang Liu

This paper introduces the Quadratic Quantum Variational Monte Carlo (Q$^2$VMC) algorithm, an innovative algorithm in quantum chemistry that significantly enhances the efficiency and accuracy of solving the Schrödinger equation. Inspired by the discretization of imaginary-time Schrödinger evolution, Q$^2$VMC employs a novel quadratic update mechanism that integrates seamlessly with neural network-based ansatzes. Our extensive experiments showcase Q$^2$VMC's superior performance, achieving faster convergence and lower ground state energies in wavefunction optimization across various molecular systems, without additional computational cost. This study not only advances the field of computational quantum chemistry but also highlights the important role of discretized evolution in variational quantum algorithms, offering a scalable and robust framework for future quantum research.

Jianqing Xu, Shen Li, Jiaying Wu, Miao Xiong, Ailin Deng, Jiazhen Ji, Yuge Huang, Guodong Mu, Wenjie Feng, Shouhong Ding 等

Synthetic face recognition (SFR) aims to generate synthetic face datasets that mimic the distribution of real face data, which allows for training face recognition models in a privacy-preserving manner. Despite the remarkable potential of diffusion models in image generation, current diffusion-based SFR models struggle with generalization to real-world faces. To address this limitation, we outline three key objectives for SFR: (1) promoting diversity across identities (inter-class diversity), (2) ensuring diversity within each identity by injecting various facial attributes (intra-class diversity), and (3) maintaining identity consistency within each identity group (intra-class identity preservation). Inspired by these goals, we introduce a diffusion-fueled SFR model termed $\text{ID}^3$. $\text{ID}^3$ employs an ID-preserving loss to generate diverse yet identity-consistent facial appearances. Theoretically, we show that minimizing this loss is equivalent to maximizing the lower bound of an adjusted conditional log-likelihood over ID-preserving data. This equivalence motivates an ID-preserving sampling algorithm, which operates over an adjusted gradient vector field, enabling the generation of fake face recognition datasets that approximate the distribution of real-world faces. Extensive experiments across five challenging benchmarks validate the advantages of $\text{ID}^3$.

Computer Vision · Segmentation

Paul Couairon, Mustafa Shukor, Jean-Emmanuel HAUGEARD, Matthieu Cord, Nicolas THOME

Foundation models have emerged as powerful tools across various domains including language, vision, and multimodal tasks. While prior works have addressed unsupervised semantic segmentation, they significantly lag behind supervised models. In this paper, we use a diffusion UNet encoder as a foundation vision encoder and introduce DiffCut, an unsupervised zero-shot segmentation method that solely harnesses the output features from the final self-attention block. Through extensive experimentation, we demonstrate that using these diffusion features in a graph based segmentation algorithm, significantly outperforms previous state-of-the-art methods on zero-shot segmentation. Specifically, we leverage a recursive Normalized Cut algorithm that regulates the granularity of detected objects and produces well-defined segmentation maps that precisely capture intricate image details. Our work highlights the remarkably accurate semantic knowledge embedded within diffusion UNet encoders that could then serve as foundation vision encoders for downstream tasks.

Generative Models · Diffusion models

Branislav Kveton, Boris Oreshkin, Youngsuk Park, Aniket Anand Deshmukh, Rui Song

Posterior sampling in contextual bandits with a Gaussian prior can be implemented exactly or approximately using the Laplace approximation. The Gaussian prior is computationally efficient but it cannot describe complex distributions. In this work, we propose approximate posterior sampling algorithms for contextual bandits with a diffusion model prior. The key idea is to sample from a chain of approximate conditional posteriors, one for each stage of the reverse diffusion process, which are obtained by the Laplace approximation. Our approximations are motivated by posterior sampling with a Gaussian prior, and inherit its simplicity and efficiency. They are asymptotically consistent and perform well empirically on a variety of contextual bandit problems.

Computer Vision · Image Generation

Xuanjia Zhao, Jian Guan, Congyi Fan, Dongli Xu, Youtian Lin, Haiwei Pan, Pengming Feng

Drag-based image editing using generative models provides precise control over image contents, enabling users to manipulate anything in an image with a few clicks. However, prevailing methods typically adopt $n$-step iterations for latent semantic optimization to achieve drag-based image editing, which is time-consuming and limits practical applications. In this paper, we introduce a novel one-step drag-based image editing method, i.e., FastDrag, to accelerate the editing process. Central to our approach is a latent warpage function (LWF), which simulates the behavior of a stretched material to adjust the location of individual pixels within the latent space. This innovation achieves one-step latent semantic optimization and hence significantly promotes editing speeds. Meanwhile, null regions emerging after applying LWF are addressed by our proposed bilateral nearest neighbor interpolation (BNNI) strategy. This strategy interpolates these regions using similar features from neighboring areas, thus enhancing semantic integrity. Additionally, a consistency-preserving strategy is introduced to maintain the consistency between the edited and original images by adopting semantic information from the original image, saved as key and value pairs in self-attention module during diffusion inversion, to guide the diffusion sampling. Our FastDrag is validated on the DragBench dataset, demonstrating substantial improvements in processing time over existing methods, while achieving enhanced editing performance.

Data-centric AI

Xinyi Xu, Shuaiqi Wang, Chuan Sheng Foo, Bryan Kian Hsiang Low, Giulia Fanti

Data valuation is a class of techniques for quantitatively assessing the value of data for applications like pricing in data marketplaces. Existing data valuation methods define a value for a discrete dataset. However, in many use cases, users are interested in not only the value of the dataset, but that of the distribution from which the dataset was sampled. For example, consider a buyer trying to evaluate whether to purchase data from different vendors. The buyer may observe (and compare) only a small preview sample from each vendor, to decide which vendor's data distribution is most useful to the buyer and purchase. The core question is how should we compare the values of data distributions from their samples? Under a Huber characterization of the data heterogeneity across vendors, we propose a maximum mean discrepancy (MMD)-based valuation method which enables theoretically principled and actionable policies for comparing data distributions from samples. We empirically demonstrate that our method is sample-efficient and effective in identifying valuable data distributions against several existing baselines, on multiple real-world datasets (e.g., network intrusion detection, credit card fraud detection) and downstream applications (classification, regression).