GenAI4ELab/papercli-papers huggingface dataset:
A Theory of Initialisation's Impact on Specialisation
Authors: Devon Jarvis; Sebastian Lee; Clémentine Carla Juliette Dominé; Andrew M Saxe; Stefano Sarao Mannelli
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Prior work has demonstrated a consistent tendency in neural networks engaged in continual learning tasks, wherein intermediate task similarity results in the highest levels of catastrophic interference. This phenomenon is attributed to the network's tendency to reuse learned features across tasks. However, this explanation heavily relies on the premise that neuron specialisation occurs, i.e. the emergence of  localised representations. Our investigation challenges the validity of this assumption. Using theoretical frameworks for the analysis of neural networks, we show a strong dependence of specialisation on the initial condition. More precisely, we show that weight imbalance and high weight entropy can favour specialised solutions. We then apply these insights in the context of continual learning, first showing the emergence of a monotonic relation between task-similarity and forgetting in non-specialised networks. Finally, we show that  specialization by weight imbalance is beneficial on the commonly employed elastic weight consolidation regularisation technique.
Manifolds, Random Matrices and Spectral Gaps: The geometric phases of generative diffusion
Authors: Enrico Ventura; Beatrice Achilli; Gianluigi Silvestri; Carlo Lucibello; Luca Ambrogioni
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: In this paper, we investigate the latent geometry of generative diffusion models under the manifold hypothesis. For this purpose, we analyze the spectrum of eigenvalues (and singular values) of the Jacobian of the score function, whose discontinuities (gaps) reveal the presence and dimensionality of distinct sub-manifolds. Using a statistical physics approach, we derive the spectral distributions and formulas for the spectral gaps under several distributional assumptions, and we compare these theoretical predictions with the spectra estimated from trained networks. Our analysis reveals the existence of three distinct qualitative phases during the generative process: a trivial phase; a manifold coverage phase where the diffusion process fits the distribution internal to the manifold; a consolidation phase where the score becomes orthogonal to the manifold and all particles are projected on the support of the data. This `division of labor' between different timescales provides an elegant explanation of why generative diffusion models are not affected by the manifold overfitting phenomenon that plagues likelihood-based models, since the internal distribution and the manifold geometry are produced at different time points during generation.
AgentSquare: Automatic LLM Agent Search in Modular Design Space
Authors: Yu Shang; Yu Li; Keyu Zhao; Likai Ma; Jiahe Liu; Fengli Xu; Yong Li
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Recent advancements in Large Language Models (LLMs) have led to a rapid growth of agentic systems capable of handling a wide range of complex tasks. However, current research largely relies on manual, task-specific design, limiting their adaptability to novel tasks. In this paper, we introduce a new research problem: Modularized LLM Agent Search (MoLAS). We propose a modular design space that abstracts existing LLM agent designs into four fundamental modules with uniform IO interface: Planning, Reasoning, Tool Use, and Memory. Building on this design space, we present a novel LLM agent search framework called AgentSquare, which introduces two core mechanisms, i.e., module evolution and recombination, to efficiently search for optimized LLM agents. To further accelerate the process, we design a performance predictor that uses in-context surrogate models to skip unpromising agent designs. Extensive experiments across six benchmarks, covering the diverse scenarios of web, embodied, tool use and game applications, show that AgentSquare substantially outperforms hand-crafted agents, achieving an average performance gain of 17.2% against best-known human designs. Moreover, AgentSquare can generate interpretable design insights, enabling a deeper understanding of agentic architecture and its impact on task performance. We believe that the modular design space and AgentSquare search framework offer a platform for fully exploiting the potential of prior successful designs and consolidate the collective efforts of research community. Code repo is available at https://github.com/tsinghua-fib-lab/AgentSquare.
Energy-based Backdoor Defense Against Federated Graph Learning
Authors: Guancheng Wan; Zitong Shi; Wenke Huang; Guibin Zhang; Dacheng Tao; Mang Ye
Venue: ICLR 2025 (ICLR 2025 Oral)

Abstract: Federated Graph Learning is rapidly evolving as a privacy-preserving collaborative approach. However, backdoor attacks are increasingly undermining federated systems by injecting carefully designed triggers that lead to the model making incorrect predictions. Trigger structures and injection locations in Federated Graph Learning are more diverse, making traditional federated defense methods less effective. In our work, we propose an effective Federated Graph Backdoor Defense using Topological Graph Energy (FedTGE). At the local client level, it injects distribution knowledge into the local model, assigning low energy to benign samples and high energy to the constructed malicious substitutes, and selects benign clients through clustering. At the global server level, the energy elements uploaded by each client are treated as new nodes to construct a global energy graph for energy propagation, making the selected clients' energy elements more similar and further adjusting the aggregation weights. Our method can handle high data heterogeneity, does not require a validation dataset, and is effective under both small and large malicious proportions. Extensive results on various settings of federated graph scenarios under backdoor attacks validate the effectiveness of this approach.
Multi-Task Corrupted Prediction for Learning Robust Audio-Visual Speech Representation
Authors: Sungnyun Kim; Sungwoo Cho; Sangmin Bae; Kangwook Jang; Se-Young Yun
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Audio-visual speech recognition (AVSR) incorporates auditory and visual modalities to improve recognition accuracy, particularly in noisy environments where audio-only speech systems are insufficient. While previous research has largely addressed audio disruptions, few studies have dealt with visual corruptions, e.g., lip occlusions or blurred videos, which are also detrimental. To address this real-world challenge, we propose CAV2vec, a novel self-supervised speech representation learning framework particularly designed to handle audio-visual joint corruption. CAV2vec employs a self-distillation approach with a corrupted prediction task, where the student model learns to predict clean targets, generated by the teacher model, with corrupted input frames. Specifically, we suggest a unimodal multi-task learning, which distills cross-modal knowledge and aligns the corrupted modalities, by predicting clean audio targets with corrupted videos, and clean video targets with corrupted audios. This strategy mitigates the dispersion in the representation space caused by corrupted modalities, leading to more reliable and robust audio-visual fusion. Our experiments on robust AVSR benchmarks demonstrate that the corrupted representation learning method significantly enhances recognition accuracy across generalized environments involving various types of corruption. Our code is available at https://github.com/sungnyun/cav2vec.
Size-Generalizable RNA Structure Evaluation by Exploring Hierarchical Geometries
Authors: Zongzhao Li; Jiacheng Cen; Wenbing Huang; Taifeng Wang; Le Song
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Understanding the 3D structure of RNA is essential for deciphering its function and developing RNA-based therapeutics. Geometric Graph Neural Networks (GeoGNNs) that conform to the $\mathrm{E}(3)$-symmetry have advanced RNA structure evaluation, a crucial step toward RNA structure prediction. However, existing GeoGNNs are still defective in two aspects: 1. inefficient or incapable of capturing the full geometries of RNA; 2. limited generalization ability when the size of RNA significantly differs between training and test datasets. In this paper, we propose EquiRNA, a novel equivariant GNN model by exploring the three-level hierarchical geometries of RNA. At its core, EquiRNA effectively addresses the size generalization challenge by reusing the representation of nucleotide, the common building block shared across RNAs of varying sizes. Moreover, by adopting a scalarization-based equivariant GNN as the backbone, our model maintains directional information while offering higher computational efficiency compared to existing GeoGNNs. Additionally, we propose a size-insensitive $K$-nearest neighbor sampling strategy to enhance the model's robustness to RNA size shifts. We test our approach on our created benchmark as well as an existing dataset. The results show that our method significantly outperforms other state-of-the-art methods, providing a robust baseline for RNA 3D structure modeling and evaluation.
Semi-Supervised Vision-Centric 3D Occupancy World Model for Autonomous Driving
Authors: Xiang Li; Pengfei Li; Yupeng Zheng; Wei Sun; Yan Wang; yilun chen
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Understanding world dynamics is crucial for planning in autonomous driving. Recent methods attempt to achieve this by learning a 3D occupancy world model that forecasts future surrounding scenes based on current observation. However, 3D occupancy labels are still required to produce promising results. Considering the high annotation cost for 3D outdoor scenes, we propose a semi-supervised vision-centric 3D occupancy world model, **PreWorld**, to leverage the potential of 2D labels through a novel two-stage training paradigm: the self-supervised pre-training stage and the fully-supervised fine-tuning stage. Specifically, during the pre-training stage, we utilize an attribute projection head to generate different attribute fields of a scene (e.g., RGB, density, semantic), thus enabling temporal supervision from 2D labels via volume rendering techniques. Furthermore, we introduce a simple yet effective state-conditioned forecasting module to recursively forecast future occupancy and ego trajectory in a direct manner. Extensive experiments on the nuScenes dataset validate the effectiveness and scalability of our method, and demonstrate that PreWorld achieves competitive performance across 3D occupancy prediction, 4D occupancy forecasting and motion planning tasks.
Efficient Interpolation between Extragradient and Proximal Methods for Weak MVIs
Authors: Thomas Pethick; Ioannis Mavrothalassitis; Volkan Cevher
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: We study nonmonotone games satisfying the weak Minty variational inequality (MVI) with parameter $\rho \in (-\tfrac{1}{L}, \infty)$, where $L$ is the Lipschitz constant of the gradient operator. An error corrected version of the inexact proximal point algorithm is proposed, with which we establish the first $\mathcal O(1/\epsilon)$ rate for the entire range $\rho \in (-\tfrac{1}{L}, \infty)$, thus removing a logarithmic factor compared with the complexity of existing methods. The scheme automatically selects the needed accuracy for the proximal computation, and can recover the relaxed extragradient method when $\rho > -\tfrac{1}{2L}$ and the relaxed proximal point algorithm (rPPA) when $\rho > -\tfrac{1}{L}$. Due to the error correction, the scheme inherits the strong properties of the _exact_ rPPA. Specifically, we show that linear convergence is automatically achieved under appropriate conditions. Tightness for the range of $\rho$ is established through a lower bound for rPPA. Central to the algorithmic construction is a halfspace projection, where the key insight is that the allowed error tolerance can both be used to correct for the proximal approximation and to enlarge the problem class.
Generative Flows on Synthetic Pathway for Drug Design
Authors: Seonghwan Seo; Minsu Kim; Tony Shen; Martin Ester; Jinkyoo Park; Sungsoo Ahn; Woo Youn Kim
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Generative models in drug discovery have recently gained attention as efficient alternatives to brute-force virtual screening. However, most existing models do not account for synthesizability, limiting their practical use in real-world scenarios. In this paper, we propose RxnFlow, which sequentially assembles molecules using predefined molecular building blocks and chemical reaction templates to constrain the synthetic chemical pathway. We then train on this sequential generating process with the objective of generative flow networks (GFlowNets) to generate both highly rewarded and diverse molecules. To mitigate the large action space of synthetic pathways in GFlowNets, we implement a novel action space subsampling method. This enables RxnFlow to learn generative flows over extensive action spaces comprising combinations of 1.2 million building blocks and 71 reaction templates without significant computational overhead. Additionally, RxnFlow can employ modified or expanded action spaces for generation without retraining, allowing for the introduction of additional objectives or the incorporation of newly discovered building blocks. We experimentally demonstrate that RxnFlow outperforms existing reaction-based and fragment-based models in pocket-specific optimization across various target pockets. Furthermore, RxnFlow achieves state-of-the-art performance on CrossDocked2020 for pocket-conditional generation, with an average Vina score of –8.85 kcal/mol and 34.8% synthesizability. Code is available at https://github.com/SeonghwanSeo/RxnFlow.
Integrating Protein Dynamics into Structure-Based Drug Design via Full-Atom Stochastic Flows
Authors: Xiangxin Zhou; Yi Xiao; Haowei Lin; Xinheng He; Jiaqi Guan; Yang Wang; Qiang Liu; Feng Zhou; Liang Wang; Jianzhu Ma
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: The dynamic nature of proteins, influenced by ligand interactions, is essential for comprehending protein function and progressing drug discovery. Traditional structure-based drug design (SBDD) approaches typically target binding sites with rigid structures, limiting their practical application in drug development. While molecular dynamics simulation can theoretically capture all the biologically relevant conformations, the transition rate is dictated by the intrinsic energy barrier between them, making the sampling process computationally expensive. To overcome the aforementioned challenges, we propose to use generative modeling for SBDD considering conformational changes of protein pockets. We curate a dataset of apo and multiple holo states of protein-ligand complexes, simulated by molecular dynamics, and propose a full-atom flow model (and a stochastic version), named DynamicFlow, that learns to transform apo pockets and noisy ligands into holo pockets and corresponding 3D ligand molecules. Our method uncovers promising ligand molecules and corresponding holo conformations of pockets. Additionally, the resultant holo-like states provide superior inputs for traditional SBDD approaches, playing a significant role in practical drug discovery.
InstantSplamp: Fast and Generalizable Stenography Framework for Generative Gaussian Splatting
Authors: Chenxin Li; Hengyu Liu; Zhiwen Fan; Wuyang Li; Yifan Liu; Panwang Pan; Yixuan Yuan
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: With the rapid development of large generative models for 3D, especially the evolution from NeRF representations to more efficient Gaussian Splatting, the synthesis of 3D assets has become increasingly fast and efficient, enabling the large-scale publication and sharing of generated 3D objects. However, while existing methods can add watermarks or steganographic information to individual 3D assets, they often require time-consuming per-scene training and optimization, leading to watermarking overheads that can far exceed the time required for asset generation itself, making deployment impractical for generating large collections of 3D objects. To address this, we propose InstantSplamp a framework that seamlessly integrates the 3D steganography pipeline into large 3D generative models without introducing explicit additional time costs. Guided by visual foundation models,InstantSplamp subtly injects hidden information like copyright tags during asset generation, enabling effective embedding and recovery of watermarks within generated 3D assets while preserving original visual quality. Experiments across various potential deployment scenarios demonstrate that \model~strikes an optimal balance between rendering quality and hiding fidelity, as well as between hiding performance and speed. Compared to existing per-scene optimization techniques for 3D assets, InstantSplamp reduces their watermarking training overheads that are multiples of generation time to nearly zero, paving the way for real-world deployment at scale. Project page: https://gaussian-stego.github.io/.
Semantics-Adaptive Activation Intervention for LLMs via Dynamic Steering Vectors
Authors: Weixuan Wang; JINGYUAN YANG; Wei Peng
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Large language models (LLMs) have achieved remarkable performance across many tasks, yet aligning them with desired behaviors remains challenging. Activation intervention has emerged as an effective and economical method to modify the behavior of LLMs. Despite considerable interest in this area, current intervention methods exclusively employ a fixed steering vector to modify model activations, lacking adaptability to diverse input semantics. To address this limitation, we propose Semantics-Adaptive Dynamic Intervention (SADI), a novel method that constructs a dynamic steering vector to intervene model activations at inference time. More specifically, SADI utilizes activation differences in contrastive pairs to precisely identify critical elements of an LLM (i.e., attention heads, hidden states, and neurons) for targeted intervention. During inference, SADI dynamically steers model behavior by scaling element-wise activations based on the directions of input semantics. Experimental results show that SADI outperforms established baselines by substantial margins, improving task performance without training. SADI's cost-effectiveness and generalizability across various LLM backbones and tasks highlight its potential as a versatile alignment technique. We will release the code to foster research in this area.
Signature Kernel Conditional Independence Tests in Causal Discovery for Stochastic Processes
Authors: Georg Manten; Cecilia Casolo; Emilio Ferrucci; Søren Wengel Mogensen; Cristopher Salvi; Niki Kilbertus
Venue: ICLR 2025 (ICLR 2025 Spotlight)

Abstract: Inferring the causal structure underlying stochastic dynamical systems from observational data holds great promise in domains ranging from science and health to finance. Such processes can often be accurately modeled via stochastic differential equations (SDEs), which naturally imply causal relationships via `which variables enter the differential of which other variables'. In this paper, we develop conditional independence (CI) constraints on coordinate processes over selected intervals that are Markov with respect to the acyclic dependence graph (allowing self-loops) induced by a general SDE model. We then provide a sound and complete causal discovery algorithm, capable of handling both fully and partially observed data, and uniquely recovering the underlying or induced ancestral graph by exploiting time directionality assuming a CI oracle. Finally, to make our algorithm practically usable, we also propose a flexible, consistent signature kernel-based CI test to infer these constraints from data. We extensively benchmark the CI test in isolation and as part of our causal discovery algorithms, outperforming existing approaches in SDE models and beyond.
ADAM Optimization with Adaptive Batch Selection
Authors: Gyu Yeol Kim; Min-hwan Oh
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Adam is a widely used optimizer in neural network training due to its adaptive learning rate. However, because different data samples influence model updates to varying degrees, treating them equally can lead to inefficient convergence. To address this, a prior work proposed adapting the sampling distribution using a bandit framework to select samples adaptively. While promising, the bandit-based variant of Adam suffers from limited theoretical guarantees.
In this paper, we introduce \textit{Adam with Combinatorial Bandit Sampling} (AdamCB), which integrates combinatorial bandit techniques into Adam to resolve these issues. AdamCB is able to fully utilize feedback from multiple samples at once, enhancing both theoretical guarantees and practical performance. Our regret analysis shows that AdamCB achieves faster convergence than Adam-based methods including the previous bandit-based variant. Numerical experiments demonstrate that AdamCB consistently outperforms existing methods.
Tailoring Mixup to Data for Calibration
Authors: Quentin Bouniot; Pavlo Mozharovskyi; Florence d'Alché-Buc
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: Among all data augmentation techniques proposed so far, linear interpolation of training samples, also called Mixup, has found to be effective for a large panel of applications. 
  Along with improved predictive performance, Mixup is also a good technique for improving calibration.
  However, mixing data carelessly can lead to manifold mismatch, i.e., synthetic data lying outside original  class manifolds, which can deteriorate calibration.
  In this work, we show that the likelihood of assigning a wrong label with mixup increases with the distance between data to mix. 
  To this end, we propose to dynamically change the underlying distributions of interpolation coefficients 
  depending on the similarity between samples to mix, and define a flexible framework to do so without losing in diversity. We provide extensive experiments for classification and regression tasks, showing that our proposed method improves predictive performance 
  and calibration of models, while being much more efficient.
MIRACLE 3D: Memory-efficient Integrated Robust Approach for Continual Learning on 3D Point Clouds via Shape Model Construction
Authors: Hossein Resani; Behrooz Nasihatkon
Venue: ICLR 2025 (ICLR 2025 Poster)

Abstract: In this paper, we introduce a novel framework for memory-efficient and privacy-preserving continual learning in 3D object classification. Unlike conventional memory-based approaches in continual learning that require storing numerous exemplars, our method constructs a compact shape model for each class, retaining only the mean shape along with a few key modes of variation. This strategy not only enables the generation of diverse training samples while drastically reducing memory usage but also enhances privacy by eliminating the need to store original data. To further improve model robustness against input variations—an issue common in 3D domains due to the absence of strong backbones and limited training data—we incorporate Gradient Mode Regularization. This technique enhances model stability and broadens classification margins, resulting in accuracy improvements. We validate our approach through extensive experiments on the ModelNet40, ShapeNet, and ScanNet datasets, where we achieve state-of-the-art performance. Notably, our method consumes only 15% of the memory required by competing methods on the ModelNet40 and ShapeNet, while achieving comparable performance on the challenging ScanNet dataset with just 8.5% of the memory. These results underscore the scalability, effectiveness, and privacy-preserving strengths of our framework for 3D object classification.