arXiv subjects

Jiaqi Han

Publications and source records attributed to Jiaqi Han.

At least 37 records · Page 2Linked to original sources

arXiv2025

CHORDS: Diffusion Sampling Accelerator with Multi-core Hierarchical ODE Solvers

Diffusion-based generative models have become dominant generators of high-fidelity images and videos but remain limited by their computationally expensive inference procedures. Existing acceleration techniques either require extensive model retraining or compromise significantly on sample quality. This paper explores a general, training-free, and model-agnostic acceleration strategy via multi-core parallelism. Our framework views multi-core diffusion sampling as an ODE solver pipeline, where slower yet accurate solvers progressively rectify faster solvers through a theoretically justified inter-core communication mechanism. This motivates our multi-core training-free diffusion sampling accelerator, CHORDS, which is compatible with various diffusion samplers, model architectures, and modalities. Through extensive experiments, CHORDS significantly accelerates sampling across diverse large-scale image and video diffusion models, yielding up to 2.1x speedup with four cores, improving by 50% over baselines, and 2.9x speedup with eight cores, all without quality degradation. This advancement enables CHORDS to establish a solid foundation for real-time, high-fidelity diffusion generation.

cs.LG↗

arXiv2025

Zero-Shot Cyclic Peptide Design via Composable Geometric Constraints

Cyclic peptides, characterized by geometric constraints absent in linear peptides, offer enhanced biochemical properties, presenting new opportunities to address unmet medical needs. However, designing target-specific cyclic peptides remains underexplored due to limited training data. To bridge the gap, we propose CP-Composer, a novel generative framework that enables zero-shot cyclic peptide generation via composable geometric constraints. Our approach decomposes complex cyclization patterns into unit constraints, which are incorporated into a diffusion model through geometric conditioning on nodes and edges. During training, the model learns from unit constraints and their random combinations in linear peptides, while at inference, novel constraint combinations required for cyclization are imposed as input. Experiments show that our model, despite trained with linear peptides, is capable of generating diverse target-binding cyclic peptides, reaching success rates from 38% to 84% on different cyclization strategies.

cs.LG↗

arXiv2025

GeoAda: Efficiently Finetune Geometric Diffusion Models with Equivariant Adapters

Geometric diffusion models have shown remarkable success in molecular dynamics and structure generation. However, efficiently fine-tuning them for downstream tasks with varying geometric controls remains underexplored. In this work, we propose an SE(3)-equivariant adapter framework ( GeoAda) that enables flexible and parameter-efficient fine-tuning for controlled generative tasks without modifying the original model architecture. GeoAda introduces a structured adapter design: control signals are first encoded through coupling operators, then processed by a trainable copy of selected pretrained model layers, and finally projected back via decoupling operators followed by an equivariant zero-initialized convolution. By fine-tuning only these lightweight adapter modules, GeoAda preserves the model's geometric consistency while mitigating overfitting and catastrophic forgetting. We theoretically prove that the proposed adapters maintain SE(3)-equivariance, ensuring that the geometric inductive biases of the pretrained diffusion model remain intact during adaptation. We demonstrate the wide applicability of GeoAda across diverse geometric control types, including frame control, global control, subgraph control, and a broad range of application domains such as particle dynamics, molecular dynamics, human motion prediction, and molecule generation. Empirical results show that GeoAda achieves state-of-the-art fine-tuning performance while preserving original task accuracy, whereas other baselines experience significant performance degradation due to overfitting and catastrophic forgetting.

cs.LG↗

arXiv2025

Fast and Distributed Equivariant Graph Neural Networks by Virtual Node Learning

Equivariant Graph Neural Networks (GNNs) have achieved remarkable success across diverse scientific applications. However, existing approaches face critical efficiency challenges when scaling to large geometric graphs and suffer significant performance degradation when the input graphs are sparsified for computational tractability. To address these limitations, we introduce FastEGNN and DistEGNN, two novel enhancements to equivariant GNNs for large-scale geometric graphs. FastEGNN employs a key innovation: a small ordered set of virtual nodes that effectively approximates the large unordered graph of real nodes. Specifically, we implement distinct message passing and aggregation mechanisms for different virtual nodes to ensure mutual distinctiveness, and minimize Maximum Mean Discrepancy (MMD) between virtual and real coordinates to achieve global distributedness. This design enables FastEGNN to maintain high accuracy while efficiently processing large-scale sparse graphs. For extremely large-scale geometric graphs, we present DistEGNN, a distributed extension where virtual nodes act as global bridges between subgraphs in different devices, maintaining consistency while dramatically reducing memory and computational overhead. We comprehensively evaluate our models across four challenging domains: N-body systems (100 nodes), protein dynamics (800 nodes), Water-3D (8,000 nodes), and our new Fluid113K benchmark (113,000 nodes). Results demonstrate superior efficiency and performance, establishing new capabilities in large-scale equivariant graph learning. Code is available at https://github.com/GLAD-RUC/DistEGNN.

cs.LG↗

arXiv2025

A Survey of Geometric Graph Neural Networks: Data Structures, Models and Applications

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

cs.LG↗

arXiv2025

Block Diffusion: Interpolating Between Autoregressive and Diffusion Language Models

Diffusion language models offer unique benefits over autoregressive models due to their potential for parallelized generation and controllability, yet they lag in likelihood modeling and are limited to fixed-length generation. In this work, we introduce a class of block diffusion language models that interpolate between discrete denoising diffusion and autoregressive models. Block diffusion overcomes key limitations of both approaches by supporting flexible-length generation and improving inference efficiency with KV caching and parallel token sampling. We propose a recipe for building effective block diffusion models that includes an efficient training algorithm, estimators of gradient variance, and data-driven noise schedules to minimize the variance. Block diffusion sets a new state-of-the-art performance among diffusion models on language modeling benchmarks and enables generation of arbitrary-length sequences. We provide the code, along with the model weights and blog post on the project page: https://m-arriola.com/bd3lms

cs.LG↗

arXiv2025

Reinforced Model Merging

The success of large language models has garnered widespread attention for model merging techniques, especially training-free methods which combine model capabilities within the parameter space. However, two challenges remain: (1) uniform treatment of all parameters leads to performance degradation; (2) search-based algorithms are often inefficient. In this paper, we present an innovative framework termed Reinforced Model Merging (RMM), which encompasses an environment and agent tailored for merging tasks. These components interact to execute layer-wise merging actions, aiming to search the optimal merging architecture. Notably, RMM operates without any gradient computations on the original models, rendering it feasible for edge devices. Furthermore, by utilizing data subsets during the evaluation process, we addressed the bottleneck in the reward feedback phase, thereby accelerating RMM by up to 100 times. Extensive experiments demonstrate that RMM achieves state-of-the-art performance across various vision and NLP datasets and effectively overcomes the limitations of the existing baseline methods. Our code is available at https://github.com/WuDiHJQ/Reinforced-Model-Merging.

cs.AI↗

arXiv2025

$f$-PO: Generalizing Preference Optimization with $f$-divergence Minimization

Preference optimization has made significant progress recently, with numerous methods developed to align language models with human preferences. This paper introduces $f$-divergence Preference Optimization ($f$-PO), a novel framework that generalizes and extends existing approaches. $f$-PO minimizes $f$-divergences between the optimized policy and the optimal policy, encompassing a broad family of alignment methods using various divergences. Our approach unifies previous algorithms like DPO and EXO, while offering new variants through different choices of $f$-divergences. We provide theoretical analysis of $f$-PO's properties and conduct extensive experiments on state-of-the-art language models using benchmark datasets. Results demonstrate $f$-PO's effectiveness across various tasks, achieving superior performance compared to existing methods on popular benchmarks such as AlpacaEval 2, Arena-Hard, MT-Bench, and Open LLM Leaderboard v2. Additionally, we present ablation studies exploring the impact of different $f$-divergences, offering insights into the trade-offs between regularization and performance in offline preference optimization. Our work contributes both practical algorithms and theoretical understanding to the field of language model alignment. Code is available at https://github.com/MinkaiXu/fPO.

cs.CL↗

arXiv2024

TFG: Unified Training-Free Guidance for Diffusion Models

Given an unconditional diffusion model and a predictor for a target property of interest (e.g., a classifier), the goal of training-free guidance is to generate samples with desirable target properties without additional training. Existing methods, though effective in various individual applications, often lack theoretical grounding and rigorous testing on extensive benchmarks. As a result, they could even fail on simple tasks, and applying them to a new problem becomes unavoidably difficult. This paper introduces a novel algorithmic framework encompassing existing methods as special cases, unifying the study of training-free guidance into the analysis of an algorithm-agnostic design space. Via theoretical and empirical investigation, we propose an efficient and effective hyper-parameter searching strategy that can be readily applied to any downstream task. We systematically benchmark across 7 diffusion models on 16 tasks with 40 targets, and improve performance by 8.5% on average. Our framework and benchmark offer a solid foundation for conditional generation in a training-free manner.

cs.LG↗

arXiv2024

Geometric Trajectory Diffusion Models

Generative models have shown great promise in generating 3D geometric systems, which is a fundamental problem in many natural science domains such as molecule and protein design. However, existing approaches only operate on static structures, neglecting the fact that physical systems are always dynamic in nature. In this work, we propose geometric trajectory diffusion models (GeoTDM), the first diffusion model for modeling the temporal distribution of 3D geometric trajectories. Modeling such distribution is challenging as it requires capturing both the complex spatial interactions with physical symmetries and temporal correspondence encapsulated in the dynamics. We theoretically justify that diffusion models with equivariant temporal kernels can lead to density with desired symmetry, and develop a novel transition kernel leveraging SE(3)-equivariant spatial convolution and temporal attention. Furthermore, to induce an expressive trajectory distribution for conditional generation, we introduce a generalized learnable geometric prior into the forward diffusion process to enhance temporal conditioning. We conduct extensive experiments on both unconditional and conditional generation in various scenarios, including physical simulation, molecular dynamics, and pedestrian motion. Empirical results on a wide suite of metrics demonstrate that GeoTDM can generate realistic geometric trajectories with significantly higher quality.

cs.CV↗

arXiv2024

CPSample: Classifier Protected Sampling for Guarding Training Data During Diffusion

Diffusion models have a tendency to exactly replicate their training data, especially when trained on small datasets. Most prior work has sought to mitigate this problem by imposing differential privacy constraints or masking parts of the training data, resulting in a notable substantial decrease in image quality. We present CPSample, a method that modifies the sampling process to prevent training data replication while preserving image quality. CPSample utilizes a classifier that is trained to overfit on random binary labels attached to the training data. CPSample then uses classifier guidance to steer the generation process away from the set of points that can be classified with high certainty, a set that includes the training data. CPSample achieves FID scores of 4.97 and 2.97 on CIFAR-10 and CelebA-64, respectively, without producing exact replicates of the training data. Unlike prior methods intended to guard the training images, CPSample only requires training a classifier rather than retraining a diffusion model, which is computationally cheaper. Moreover, our technique provides diffusion models with greater robustness against membership inference attacks, wherein an adversary attempts to discern which images were in the model's training dataset. We show that CPSample behaves like a built-in rejection sampler, and we demonstrate its capabilities to prevent mode collapse in Stable Diffusion.

cs.LG↗

arXiv2024

RelBench: A Benchmark for Deep Learning on Relational Databases

We present RelBench, a public benchmark for solving predictive tasks over relational databases with graph neural networks. RelBench provides databases and tasks spanning diverse domains and scales, and is intended to be a foundational infrastructure for future research. We use RelBench to conduct the first comprehensive study of Relational Deep Learning (RDL) (Fey et al., 2024), which combines graph neural network predictive models with (deep) tabular models that extract initial entity-level representations from raw tables. End-to-end learned RDL models fully exploit the predictive signal encoded in primary-foreign key links, marking a significant shift away from the dominant paradigm of manual feature engineering combined with tabular models. To thoroughly evaluate RDL against this prior gold-standard, we conduct an in-depth user study where an experienced data scientist manually engineers features for each task. In this study, RDL learns better models whilst reducing human work needed by more than an order of magnitude. This demonstrates the power of deep learning for solving predictive tasks over relational databases, opening up many new research opportunities enabled by RelBench.

cs.LG↗

arXiv2024

Algebraic solitons in the massive Thirring model

We present exact solutions describing dynamics of two algebraic solitons in the massive Thirring model. Each algebraic soliton corresponds to a simple embedded eigenvalue in the Kaup--Newell spectral problem and attains the maximal mass among the family of solitary waves traveling with the same speed. By coalescence of speeds of the two algebraic solitons, we find a new solution for an algebraic double-soliton which corresponds to a double embedded eigenvalue. We show that the double-soliton attains the double mass of a single soliton and describes a slow interaction of two identical algebraic solitons.

nlin.SI↗

arXiv2024

Equivariant Graph Neural Operator for Modeling 3D Dynamics

Modeling the complex three-dimensional (3D) dynamics of relational systems is an important problem in the natural sciences, with applications ranging from molecular simulations to particle mechanics. Machine learning methods have achieved good success by learning graph neural networks to model spatial interactions. However, these approaches do not faithfully capture temporal correlations since they only model next-step predictions. In this work, we propose Equivariant Graph Neural Operator (EGNO), a novel and principled method that directly models dynamics as trajectories instead of just next-step prediction. Different from existing methods, EGNO explicitly learns the temporal evolution of 3D dynamics where we formulate the dynamics as a function over time and learn neural operators to approximate it. To capture the temporal correlations while keeping the intrinsic SE(3)-equivariance, we develop equivariant temporal convolutions parameterized in the Fourier space and build EGNO by stacking the Fourier layers over equivariant networks. EGNO is the first operator learning framework that is capable of modeling solution dynamics functions over time while retaining 3D equivariance. Comprehensive experiments in multiple domains, including particle simulations, human motion capture, and molecular dynamics, demonstrate the significantly superior performance of EGNO against existing methods, thanks to the equivariant temporal modeling. Our code is available at https://github.com/MinkaiXu/egno.

cs.LG↗

arXiv2024

Crystal Structure Prediction by Joint Equivariant Diffusion

Crystal Structure Prediction (CSP) is crucial in various scientific disciplines. While CSP can be addressed by employing currently-prevailing generative models (e.g. diffusion models), this task encounters unique challenges owing to the symmetric geometry of crystal structures -- the invariance of translation, rotation, and periodicity. To incorporate the above symmetries, this paper proposes DiffCSP, a novel diffusion model to learn the structure distribution from stable crystals. To be specific, DiffCSP jointly generates the lattice and atom coordinates for each crystal by employing a periodic-E(3)-equivariant denoising model, to better model the crystal geometry. Notably, different from related equivariant generative approaches, DiffCSP leverages fractional coordinates other than Cartesian coordinates to represent crystals, remarkably promoting the diffusion and the generation process of atom positions. Extensive experiments verify that our DiffCSP significantly outperforms existing CSP methods, with a much lower computation cost in contrast to DFT-based methods. Moreover, the superiority of DiffCSP is also observed when it is extended for ab initio crystal generation.

cond-mat.mtrl-sci↗

arXiv2024

An Empirical Study of Data Ability Boundary in LLMs' Math Reasoning

Large language models (LLMs) are displaying emergent abilities for math reasoning tasks,and there is a growing attention on enhancing the ability of open-source LLMs through supervised fine-tuning (SFT).In this paper, we aim to explore a general data strategy for supervised data to help optimize and expand math reasoning ability.Firstly, we determine the ability boundary of reasoning paths augmentation by identifying these paths' minimal optimal set.Secondly, we validate that different abilities of the model can be cumulatively enhanced by Mix of Minimal Optimal Sets of corresponding types of data, while our models MMOS achieve SOTA performance on series base models under much lower construction costs.Besides, we point out GSM-HARD is not really hard and today's LLMs no longer lack numerical robustness.Also, we provide an Auto Problem Generator for robustness testing and educational applications.Our code and data are publicly available at https://github.com/cyzhh/MMOS.

cs.CL↗

arXiv2023

Structure-Aware DropEdge Towards Deep Graph Convolutional Networks

It has been discovered that Graph Convolutional Networks (GCNs) encounter a remarkable drop in performance when multiple layers are piled up. The main factor that accounts for why deep GCNs fail lies in over-smoothing, which isolates the network output from the input with the increase of network depth, weakening expressivity and trainability. In this paper, we start by investigating refined measures upon DropEdge -- an existing simple yet effective technique to relieve over-smoothing. We term our method as DropEdge++ for its two structure-aware samplers in contrast to DropEdge: layer-dependent sampler and feature-dependent sampler. Regarding the layer-dependent sampler, we interestingly find that increasingly sampling edges from the bottom layer yields superior performance than the decreasing counterpart as well as DropEdge. We theoretically reveal this phenomenon with Mean-Edge-Number (MEN), a metric closely related to over-smoothing. For the feature-dependent sampler, we associate the edge sampling probability with the feature similarity of node pairs, and prove that it further correlates the convergence subspace of the output layer with the input features. Extensive experiments on several node classification benchmarks, including both full- and semi- supervised tasks, illustrate the efficacy of DropEdge++ and its compatibility with a variety of backbones by achieving generally better performance over DropEdge and the no-drop version.

cs.LG↗

arXiv2023

Subequivariant Graph Reinforcement Learning in 3D Environments

Learning a shared policy that guides the locomotion of different agents is of core interest in Reinforcement Learning (RL), which leads to the study of morphology-agnostic RL. However, existing benchmarks are highly restrictive in the choice of starting point and target point, constraining the movement of the agents within 2D space. In this work, we propose a novel setup for morphology-agnostic RL, dubbed Subequivariant Graph RL in 3D environments (3D-SGRL). Specifically, we first introduce a new set of more practical yet challenging benchmarks in 3D space that allows the agent to have full Degree-of-Freedoms to explore in arbitrary directions starting from arbitrary configurations. Moreover, to optimize the policy over the enlarged state-action space, we propose to inject geometric symmetry, i.e., subequivariance, into the modeling of the policy and Q-function such that the policy can generalize to all directions, improving exploration efficiency. This goal is achieved by a novel SubEquivariant Transformer (SET) that permits expressive message exchange. Finally, we evaluate the proposed method on the proposed benchmarks, where our method consistently and significantly outperforms existing approaches on single-task, multi-task, and zero-shot generalization scenarios. Extensive ablations are also conducted to verify our design. Code and videos are available on our project page: https://alpc91.github.io/SGRL/.

cs.LG↗