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Jan 26

Structure-Preserving Operator Learning

Learning complex dynamics driven by partial differential equations directly from data holds great promise for fast and accurate simulations of complex physical systems. In most cases, this problem can be formulated as an operator learning task, where one aims to learn the operator representing the physics of interest, which entails discretization of the continuous system. However, preserving key continuous properties at the discrete level, such as boundary conditions, and addressing physical systems with complex geometries is challenging for most existing approaches. We introduce a family of operator learning architectures, structure-preserving operator networks (SPONs), that allows to preserve key mathematical and physical properties of the continuous system by leveraging finite element (FE) discretizations of the input-output spaces. SPONs are encode-process-decode architectures that are end-to-end differentiable, where the encoder and decoder follows from the discretizations of the input-output spaces. SPONs can operate on complex geometries, enforce certain boundary conditions exactly, and offer theoretical guarantees. Our framework provides a flexible way of devising structure-preserving architectures tailored to specific applications, and offers an explicit trade-off between performance and efficiency, all thanks to the FE discretization of the input-output spaces. Additionally, we introduce a multigrid-inspired SPON architecture that yields improved performance at higher efficiency. Finally, we release a software to automate the design and training of SPON architectures.

  • 2 authors
·
Oct 1, 2024

Regression Transformer: Concurrent sequence regression and generation for molecular language modeling

Despite significant progress of generative models in the natural sciences, their controllability remains challenging. One fundamentally missing aspect of molecular or protein generative models is an inductive bias that can reflect continuous properties of interest. To that end, we propose the Regression Transformer (RT), a novel method that abstracts regression as a conditional sequence modeling problem. This introduces a new paradigm of multitask language models which seamlessly bridge sequence regression and conditional sequence generation. We thoroughly demonstrate that, despite using a nominal-scale training objective, the RT matches or surpasses the performance of conventional regression models in property prediction tasks of small molecules, proteins and chemical reactions. Critically, priming the same model with continuous properties yields a highly competitive conditional generative model that outperforms specialized approaches in a substructure-constrained, property-driven molecule generation benchmark. Our dichotomous approach is facilitated by a novel, alternating training scheme that enables the model to decorate seed sequences by desired properties, e.g., to optimize reaction yield. In sum, the RT is the first report of a multitask model that concurrently excels at predictive and generative tasks in biochemistry. This finds particular application in property-driven, local exploration of the chemical or protein space and could pave the road toward foundation models in material design. The code to reproduce all experiments of the paper is available at: https://github.com/IBM/regression-transformer

  • 2 authors
·
Feb 1, 2022

OmniEAR: Benchmarking Agent Reasoning in Embodied Tasks

Large language models excel at abstract reasoning but their capacity for embodied agent reasoning remains largely unexplored. We present OmniEAR, a comprehensive framework for evaluating how language models reason about physical interactions, tool usage, and multi-agent coordination in embodied tasks. Unlike existing benchmarks that provide predefined tool sets or explicit collaboration directives, OmniEAR requires agents to dynamically acquire capabilities and autonomously determine coordination strategies based on task demands. Through text-based environment representation, we model continuous physical properties and complex spatial relationships across 1,500 scenarios spanning household and industrial domains. Our systematic evaluation reveals severe performance degradation when models must reason from constraints: while achieving 85-96% success with explicit instructions, performance drops to 56-85% for tool reasoning and 63-85% for implicit collaboration, with compound tasks showing over 50% failure rates. Surprisingly, complete environmental information degrades coordination performance, indicating models cannot filter task-relevant constraints. Fine-tuning improves single-agent tasks dramatically (0.6% to 76.3%) but yields minimal multi-agent gains (1.5% to 5.5%), exposing fundamental architectural limitations. These findings demonstrate that embodied reasoning poses fundamentally different challenges than current models can address, establishing OmniEAR as a rigorous benchmark for evaluating and advancing embodied AI systems. Our code and data are included in the supplementary materials and will be open-sourced upon acceptance.

  • 10 authors
·
Aug 7, 2025 2

PointRAFT: 3D deep learning for high-throughput prediction of potato tuber weight from partial point clouds

Potato yield is a key indicator for optimizing cultivation practices in agriculture. Potato yield can be estimated on harvesters using RGB-D cameras, which capture three-dimensional (3D) information of individual tubers moving along the conveyor belt. However, point clouds reconstructed from RGB-D images are incomplete due to self-occlusion, leading to systematic underestimation of tuber weight. To address this, we introduce PointRAFT, a high-throughput point cloud regression network that directly predicts continuous 3D shape properties, such as tuber weight, from partial point clouds. Rather than reconstructing full 3D geometry, PointRAFT infers target values directly from raw 3D data. Its key architectural novelty is an object height embedding that incorporates tuber height as an additional geometric cue, improving weight prediction under practical harvesting conditions. PointRAFT was trained and evaluated on 26,688 partial point clouds collected from 859 potato tubers across four cultivars and three growing seasons on an operational harvester in Japan. On a test set of 5,254 point clouds from 172 tubers, PointRAFT achieved a mean absolute error of 12.0 g and a root mean squared error of 17.2 g, substantially outperforming a linear regression baseline and a standard PointNet++ regression network. With an average inference time of 6.3 ms per point cloud, PointRAFT supports processing rates of up to 150 tubers per second, meeting the high-throughput requirements of commercial potato harvesters. Beyond potato weight estimation, PointRAFT provides a versatile regression network applicable to a wide range of 3D phenotyping and robotic perception tasks. The code, network weights, and a subset of the dataset are publicly available at https://github.com/pieterblok/pointraft.git.

  • 6 authors
·
Dec 30, 2025

Continuous Speculative Decoding for Autoregressive Image Generation

Continuous-valued Autoregressive (AR) image generation models have demonstrated notable superiority over their discrete-token counterparts, showcasing considerable reconstruction quality and higher generation fidelity. However, the computational demands of the autoregressive framework result in significant inference overhead. While speculative decoding has proven effective in accelerating Large Language Models (LLMs), their adaptation to continuous-valued visual autoregressive models remains unexplored. This work generalizes the speculative decoding algorithm from discrete tokens to continuous space. By analyzing the intrinsic properties of output distribution, we establish a tailored acceptance criterion for the diffusion distributions prevalent in such models. To overcome the inconsistency that occurred in speculative decoding output distributions, we introduce denoising trajectory alignment and token pre-filling methods. Additionally, we identify the hard-to-sample distribution in the rejection phase. To mitigate this issue, we propose a meticulous acceptance-rejection sampling method with a proper upper bound, thereby circumventing complex integration. Experimental results show that our continuous speculative decoding achieves a remarkable 2.33times speed-up on off-the-shelf models while maintaining the output distribution. Codes will be available at https://github.com/MarkXCloud/CSpD

  • 6 authors
·
Nov 18, 2024 3

Chain-of-Visual-Thought: Teaching VLMs to See and Think Better with Continuous Visual Tokens

Vision-Language Models (VLMs) excel at reasoning in linguistic space but struggle with perceptual understanding that requires dense visual perception, e.g., spatial reasoning and geometric awareness. This limitation stems from the fact that current VLMs have limited mechanisms to capture dense visual information across spatial dimensions. We introduce Chain-of-Visual-Thought (COVT), a framework that enables VLMs to reason not only in words but also through continuous visual tokens-compact latent representations that encode rich perceptual cues. Within a small budget of roughly 20 tokens, COVT distills knowledge from lightweight vision experts, capturing complementary properties such as 2D appearance, 3D geometry, spatial layout, and edge structure. During training, the VLM with COVT autoregressively predicts these visual tokens to reconstruct dense supervision signals (e.g., depth, segmentation, edges, and DINO features). At inference, the model reasons directly in the continuous visual token space, preserving efficiency while optionally decoding dense predictions for interpretability. Evaluated across more than ten diverse perception benchmarks, including CV-Bench, MMVP, RealWorldQA, MMStar, WorldMedQA, and HRBench, integrating COVT into strong VLMs such as Qwen2.5-VL and LLaVA consistently improves performance by 3% to 16% and demonstrates that compact continuous visual thinking enables more precise, grounded, and interpretable multimodal intelligence.

TopoReformer: Mitigating Adversarial Attacks Using Topological Purification in OCR Models

Adversarially perturbed images of text can cause sophisticated OCR systems to produce misleading or incorrect transcriptions from seemingly invisible changes to humans. Some of these perturbations even survive physical capture, posing security risks to high-stakes applications such as document processing, license plate recognition, and automated compliance systems. Existing defenses, such as adversarial training, input preprocessing, or post-recognition correction, are often model-specific, computationally expensive, and affect performance on unperturbed inputs while remaining vulnerable to unseen or adaptive attacks. To address these challenges, TopoReformer is introduced, a model-agnostic reformation pipeline that mitigates adversarial perturbations while preserving the structural integrity of text images. Topology studies properties of shapes and spaces that remain unchanged under continuous deformations, focusing on global structures such as connectivity, holes, and loops rather than exact distance. Leveraging these topological features, TopoReformer employs a topological autoencoder to enforce manifold-level consistency in latent space and improve robustness without explicit gradient regularization. The proposed method is benchmarked on EMNIST, MNIST, against standard adversarial attacks (FGSM, PGD, Carlini-Wagner), adaptive attacks (EOT, BDPA), and an OCR-specific watermark attack (FAWA).

  • 5 authors
·
Nov 19, 2025

Reliable Unlearning Harmful Information in LLMs with Metamorphosis Representation Projection

While Large Language Models (LLMs) have demonstrated impressive performance in various domains and tasks, concerns about their safety are becoming increasingly severe. In particular, since models may store unsafe knowledge internally, machine unlearning has emerged as a representative paradigm to ensure model safety. Existing approaches employ various training techniques, such as gradient ascent and negative preference optimization, in attempts to eliminate the influence of undesired data on target models. However, these methods merely suppress the activation of undesired data through parametric training without completely eradicating its informational traces within the model. This fundamental limitation makes it difficult to achieve effective continuous unlearning, rendering these methods vulnerable to relearning attacks. To overcome these challenges, we propose a Metamorphosis Representation Projection (MRP) approach that pioneers the application of irreversible projection properties to machine unlearning. By implementing projective transformations in the hidden state space of specific network layers, our method effectively eliminates harmful information while preserving useful knowledge. Experimental results demonstrate that our approach enables effective continuous unlearning and successfully defends against relearning attacks, achieving state-of-the-art performance in unlearning effectiveness while preserving natural performance. Our code is available in https://github.com/ChengcanWu/MRP.

  • 5 authors
·
Aug 21, 2025

PepTune: De Novo Generation of Therapeutic Peptides with Multi-Objective-Guided Discrete Diffusion

Peptide therapeutics, a major class of medicines, have achieved remarkable success across diseases such as diabetes and cancer, with landmark examples such as GLP-1 receptor agonists revolutionizing the treatment of type-2 diabetes and obesity. Despite their success, designing peptides that satisfy multiple conflicting objectives, such as target binding affinity, solubility, and membrane permeability, remains a major challenge. Classical drug development and structure-based design are ineffective for such tasks, as they fail to optimize global functional properties critical for therapeutic efficacy. Existing generative frameworks are largely limited to continuous spaces, unconditioned outputs, or single-objective guidance, making them unsuitable for discrete sequence optimization across multiple properties. To address this, we present PepTune, a multi-objective discrete diffusion model for the simultaneous generation and optimization of therapeutic peptide SMILES. Built on the Masked Discrete Language Model (MDLM) framework, PepTune ensures valid peptide structures with state-dependent masking schedules and penalty-based objectives. To guide the diffusion process, we propose a Monte Carlo Tree Search (MCTS)-based strategy that balances exploration and exploitation to iteratively refine Pareto-optimal sequences. MCTS integrates classifier-based rewards with search-tree expansion, overcoming gradient estimation challenges and data sparsity inherent to discrete spaces. Using PepTune, we generate diverse, chemically-modified peptides optimized for multiple therapeutic properties, including target binding affinity, membrane permeability, solubility, hemolysis, and non-fouling characteristics on various disease-relevant targets. In total, our results demonstrate that MCTS-guided discrete diffusion is a powerful and modular approach for multi-objective sequence design in discrete state spaces.

  • 3 authors
·
Dec 23, 2024 2

Semantic Concentration for Self-Supervised Dense Representations Learning

Recent advances in image-level self-supervised learning (SSL) have made significant progress, yet learning dense representations for patches remains challenging. Mainstream methods encounter an over-dispersion phenomenon that patches from the same instance/category scatter, harming downstream performance on dense tasks. This work reveals that image-level SSL avoids over-dispersion by involving implicit semantic concentration. Specifically, the non-strict spatial alignment ensures intra-instance consistency, while shared patterns, i.e., similar parts of within-class instances in the input space, ensure inter-image consistency. Unfortunately, these approaches are infeasible for dense SSL due to their spatial sensitivity and complicated scene-centric data. These observations motivate us to explore explicit semantic concentration for dense SSL. First, to break the strict spatial alignment, we propose to distill the patch correspondences. Facing noisy and imbalanced pseudo labels, we propose a noise-tolerant ranking loss. The core idea is extending the Average Precision (AP) loss to continuous targets, such that its decision-agnostic and adaptive focusing properties prevent the student model from being misled. Second, to discriminate the shared patterns from complicated scenes, we propose the object-aware filter to map the output space to an object-based space. Specifically, patches are represented by learnable prototypes of objects via cross-attention. Last but not least, empirical studies across various tasks soundly support the effectiveness of our method. Code is available in https://github.com/KID-7391/CoTAP.

  • 5 authors
·
Sep 11, 2025

DragMesh: Interactive 3D Generation Made Easy

While generative models have excelled at creating static 3D content, the pursuit of systems that understand how objects move and respond to interactions remains a fundamental challenge. Current methods for articulated motion lie at a crossroads: they are either physically consistent but too slow for real-time use, or generative but violate basic kinematic constraints. We present DragMesh, a robust framework for real-time interactive 3D articulation built around a lightweight motion generation core. Our core contribution is a novel decoupled kinematic reasoning and motion generation framework. First, we infer the latent joint parameters by decoupling semantic intent reasoning (which determines the joint type) from geometric regression (which determines the axis and origin using our Kinematics Prediction Network (KPP-Net)). Second, to leverage the compact, continuous, and singularity-free properties of dual quaternions for representing rigid body motion, we develop a novel Dual Quaternion VAE (DQ-VAE). This DQ-VAE receives these predicted priors, along with the original user drag, to generate a complete, plausible motion trajectory. To ensure strict adherence to kinematics, we inject the joint priors at every layer of the DQ-VAE's non-autoregressive Transformer decoder using FiLM (Feature-wise Linear Modulation) conditioning. This persistent, multi-scale guidance is complemented by a numerically-stable cross-product loss to guarantee axis alignment. This decoupled design allows DragMesh to achieve real-time performance and enables plausible, generative articulation on novel objects without retraining, offering a practical step toward generative 3D intelligence. Code: https://github.com/AIGeeksGroup/DragMesh. Website: https://aigeeksgroup.github.io/DragMesh.

PekingUniversity Peking University
·
Dec 6, 2025 2

On the Continuity of Rotation Representations in Neural Networks

In neural networks, it is often desirable to work with various representations of the same space. For example, 3D rotations can be represented with quaternions or Euler angles. In this paper, we advance a definition of a continuous representation, which can be helpful for training deep neural networks. We relate this to topological concepts such as homeomorphism and embedding. We then investigate what are continuous and discontinuous representations for 2D, 3D, and n-dimensional rotations. We demonstrate that for 3D rotations, all representations are discontinuous in the real Euclidean spaces of four or fewer dimensions. Thus, widely used representations such as quaternions and Euler angles are discontinuous and difficult for neural networks to learn. We show that the 3D rotations have continuous representations in 5D and 6D, which are more suitable for learning. We also present continuous representations for the general case of the n-dimensional rotation group SO(n). While our main focus is on rotations, we also show that our constructions apply to other groups such as the orthogonal group and similarity transforms. We finally present empirical results, which show that our continuous rotation representations outperform discontinuous ones for several practical problems in graphics and vision, including a simple autoencoder sanity test, a rotation estimator for 3D point clouds, and an inverse kinematics solver for 3D human poses.

  • 5 authors
·
Dec 17, 2018

Denotational validation of higher-order Bayesian inference

We present a modular semantic account of Bayesian inference algorithms for probabilistic programming languages, as used in data science and machine learning. Sophisticated inference algorithms are often explained in terms of composition of smaller parts. However, neither their theoretical justification nor their implementation reflects this modularity. We show how to conceptualise and analyse such inference algorithms as manipulating intermediate representations of probabilistic programs using higher-order functions and inductive types, and their denotational semantics. Semantic accounts of continuous distributions use measurable spaces. However, our use of higher-order functions presents a substantial technical difficulty: it is impossible to define a measurable space structure over the collection of measurable functions between arbitrary measurable spaces that is compatible with standard operations on those functions, such as function application. We overcome this difficulty using quasi-Borel spaces, a recently proposed mathematical structure that supports both function spaces and continuous distributions. We define a class of semantic structures for representing probabilistic programs, and semantic validity criteria for transformations of these representations in terms of distribution preservation. We develop a collection of building blocks for composing representations. We use these building blocks to validate common inference algorithms such as Sequential Monte Carlo and Markov Chain Monte Carlo. To emphasize the connection between the semantic manipulation and its traditional measure theoretic origins, we use Kock's synthetic measure theory. We demonstrate its usefulness by proving a quasi-Borel counterpart to the Metropolis-Hastings-Green theorem.

  • 10 authors
·
Nov 8, 2017