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Deep Learning · Graph Neural Networks

Dai Shi, Lequan Lin, Andi Han, Zhiyong Wang, Yi Guo, Junbin Gao

Graph Neural Networks (GNNs) have emerged as fundamental tools for a wide range of prediction tasks on graph-structured data. Recent studies have drawn analogies between GNN feature propagation and diffusion processes, which can be interpreted as dynamical systems. In this paper, we delve deeper into this perspective by connecting the dynamics in GNNs to modern Koopman theory and its numerical method, Dynamic Mode Decomposition (DMD). We illustrate how DMD can estimate a low-rank, finite-dimensional linear operator based on multiple states of the system, effectively approximating potential nonlinear interactions between nodes in the graph. This approach allows us to capture complex dynamics within the graph accurately and efficiently. We theoretically establish a connection between the DMD-estimated operator and the original dynamic operator between system states. Building upon this foundation, we introduce a family of DMD-GNN models that effectively leverage the low-rank eigenfunctions provided by the DMD algorithm. We further discuss the potential of enhancing our approach by incorporating domain-specific constraints such as symmetry into the DMD computation, allowing the corresponding GNN models to respect known physical properties of the underlying system. Our work paves the path for applying advanced dynamical system analysis tools via GNNs. We validate our approach through extensive experiments on various learning tasks, including directed graphs, large-scale graphs, long-range interactions, and spatial-temporal graphs. We also empirically verify that our proposed models can serve as powerful encoders for link prediction tasks. The results demonstrate that our DMD-enhanced GNNs achieve state-of-the-art performance, highlighting the effectiveness of integrating DMD into GNN frameworks.

Applications · Computer Vision

Qingxuan Wu, Zhiyang Dou, Sirui Xu, Soshi Shimada, Chen Wang, Zhengming Yu, Yuan Liu, Cheng Lin, Zeyu Cao, Taku Komura 等

Reconstructing 3D hand-face interactions with deformations from a single image is a challenging yet crucial task with broad applications in AR, VR, and gaming. The challenges stem from self-occlusions during single-view hand-face interactions, diverse spatial relationships between hands and face, complex deformations, and the ambiguity of the single-view setting. The previous state-of-the-art, Decaf, employs a global fitting optimization guided by contact and deformation estimation networks trained on studio-collected data with 3D annotations. However, Decaf suffers from a time-consuming optimization process and limited generalization capability due to its reliance on 3D annotations of hand-face interaction data. To address these issues, we present DICE, the first end-to-end method for Deformation-aware hand-face Interaction reCovEry from a single image. DICE estimates the poses of hands and faces, contacts, and deformations simultaneously using a Transformer-based architecture. It features disentangling the regression of local deformation fields and global mesh vertex locations into two network branches, enhancing deformation and contact estimation for precise and robust hand-face mesh recovery. To improve generalizability, we propose a weakly-supervised training approach that augments the training set using in-the-wild images without 3D ground-truth annotations, employing the depths of 2D keypoints estimated by off-the-shelf models and adversarial priors of poses for supervision. Our experiments demonstrate that DICE achieves state-of-the-art performance on a standard benchmark and in-the- wild data in terms of accuracy and physical plausibility. Additionally, our method operates at an interactive rate (20 fps) on an Nvidia 4090 GPU, whereas Decaf requires more than 15 seconds for a single image. The code will be available at: https://github.com/Qingxuan-Wu/DICE.

Deep Learning · Algorithms

Parshin Shojaee, Kazem Meidani, Shashank Gupta, Amir Barati Farimani, Chandan Reddy

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely large combinatorial hypothesis spaces. Current methods of equation discovery, commonly known as symbolic regression techniques, largely focus on extracting equations from data alone, often neglecting the domain-specific prior knowledge that scientists typically depend on. They also employ limited representations such as expression trees, constraining the search space and expressiveness of equations. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeleton hypotheses, drawing from its domain knowledge, which are then optimized against data to estimate parameters. We evaluate LLM-SR on four benchmark problems across diverse scientific domains (e.g., physics, biology), which we carefully designed to simulate the discovery process and prevent LLM recitation. Our results demonstrate that LLM-SR discovers physically accurate equations that significantly outperform state-of-the-art symbolic regression baselines, particularly in out-of-domain test settings. We also show that LLM-SR's incorporation of scientific priors enables more efficient equation space exploration than the baselines.

Parshin Shojaee, Kazem Meidani, Shashank Gupta, Amir Barati Farimani, Chandan Reddy

Mathematical equations have been unreasonably effective in describing complex natural phenomena across various scientific disciplines. However, discovering such insightful equations from data presents significant challenges due to the necessity of navigating extremely large combinatorial hypothesis spaces. Current methods of equation discovery, commonly known as symbolic regression techniques, largely focus on extracting equations from data alone, often neglecting the domain-specific prior knowledge that scientists typically depend on. They also employ limited representations such as expression trees, constraining the search space and expressiveness of equations. To bridge this gap, we introduce LLM-SR, a novel approach that leverages the extensive scientific knowledge and robust code generation capabilities of Large Language Models (LLMs) to discover scientific equations from data. Specifically, LLM-SR treats equations as programs with mathematical operators and combines LLMs' scientific priors with evolutionary search over equation programs. The LLM iteratively proposes new equation skeleton hypotheses, drawing from its domain knowledge, which are then optimized against data to estimate parameters. We evaluate LLM-SR on four benchmark problems across diverse scientific domains (e.g., physics, biology), which we carefully designed to simulate the discovery process and prevent LLM recitation. Our results demonstrate that LLM-SR discovers physically accurate equations that significantly outperform state-of-the-art symbolic regression baselines, particularly in out-of-domain test settings. We also show that LLM-SR's incorporation of scientific priors enables more efficient equation space exploration than the baselines.

Applications · Language, Speech and Dialog

Peiwen Sun, Sitong Cheng, Xiangtai Li, Zhen Ye, Huadai Liu, Honggang Zhang, Wei Xue, Yike Guo

Recently, diffusion models have achieved great success in mono-channel audio generation.However, when it comes to stereo audio generation, the soundscapes often have a complex scene of multiple objects and directions.Controlling stereo audio with spatial contexts remains challenging due to high data costs and unstable generative models. To the best of our knowledge, this work represents the first attempt to address these issues.We first construct a large-scale, simulation-based, and GPT-assisted dataset, BEWO-1M, with abundant soundscapes and descriptions even including moving and multiple sources.Beyond text modality, we have also acquired a set of images and rationally paired stereo audios through retrieval to advance multimodal generation. Existing audio generation models tend to generate rather random and indistinct spatial audio. To provide accurate guidance for Latent Diffusion Models, we introduce the SpatialSonic model utilizing spatial-aware encoders and azimuth state matrices to reveal reasonable spatial guidance. By leveraging spatial guidance, our model not only achieves the objective of generating immersive and controllable spatial audio from text but also extends to other modalities as the pioneer attempt.Finally, under fair settings, we conduct subjective and objective evaluations on simulated and real-world data to compare our approach with prevailing methods. The results demonstrate the effectiveness of our method, highlighting its capability to generate spatial audio that adheres to physical rules.

Alexey Gorbatovski, Boris Shaposhnikov, Alexey Malakhov, Nikita Surnachev, Yaroslav Aksenov, Ian Maksimov, Nikita Balagansky, Daniil Gavrilov

Despite the fact that offline methods for Large Language Models (LLMs) alignment do not require a direct reward model, they remain susceptible to overoptimization. This issue arises when the trained model deviates excessively from the reference policy, leading to a decrease in sample quality. We propose a novel approach of offline alignment methods, called Trust Region (including variants TR-DPO, TR-IPO, TR-KTO), which dynamically updates the reference policy throughout the training process. Our results show that TR alignment methods effectively mitigate overoptimization, enabling models to maintain strong performance even when substantially deviating from the initial reference policy. We demonstrate the efficacy of these approaches not only through toy examples that exhibit reduced overoptimization, but also through direct, side-by-side comparisons in specific tasks such as helpful and harmless dialogue, as well as summarization, where they surpass conventional methods. Additionally, we report significant improvements in general-purpose assistant setups with the Llama3 model on the AlpacaEval 2 and Arena-Hard benchmarks, highlighting the advantages of Trust Region methods over classical approaches.

Deep Learning · Large Language Models

Hao Cui, Zahra Shamsi, Gowoon Cheon, Xuejian Ma, Shutong Li, Maria Tikhanovskaya, Peter Norgaard, Nayantara Mudur, Martyna Plomecka, Paul Raccuglia 等

Scientific problem-solving involves synthesizing information while applying expert knowledge. We introduce CURIE, a scientific long-Context Understanding, Reasoning, and Information Extraction benchmark to measure the potential of Large Language Models (LLMs) in scientific problem-solving and assisting scientists in realistic workflows. This benchmark introduces ten challenging tasks with a total of 580 problems and solution pairs curated by experts in six disciplines - materials science, condensed matter physics, quantum computing, geo-spatial analysis, biodiversity, and proteins - covering both experimental and theoretical work-flows in science. We evaluate a range of closed and open LLMs on tasks in CURIE which requires domain expertise, comprehension of long in-context information,and multi-step reasoning. While Gemini Flash 2.0 and Claude-3 show consistent high comprehension across domains, the popular GPT-4o and command-R+ fail dramatically on protein sequencing tasks. With the best performance at 32% there is much room for improvement for all models. We hope that insights gained from CURIE can guide the future development of LLMs in sciences. Links to the data and evaluation code are in https://github.com/google/curie

Applications · Computer Vision

Haodong Hong, Yanyuan Qiao, Sen Wang, Jiajun Liu, Qi Wu

Vision-and-Language Navigation (VLN) tasks mainly evaluate agents based on one-time execution of individual instructions across multiple environments, aiming to develop agents capable of functioning in any environment in a zero-shot manner. However, real-world navigation robots often operate in persistent environments with relatively consistent physical layouts, visual observations, and language styles from instructors. Such a gap in the task setting presents an opportunity to improve VLN agents by incorporating continuous adaptation to specific environments. To better reflect these real-world conditions, we introduce GSA-VLN (General Scene Adaptation for VLN), a novel task requiring agents to execute navigation instructions within a specific scene and simultaneously adapt to it for improved performance over time. To evaluate the proposed task, one has to address two challenges in existing VLN datasets: the lack of out-of-distribution (OOD) data, and the limited number and style diversity of instructions for each scene. Therefore, we propose a new dataset, GSA-R2R, which significantly expands the diversity and quantity of environments and instructions for the Room-to-Room (R2R) dataset to evaluate agent adaptability in both ID and OOD contexts. Furthermore, we design a three-stage instruction orchestration pipeline that leverages large language models (LLMs) to refine speaker-generated instructions and apply role-playing techniques to rephrase instructions into different speaking styles. This is motivated by the observation that each individual user often has consistent signatures or preferences in their instructions, taking the use case of home robotic assistants as an example. We conducted extensive experiments on GSA-R2R to thoroughly evaluate our dataset and benchmark various methods, revealing key factors enabling agents to adapt to specific environments. Based on our findings, we propose a novel method, Graph-Retained DUET (GR-DUET), which incorporates memory-based navigation graphs with an environment-specific training strategy, achieving state-of-the-art results on all GSA-R2R splits.

Applications · Computer Vision

Long Peng, Wenbo Li, Renjing Pei, Jingjing Ren, Jiaqi Xu, Yang Wang, Yang Cao, Zheng-Jun Zha

Existing image super-resolution (SR) techniques often fail to generalize effectively in complex real-world settings due to the significant divergence between training data and practical scenarios. To address this challenge, previous efforts have either manually simulated intricate physical-based degradations or utilized learning-based techniques, yet these approaches remain inadequate for producing large-scale, realistic, and diverse data simultaneously. In this paper, we introduce a novel Realistic Decoupled Data Generator (RealDGen), an unsupervised learning data generation framework designed for real-world super-resolution. We meticulously develop content and degradation extraction strategies, which are integrated into a novel content-degradation decoupled diffusion model to create realistic low-resolution images from unpaired real LR and HR images. Extensive experiments demonstrate that RealDGen excels in generating large-scale, high-quality paired data that mirrors real-world degradations, significantly advancing the performance of popular SR models on various real-world benchmarks.

Deep Learning · Generative Models and Autoencoders

Berthy Feng, Ricardo Baptista, Katherine Bouman

Diffusion models excel at creating visually-convincing images, but they often struggle to meet subtle constraints inherent in the training data. Such constraints could be physics-based (e.g., satisfying a PDE), geometric (e.g., respecting symmetry), or semantic (e.g., including a particular number of objects). When the training data all satisfy a certain constraint, enforcing this constraint on a diffusion model makes it more reliable for generating valid synthetic data and solving constrained inverse problems. However, existing methods for constrained diffusion models are restricted in the constraints they can handle. For instance, recent work proposed to learn mirror diffusion models (MDMs), but analytical mirror maps only exist for convex constraints and can be challenging to derive. We propose *neural approximate mirror maps* (NAMMs) for general, possibly non-convex constraints. Our approach only requires a differentiable distance function from the constraint set. We learn an approximate mirror map that transforms data into an unconstrained space and a corresponding approximate inverse that maps data back to the constraint set. A generative model, such as an MDM, can then be trained in the learned mirror space and its samples restored to the constraint set by the inverse map. We validate our approach on a variety of constraints, showing that compared to an unconstrained diffusion model, a NAMM-based MDM substantially improves constraint satisfaction. We also demonstrate how existing diffusion-based inverse-problem solvers can be easily applied in the learned mirror space to solve constrained inverse problems.

Applications · Physics

Chaoran Cheng, Boran Han, Danielle Maddix, Abdul Fatir Ansari, Andrew Stuart, Michael W Mahoney, Bernie Wang

Generative models that satisfy hard constraints are critical in many scientific and engineering applications, where physical laws or system requirements must be strictly respected. Many existing constrained generative models, especially those developed for computer vision, rely heavily on gradient information, which is often sparse or computationally expensive in some fields, e.g., partial differential equations (PDEs). In this work, we introduce a novel framework for adapting pre-trained, unconstrained flow-matching models to satisfy constraints exactly in a zero-shot manner without requiring expensive gradient computations or fine-tuning. Our framework, *ECI sampling*, alternates between extrapolation (E), correction (C), and interpolation (I) stages during each iterative sampling step of flow matching sampling to ensure accurate integration of constraint information while preserving the validity of the generation. We demonstrate the effectiveness of our approach across various PDE systems, showing that ECI-guided generation strictly adheres to physical constraints and accurately captures complex distribution shifts induced by these constraints. Empirical results demonstrate that our framework consistently outperforms baseline approaches in various zero-shot constrained generation tasks and also achieves competitive results in the regression tasks without additional fine-tuning.

Applications · Physics

Ruikun Li, Huandong Wang, Qingmin Liao, Yong Li

Energy landscapes play a crucial role in shaping dynamics of many real-world complex systems. System evolution is often modeled as particles moving on a landscape under the combined effect of energy-driven drift and noise-induced diffusion, where the energy governs the long-term motion of the particles.Estimating the energy landscape of a system has been a longstanding interdisciplinary challenge, hindered by the high operational costs or the difficulty of obtaining supervisory signals. Therefore, the question of how to infer the energy landscape in the absence of true energy values is critical. In this paper, we propose a physics-informed self-supervised learning method to learn the energy landscape from the evolution trajectories of the system. It first maps the system state from the observation space to a discrete landscape space by an adaptive codebook, and then explicitly integrates energy into the graph neural Fokker-Planck equation, enabling the joint learning of energy estimation and evolution prediction. Experimental results across interdisciplinary systems demonstrate that our estimated energy has a correlation coefficient above 0.9 with the ground truth, and evolution prediction accuracy exceeds the baseline by an average of 17.65\%. The code is available at https://github.com/tsinghua-fib-lab/PESLA.

Li Huaqiu, HuXiaowan, Haoqian Wang

Real-world low-light images often suffer from complex degradations such as local overexposure, low brightness, noise, and uneven illumination. Supervised methods tend to overfit to specific scenarios, while unsupervised methods, though better at generalization, struggle to model these degradations due to the lack of reference images. To address this issue, we propose an interpretable, zero-reference joint denoising and low-light enhancement framework tailored for real-world scenarios. Our method derives a training strategy based on paired sub-images with varying illumination and noise levels, grounded in physical imaging principles and retinex theory. Additionally, we leverage the Discrete Cosine Transform (DCT) to perform frequency domain decomposition in the sRGB space, and introduce an implicit-guided hybrid representation strategy that effectively separates intricate compounded degradations. In the backbone network design, we develop retinal decomposition network guided by implicit degradation representation mechanisms. Extensive experiments demonstrate the superiority of our method. Code will be available at https://github.com/huaqlili/unsupervised-light-enhance-ICLR2025.

Applications · Physics

Sifan Wang, Jacob Seidman, Shyam Sankaran, Hanwen Wang, George Pappas, Paris Perdikaris

Operator learning, which aims to approximate maps between infinite-dimensional function spaces, is an important area in scientific machine learning with applications across various physical domains. Here we introduce the Continuous Vision Transformer (CViT), a novel neural operator architecture that leverages advances in computer vision to address challenges in learning complex physical systems. CViT combines a vision transformer encoder, a novel grid-based coordinate embedding, and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. This design allows for flexible output representations and consistent evaluation at arbitrary resolutions. We demonstrate CViT's effectiveness across a diverse range of partial differential equation (PDE) systems, including fluid dynamics, climate modeling, and reaction-diffusion processes. Our comprehensive experiments show that CViT achieves state-of-the-art performance on multiple benchmarks, often surpassing larger foundation models, even without extensive pretraining and roll-out fine-tuning. Taken together, CViT exhibits robust handling of discontinuous solutions, multi-scale features, and intricate spatio-temporal dynamics. Our contributions can be viewed as a significant step towards adapting advanced computer vision architectures for building more flexible and accurate machine learning models in the physical sciences.

Applications · Physics

Bocheng Zeng, Qi Wang, Mengtao Yan, Yang Liu, Ruizhi Chengze, Yi Zhang, Hongsheng Liu, Zidong Wang, Hao Sun

Solving partial differential equations (PDEs) serves as a cornerstone for modeling complex dynamical systems. Recent progresses have demonstrated grand benefits of data-driven neural-based models for predicting spatiotemporal dynamics (e.g., tremendous speedup gain compared with classical numerical methods). However, most existing neural models rely on rich training data, have limited extrapolation and generalization abilities, and suffer to produce precise or reliable physical prediction under intricate conditions (e.g., irregular mesh or geometry, complex boundary conditions, diverse PDE parameters, etc.). To this end, we propose a new graph learning approach, namely, Physics-encoded Message Passing Graph Network (PhyMPGN), to model spatiotemporal PDE systems on irregular meshes given small training datasets. Specifically, we incorporate a GNN into a numerical integrator to approximate the temporal marching of spatiotemporal dynamics for a given PDE system. Considering that many physical phenomena are governed by diffusion processes, we further design a learnable Laplace block, which encodes the discrete Laplace-Beltrami operator, to aid and guide the GNN learning in a physically feasible solution space. A boundary condition padding strategy is also designed to improve the model convergence and accuracy. Extensive experiments demonstrate that PhyMPGN is capable of accurately predicting various types of spatiotemporal dynamics on coarse unstructured meshes, consistently achieves the state-of-the-art results, and outperforms other baselines with considerable gains.

Applications · Chemistry and Drug Discovery

Zhengxi Lu, Shizhuo Cheng, Yuru Jiang, Yan Zhang, Min Zhang

Recent advances in protein backbone generation have achieved promising results under structural, functional, or physical constraints. However, existing methods lack the flexibility for precise topology control, limiting navigation of the backbone space. We present $\textbf{ProtPainter}$, a diffusion-based approach for generating protein backbones conditioned on 3D curves. ProtPainter follows a two-stage process: curve-based sketching and sketch-guided backbone generation. For the first stage, we propose $\textbf{CurveEncoder}$, which predicts secondary structure annotations from a curve to parametrize sketch generation. For the second stage, the sketch guides the generative process in Denoising Diffusion Probabilistic Modeling (DDPM) to generate backbones. During the process, we further introduce a fusion scheduling scheme, Helix-Gating, to control the scaling factors. To evaluate, we propose the first benchmark for topology-conditioned protein generation, introducing Protein Restoration Task and a new metric, self-consistency Topology Fitness (scTF). Experiments demonstrate ProtPainter's ability to generate topology-fit (scTF $>$ 0.8) and designable (scTM $>$ 0.5) backbones, with drawing and dragging tasks showcasing its flexibility and versatility.

Applications · Physics

Nils Wandel, Stefan Schulz, Reinhard Klein

Efficient physics simulations are essential for numerous applications, ranging from realistic cloth animations in video games, to analyzing pollutant dispersion in environmental sciences, to calculating vehicle drag coefficients in engineering applications. Unfortunately, analytical solutions to the underlying physical equations are rarely available, and numerical solutions are computationally demanding. Latest developments in the field of physics-based Deep Learning have led to promising efficiency gains but still suffer from limited generalization capabilities across multiple different PDEs. Thus, in this work, we introduce **Metamizer**, a novel neural optimizer that iteratively solves a wide range of physical systems without retraining by minimizing a physics-based loss function. To this end, our approach leverages a scale-invariant architecture that enhances gradient descent updates to accelerate convergence. Since the neural network itself acts as an optimizer, training this neural optimizer falls into the category of meta-optimization approaches. We demonstrate that Metamizer achieves high accuracy across multiple PDEs after training on the Laplace, advection-diffusion and incompressible Navier-Stokes equation as well as on cloth simulations. Remarkably, the model also generalizes to PDEs that were not covered during training such as the Poisson, wave and Burgers equation.

Applications · Physics

Long Wei, Haodong Feng, Yuchen Yang, Ruiqi Feng, Peiyan Hu, Xiang Zheng, Tao Zhang, Dixia Fan, Tailin Wu

The control problems of complex physical systems have broad applications in science and engineering. Previous studies have shown that generative control methods based on diffusion models offer significant advantages for solving these problems. However, existing generative control approaches face challenges in both performance and efficiency when extended to the closed-loop setting, which is essential for effective control. In this paper, we propose an efficient Closed-Loop Diffusion method for Physical systems Control (CL-DiffPhyCon). By employing an asynchronous denoising framework for different physical time steps, CL-DiffPhyCon generates control signals conditioned on real-time feedback from the system with significantly reduced computational cost during sampling. Additionally, the control process could be further accelerated by incorporating fast sampling techniques, such as DDIM. We evaluate CL-DiffPhyCon on two tasks: 1D Burgers' equation control and 2D incompressible fluid control. The results demonstrate that CL-DiffPhyCon achieves superior control performance with significant improvements in sampling efficiency. The code can be found at https://github.com/AI4Science-WestlakeU/CL_DiffPhyCon.

Applications · Physics

Peiyan Hu, Rui Wang, Xiang Zheng, Tao Zhang, Haodong Feng, Ruiqi Feng, Long Wei, Yue Wang, Zhi-Ming Ma, Tailin Wu

Simulating and controlling physical systems described by partial differential equations (PDEs) are crucial tasks across science and engineering. Recently, diffusion generative models have emerged as a competitive class of methods for these tasks due to their ability to capture long-term dependencies and model high-dimensional states. However, diffusion models typically struggle with handling system states with abrupt changes and generalizing to higher resolutions. In this work, we propose Wavelet Diffusion Neural Operator (WDNO), a novel PDE simulation and control framework that enhances the handling of these complexities. WDNO comprises two key innovations. Firstly, WDNO performs diffusion-based generative modeling in the wavelet domain for the entire trajectory to handle abrupt changes and long-term dependencies effectively. Secondly, to address the issue of poor generalization across different resolutions, which is one of the fundamental tasks in modeling physical systems, we introduce multi-resolution training. We validate WDNO on five physical systems, including 1D advection equation, three challenging physical systems with abrupt changes (1D Burgers' equation, 1D compressible Navier-Stokes equation and 2D incompressible fluid), and a real-world dataset ERA5, which demonstrates superior performance on both simulation and control tasks over state-of-the-art methods, with significant improvements in long-term and detail prediction accuracy. Remarkably, in the challenging context of the 2D high-dimensional and indirect control task aimed at reducing smoke leakage, WDNO reduces the leakage by 33.2% compared to the second-best baseline.

Applications · Genetics, Cell Biology, Health, etc

Ziwei Yang, Zheng Chen, XIN LIU, Rikuto Kotoge, Peng Chen, Yasuko Matsubara, Yasushi Sakurai, Jimeng Sun

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail to effectively integrate gene interaction knowledge from databases or explicitly learn subtype-specific interactions. To address this mismatch, we propose GeSubNet, which learns a unified representation capable of predicting gene interactions while distinguishing between different disease subtypes. Graphs generated by such representations can be considered subtype-specific networks. GeSubNet is a multi-step representation learning framework with three modules: First, a deep generative model learns distinct disease subtypes from patient gene expression profiles. Second, a graph neural network captures representations of prior gene networks from knowledge databases, ensuring accurate physical gene interactions. Finally, we integrate these two representations using an inference loss that leverages graph generation capabilities, conditioned on the patient separation loss, to refine subtype-specific information in the learned representation. GeSubNet consistently outperforms traditional methods, with average improvements of 30.6%, 21.0%, 20.1%, and 56.6% across four graph evaluation metrics, averaged over four cancer datasets. Particularly, we conduct a biological simulation experiment to assess how the behavior of selected genes from over 11,000 candidates affects subtypes or patient distributions. The results show that the generated network has the potential to identify subtype-specific genes with an 83% likelihood of impacting patient distribution shifts.