ICLR 2025 Papers

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of around 40k protein density maps at various resolutions. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CryoFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

Multimodal Large Language Models (MLLMs) are thriving through continuous fine-tuning by LLMs. Driven by the law that "scale is everything", MLLMs expand their training sets during version iterations. In this paper, we propose a large-scale training data engine built around an evaluating-exploring-evolving (E3) loop. Evaluating the data provides insights into its characteristics. Exploring quality rules helps identify which data enhances training. Together, these processes facilitate the systematic evolution of new, high-quality data. With the E3 loop, we introduce ZooProbe, an efficient data engine for MLLMs. First, the problem of data expansion is formalized as a tree of sampling and growth. ZooProbe introduces a small-scale model *zoo* to obtain comprehensive evaluations for child datasets. From multiple perspectives, visual, textual, and multimodal models cover over 50 dimensions of intrinsic and meta attributes, such as object and topic distribution, and higher-level properties, like annotation quality and scene complexity. ZooProbe constructs based on A$^\star$ search, modeling the heuristic function as a quality estimate from data evaluation results. It dynamically explores the rule of data quality based on the model state of the *probe* datasets. Additionally, it evolves new targeted data with identified high-quality rules. We also develop an extra heuristic quality ranker with the data utilized and discarded during the expansion. Our experiments show that ZooProbe significantly breaks the scaling law in multimodal instruction fine-tuning at scales of 260$k$ and below. ZooProbe generates high-quality data that accelerates MLLM training and enhances performance, automating the evolution of large-scale training data.

The Transformer architecture is widely deployed in many popular and impactful Large Language Models. At its core is the attention mechanism for calculating correlations between pairs of tokens. Performing an attention computation takes quadratic time in the input size, and had become the time bottleneck for transformer operations. In order to circumvent this, researchers have used a variety of approaches, including designing heuristic algorithms for performing attention computations faster, and proposing alternatives to the attention mechanism which can be computed more quickly. For instance, state space models such as Mamba were designed to replace attention with an almost linear time alternative. In this paper, we prove that any such approach cannot perform important tasks that Transformer is able to perform (assuming a popular conjecture from fine-grained complexity theory). We focus on document similarity tasks, where one is given as input many documents and would like to find a pair which is (approximately) the most similar. We prove that Transformer is able to perform this task, and we prove that this task cannot be performed in truly subquadratic time by any algorithm. Thus, any model which can be evaluated in subquadratic time – whether because of subquadratic-time heuristics for attention, faster attention replacements like Mamba, or any other reason – cannot perform this task. In other words, in order to perform tasks that (implicitly or explicitly) involve document similarity, one may as well use Transformer and cannot avoid its quadratic running time.

The Sparse Mixture of Experts (SMoE) has been widely employed to enhance the efficiency of training and inference for Transformer-based foundational models, yielding promising results. However, the performance of SMoE heavily depends on the choice of hyper-parameters, such as the number of experts and the number of experts to be activated (referred to as top-$k$), resulting in significant computational overhead due to the extensive model training by searching over various hyper-parameter configurations. As a remedy, we introduce the Dynamic Mixture of Experts (DynMoE) technique. DynMoE incorporates (1) a novel gating method that enables each token to automatically determine the number of experts to activate. (2) An adaptive process automatically adjusts the number of experts during training. Extensive numerical results across Vision, Language, and Vision-Language tasks demonstrate the effectiveness of our approach to achieve competitive performance compared to GMoE for vision and language tasks, and MoE-LLaVA for vision-language tasks, while maintaining efficiency by activating fewer parameters. Our code is available at \url{https://github.com/LINs-lab/DynMoE}.

A significant aspiration of offline reinforcement learning (RL) is to develop a generalist agent with high capabilities from large and heterogeneous datasets. However, prior approaches that scale offline RL either rely heavily on expert trajectories or struggle to generalize to diverse unseen tasks. Inspired by the excellent generalization of world model in conditional video generation, we explore the potential of image observation-based world model for scaling offline RL and enhancing generalization on novel tasks. In this paper, we introduce JOWA: Jointly-Optimized World-Action model, an offline model-based RL agent pretrained on multiple Atari games with 6 billion tokens data to learn general-purpose representation and decision-making ability. Our method jointly optimizes a world-action model through a shared transformer backbone, which stabilize temporal difference learning with large models during pretraining. Moreover, we propose a provably efficient and parallelizable planning algorithm to compensate for the Q-value estimation error and thus search out better policies. Experimental results indicate that our largest agent, with 150 million parameters, achieves 78.9% human-level performance on pretrained games using only 10% subsampled offline data, outperforming existing state-of-the-art large-scale offline RL baselines by 31.6% on averange. Furthermore, JOWA scales favorably with model capacity and can sample-efficiently transfer to novel games using only 5k offline fine-tuning data (approximately 4 trajectories) per game, demonstrating superior generalization.

Large-scale diffusion models have achieved remarkable performance in generative tasks. Beyond their initial training applications, these models have proven their ability to function as versatile plug-and-play priors. For instance, 2D diffusion models can serve as loss functions to optimize 3D implicit models. Rectified Flow, a novel class of generative models, has demonstrated superior performance across various domains. Compared to diffusion-based methods, rectified flow approaches surpass them in terms of generation quality and efficiency. In this work, we present theoretical and experimental evidence demonstrating that rectified flow based methods offer similar functionalities to diffusion models — they can also serve as effective priors. Besides the generative capabilities of diffusion priors, motivated by the unique time-symmetry properties of rectified flow models, a variant of our method can additionally perform image inversion. Experimentally, our rectified flow based priors outperform their diffusion counterparts — the SDS and VSD losses — in text-to-3D generation. Our method also displays competitive performance in image inversion and editing. Code is available at: https://github.com/yangxiaofeng/rectified_flow_prior.

Node Anomaly Detection (NAD) has gained significant attention in the deep learning community due to its diverse applications in real-world scenarios. Existing NAD methods primarily embed graphs within a single Euclidean space, while overlooking the potential of non-Euclidean spaces. Besides, to address the prevalent issue of limited supervision in real NAD tasks, previous methods tend to leverage synthetic data to collect auxiliary information, which is not an effective solution as shown in our experiments. To overcome these challenges, we introduce a novel SpaceGNN model designed for NAD tasks with extremely limited labels. Specifically, we provide deeper insights into a task-relevant framework by empirically analyzing the benefits of different spaces for node representations, based on which, we design a Learnable Space Projection function that effectively encodes nodes into suitable spaces. Besides, we introduce the concept of weighted homogeneity, which we empirically and theoretically validate as an effective coefficient during information propagation. This concept inspires the design of the Distance Aware Propagation module. Furthermore, we propose the Multiple Space Ensemble module, which extracts comprehensive information for NAD under conditions of extremely limited supervision. Our findings indicate that this module is more beneficial than data augmentation techniques for NAD. Extensive experiments conducted on 9 real datasets confirm the superiority of SpaceGNN, which outperforms the best rival by an average of 8.55% in AUC and 4.31% in F1 scores. Our code is available at https://github.com/xydong127/SpaceGNN.

This paper explores alternative formulations of the Kolmogorov Superposition Theorem (KST) as a foundation for neural network design. The original KST formulation, while mathematically elegant, presents practical challenges due to its limited insight into the structure of inner and outer functions and the large number of unknown variables it introduces. Kolmogorov-Arnold Networks (KANs) leverage KST for function approximation, but they have faced scrutiny due to mixed results compared to traditional multilayer perceptrons (MLPs) and practical limitations imposed by the original KST formulation. To address these issues, we introduce ActNet, a scalable deep learning model that builds on the KST and overcomes some of the drawbacks of Kolmogorov's original formulation. We evaluate ActNet in the context of Physics-Informed Neural Networks (PINNs), a framework well-suited for leveraging KST's strengths in low-dimensional function approximation, particularly for simulating partial differential equations (PDEs). In this challenging setting, where models must learn latent functions without direct measurements, ActNet consistently outperforms KANs across multiple benchmarks and is competitive against the current best MLP-based approaches. These results present ActNet as a promising new direction for KST-based deep learning applications, particularly in scientific computing and PDE simulation tasks.

The large-scale training of multi-modal models on data scraped from the web has shown outstanding utility in infusing these models with the required world knowledge to perform effectively on multiple downstream tasks. However, one downside of scraping data from the web can be the potential sacrifice of the benchmarks on which the abilities of these models are often evaluated. To safeguard against test data contamination and to truly test the abilities of these foundation models we propose LiveXiv: A scalable evolving live benchmark based on scientific ArXiv papers. LiveXiv accesses domain-specific manuscripts at any given timestamp and proposes to automatically generate visual question-answer pairs (VQA). This is done without any human-in-the-loop, using the multi-modal content in the manuscripts, like graphs, charts, and tables. Moreover, we introduce an efficient evaluation approach that estimates the performance of all models on the evolving benchmark using evaluations of only a subset of models. This significantly reduces the overall evaluation cost. We benchmark multiple open and proprietary Large Multi-modal Models (LMMs) on the first version of our benchmark, showing its challenging nature and exposing the models’ true abilities, avoiding contamination. Lastly, in our commitment to high quality, we have collected and evaluated a manually verified subset. By comparing its overall results to our automatic annotations, we have found that the performance variance is indeed minimal (<2.5%). Our dataset is available online on HuggingFace, and our code is available here.

Recent work has shown that diffusion models memorize and reproduce training data examples. At the same time, large copyright lawsuits and legislation such as GDPR have highlighted the need for erasing datapoints from diffusion models. However, retraining from scratch is often too expensive. This motivates the setting of data unlearning, i.e., the study of efficient techniques for unlearning specific datapoints from the training set. Existing concept unlearning techniques require an anchor prompt/class/distribution to guide unlearning, which is not available in the data unlearning setting. General-purpose machine unlearning techniques were found to be either unstable or failed to unlearn data. We therefore propose a family of new loss functions called Subtracted Importance Sampled Scores (SISS) that utilize importance sampling and are the first method to unlearn data with theoretical guarantees. SISS is constructed as a weighted combination between simpler objectives that are responsible for preserving model quality and unlearning the targeted datapoints. When evaluated on CelebA-HQ and MNIST, SISS achieved Pareto optimality along the quality and unlearning strength dimensions. On Stable Diffusion, SISS successfully mitigated memorization on nearly 90% of the prompts we tested. We release our code online.

This work tackles an intriguing and fundamental open challenge in representation learning: Given a well-trained deep learning model, can it be reprogrammed to enhance its robustness against adversarial or noisy input perturbations without altering its parameters? To explore this, we revisit the core feature transformation mechanism in representation learning and propose a novel non-linear robust pattern matching technique as a robust alternative. Furthermore, we introduce three model reprogramming paradigms to offer flexible control of robustness under different efficiency requirements. Comprehensive experiments and ablation studies across diverse learning models ranging from basic linear model and MLPs to shallow and modern deep ConvNets demonstrate the effectiveness of our approaches. This work not only opens a promising and orthogonal direction for improving adversarial defenses in deep learning beyond existing methods but also provides new insights into designing more resilient AI systems with robust statistics. Our implementation is available at https://github.com/chris-hzc/Robustness-Reprogramming.

Backtracking line search is foundational in numerical optimization. The basic idea is to adjust the step size of an algorithm by a {\em constant} factor until some chosen criterion (e.g. Armijo, Descent Lemma) is satisfied. We propose a novel way to adjust step sizes, replacing the constant factor used in regular backtracking with one that takes into account the degree to which the chosen criterion is violated, with no additional computational burden. This light-weight adjustment leads to significantly faster optimization, which we confirm by performing a variety of experiments on over fifteen real world datasets. For convex problems, we prove adaptive backtracking requires no more adjustments to produce a feasible step size than regular backtracking does. For nonconvex smooth problems, we prove adaptive backtracking enjoys the same guarantees of regular backtracking. %same lower bounds that step sizes produced by regular backtracking do. Furthermore, we prove adaptive backtracking preserves the convergence rates of gradient descent and its accelerated variant.

Neural fields are an emerging paradigm that represent data as continuous functions parameterized by neural networks. Despite many advantages, neural fields often have a high training cost, which prevents a broader adoption. In this paper, we focus on a popular family of neural fields, called sinusoidal neural fields (SNFs), and study how it should be initialized to maximize the training speed. We find that the standard initialization scheme for SNFs---designed based on the signal propagation principle---is suboptimal. In particular, we show that by simply multiplying each weight (except for the last layer) by a constant, we can accelerate SNF training by 10$\times$. This method, coined _weight scaling_, consistently provides a significant speedup over various data domains, allowing the SNFs to train faster than more recently proposed architectures. To understand why the weight scaling works well, we conduct extensive theoretical and empirical analyses which reveal that the weight scaling not only resolves the spectral bias quite effectively but also enjoys a well-conditioned optimization trajectory.

With the growing capabilities of large language models (LLMs), they are increasingly applied in areas like intelligent customer service, code generation, and knowledge management. Natural language (NL) prompts act as the ``APIs'' for human-LLM interaction. To improve prompt quality, best practices for prompt engineering (PE) have been developed, including writing guidelines and templates. Building on this, we propose Controlled NL for Prompt (CNL-P), which not only incorporates PE best practices but also draws on key principles from software engineering (SE). CNL-P introduces precise grammar structures and strict semantic norms, further eliminating NL's ambiguity, allowing for a declarative but structured and accurate expression of user intent. This helps LLMs better interpret and execute the prompts, leading to more consistent and higher-quality outputs. We also introduce an NL2CNL-P conversion tool based on LLMs, enabling users to write prompts in NL, which are then transformed into CNL-P format, thus lowering the learning curve of CNL-P. In particular, we develop a linting tool that checks CNL-P prompts for syntactic and semantic accuracy, applying static analysis techniques to NL for the first time. Extensive experiments demonstrate that CNL-P enhances the quality of LLM responses through the novel and organic synergy of PE and SE. We believe that CNL-P can bridge the gap between emerging PE and traditional SE, laying the foundation for a new programming paradigm centered around NL. To further demonstrate the effectiveness of CNL-P, we develop the AI-native CNL-P IDE, UGAiForge that leverages CNL-P to enable users to Think, Describe, and Build with AI and for AI. For detailed information, please refer https://ugaiforge.ai.

Attention-based transformers have achieved tremendous success across a variety of disciplines including natural languages. To deepen our understanding of their sequential modeling capabilities, there is a growing interest in using Markov input processes to study them. A key finding is that when trained on first-order Markov chains, transformers with two or more layers consistently develop an induction head mechanism to estimate the in-context bigram conditional distribution. In contrast, single-layer transformers, unable to form an induction head, directly learn the Markov kernel but often face a surprising challenge: they become trapped in local minima representing the unigram distribution, whereas deeper models reliably converge to the ground-truth bigram. While single-layer transformers can theoretically model first-order Markov chains, their empirical failure to learn this simple kernel in practice remains a curious phenomenon. To explain this contrasting behavior of single-layer models, in this paper we introduce a new framework for a principled analysis of transformers via Markov chains. Leveraging our framework, we theoretically characterize the loss landscape of single-layer transformers and show the existence of global minima (bigram) and bad local minima (unigram) contingent on data properties and model architecture. We precisely delineate the regimes under which these local optima occur. Backed by experiments, we demonstrate that our theoretical findings are in congruence with the empirical results. Finally, we outline several open problems in this arena.

3D point clouds directly collected from objects through sensors are often incomplete due to self-occlusion. Conventional methods for completing these partial point clouds rely on manually organized training sets and are usually limited to object categories seen during training. In this work, we propose a test-time framework for completing partial point clouds across unseen categories without any requirement for training. Leveraging point rendering via Gaussian Splatting, we develop techniques of Partial Gaussian Initialization, Zero-shot Fractal Completion, and Point Cloud Extraction that utilize priors from pre-trained 2D diffusion models to infer missing regions and extract uniform completed point clouds. Experimental results on both synthetic and real-world scanned point clouds demonstrate that our approach outperforms existing methods in completing a variety of objects. Our project page is at \url{https://tianxinhuang.github.io/projects/ComPC/}.

Protecting the intellectual property of open-source Large Language Models (LLMs) is very important, because training LLMs costs extensive computational resources and data. Therefore, model owners and third parties need to identify whether a suspect model is a subsequent development of the victim model. To this end, we propose a training-free REEF to identify the relationship between the suspect and victim models from the perspective of LLMs' feature representations. Specifically, REEF computes and compares the centered kernel alignment similarity between the representations of a suspect model and a victim model on the same samples. This training-free REEF does not impair the model's general capabilities and is robust to sequential fine-tuning, pruning, model merging, and permutations. In this way, REEF provides a simple and effective way for third parties and models' owners to protect LLMs' intellectual property together. Our code is publicly accessible at https://github.com/AI45Lab/REEF.

Graph limit models, like *graphons* for limits of dense graphs, have recently been used to study size transferability of graph neural networks (GNNs). While most literature focuses on message passing GNNs (MPNNs), in this work we attend to the more powerful *higher-order* GNNs. First, we extend the $k$-WL test for graphons (Böker, 2023) to the graphon-signal space and introduce *signal-weighted homomorphism densities* as a key tool. As an exemplary focus, we generalize *Invariant Graph Networks* (IGNs) to graphons, proposing *Invariant Graphon Networks* (IWNs) defined via a subset of the IGN basis corresponding to bounded linear operators. Even with this restricted basis, we show that IWNs of order $k$ are at least as powerful as the $k$-WL test, and we establish universal approximation results for graphon-signals in $L^p$ distances. This significantly extends the prior work of Cai & Wang (2022), showing that IWNs—a subset of their *IGN-small*—retain effectively the same expressivity as the full IGN basis in the limit. In contrast to their approach, our blueprint of IWNs also aligns better with the geometry of graphon space, for example facilitating comparability to MPNNs. We highlight that, while typical higher-order GNNs are discontinuous w.r.t. cut distance—which causes their lack of convergence and is inherently tied to the definition of $k$-WL—transferability remains achievable.

Accurate protein identification from mass spectrometry (MS) data is fundamental to unraveling the complex roles of proteins in biological systems, with peptide sequencing being a pivotal step in this process. The two main paradigms for peptide sequencing are database search, which matches experimental spectra with peptide sequences from databases, and \emph{de novo} sequencing, which infers peptide sequences directly from MS without relying on pre-constructed database. Although database search methods are highly accurate, they are limited by their inability to identify novel, modified, or mutated peptides absent from the database. In contrast, \emph{de novo} sequencing is adept at discovering novel peptides but often struggles with missing peaks issue, further leading to lower precision. We introduce SearchNovo, a novel framework that synergistically integrates the strengths of database search and \emph{de novo} sequencing to enhance peptide sequencing. SearchNovo employs an efficient search mechanism to retrieve the most similar peptide spectrum match (PSM) from a database for each query spectrum, followed by a fusion module that utilizes the reference peptide sequence to guide the generation of the target sequence. Furthermore, we observed that dissimilar (noisy) reference peptides negatively affect model performance. To mitigate this, we constructed pseudo reference PSMs to minimize their impact. Comprehensive evaluations on multiple datasets reveal that SearchNovo significantly outperforms state-of-the-art models. Also, analysis indicates that many retrieved spectra contain missing peaks absent in the query spectra, and the retrieved reference peptides often share common fragments with the target peptides. These are key elements in the recipe for SearchNovo’s success. The code is available at: \textcolor{magenta}{\url{https://github.com/junxia97/SearchNovo}}.