ICLR 2025 论文列表

The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the limited scope of reference databases. Currently, the vast majority of spectral measurements remain in the "dark chemical space" without structural annotations. To improve annotation, we propose MADGEN (Mass-spec Attends to De Novo Molecular GENeration), a scaffold-based method for de novo molecular structure generation guided by mass spectrometry data. MADGEN operates in two stages: scaffold retrieval and spectra-conditioned molecular generation starting with the scaffold. In the first stage, given an MS/MS spectrum, we formulate scaffold retrieval as a ranking problem and employ contrastive learning to align mass spectra with candidate molecular scaffolds. In the second stage, starting from the retrieved scaffold, we employ the MS/MS spectrum to guide an attention-based generative model to generate the final molecule. Our approach constrains the molecular generation search space, reducing its complexity and improving generation accuracy. We evaluate MADGEN on three datasets (NIST23, CANOPUS, and MassSpecGym) and evaluate MADGEN's performance with a predictive scaffold retriever and with an oracle retriever. We demonstrate the effectiveness of using attention to integrate spectral information throughout the generation process to achieve strong results with the oracle retriever.

Test-time adaptation (TTA) updates the model weights during the inference stage using testing data to enhance generalization. However, this practice exposes TTA to adversarial risks. Existing studies have shown that when TTA is updated with crafted adversarial test samples, also known as test-time poisoned data, the performance on benign samples can deteriorate. Nonetheless, the perceived adversarial risk may be overstated if the poisoned data is generated under overly strong assumptions. In this work, we first review realistic assumptions for test-time data poisoning, including white-box versus grey-box attacks, access to benign data, attack order, and more. We then propose an effective and realistic attack method that better produces poisoned samples without access to benign samples, and derive an effective in-distribution attack objective. We also design two TTA-aware attack objectives. Our benchmarks of existing attack methods reveal that the TTA methods are more robust than previously believed. In addition, we analyze effective defense strategies to help develop adversarially robust TTA methods. The source code is available at https://github.com/Gorilla-Lab-SCUT/RTTDP.

Recent studies indicate that effectively utilizing inference-time compute is crucial for attaining good performance from large language models (LLMs). Specifically, the Best-of-N (BoN) inference strategy, where an LLM generates multiple responses and a verifier selects the best, has shown strong empirical performance. Motivated by this, we develop a novel inference-aware fine-tuning paradigm, which encompasses the BoN-aware inference framework as a special case. We devise the first imitation learning and reinforcement learning (RL) methods for fine-tuning LLMs using BoN, overcoming the challenging, non-differentiable argmax operator in BoN. We empirically demonstrate that our BoN-aware models implicitly learn a per-example "meta-strategy", which interleaves best responses with more diverse responses that might be better suited to a test-time input—a process reminiscent of the exploration-exploitation trade-off in RL. Our experiments demonstrate the effectiveness of BoN-aware fine-tuning in terms of improved performance and inference-time compute. In particular, we show that our methods improve the BoN performance of Gemma 2B on Hendrycks MATH from 26.8% to 30.8%, and Pass@K from 60% to 67%.

Mainstream test-time adaptation (TTA) techniques endeavor to mitigate distribution shifts via entropy minimization for multi-class classification, inherently increasing the probability of the most confident class. However, when encountering multi-label instances, the primary challenge stems from the varying number of labels per image, and prioritizing only the highest probability class inevitably undermines the adaptation of other positive labels. To address this issue, we investigate TTA within multi-label scenario (ML--TTA), developing Bound Entropy Minimization (BEM) objective to simultaneously increase the confidence of multiple top predicted labels. Specifically, to determine the number of labels for each augmented view, we retrieve a paired caption with yielded textual labels for that view. These labels are allocated to both the view and caption, called weak label set and strong label set with the same size k. Following this, the proposed BEM considers the highest top-k predicted labels from view and caption as a single entity, respectively, learning both view and caption prompts concurrently. By binding top-k predicted labels, BEM overcomes the limitation of vanilla entropy minimization, which exclusively optimizes the most confident class. Across the MSCOCO, VOC, and NUSWIDE multi-label datasets, our ML--TTA framework equipped with BEM exhibits superior performance compared to the latest SOTA methods, across various model architectures, prompt initialization, and varying label scenarios. The code is available at https://github.com/Jinx630/ML-TTA.

Large multimodal models such as Stable Diffusion can generate, detect, and classify new visual concepts after optimizing just the prompt. How are prompt embeddings for visual concepts found by prompt tuning methods different from typical discrete prompts? We conduct a large-scale analysis on three state-of-the-art models in text-to-image generation, open-set object detection, and zero-shot classification, and find that prompts optimized to represent new visual concepts are akin to an adversarial attack on the text encoder. Across 4,800 new embeddings trained for 40 diverse visual concepts on four standard datasets, we find perturbations within an $\epsilon$-ball to any prompt that reprogram models to generate, detect, and classify arbitrary subjects. These perturbations target the final-layers in text encoders, and steer pooling tokens towards the subject. We explore the transferability of these prompts, and find that perturbations reprogramming multimodal models are initialization-specific, and model-specific. Code for reproducing our work is available at the following site: https://wayward-concepts.github.io.

This paper introduces a novel hierarchical autoencoder that maps 3D models into a highly compressed latent space. The hierarchical autoencoder is specifically designed to tackle the challenges arising from large-scale datasets and generative modeling using diffusion. Different from previous approaches that only work on a regular image or volume grid, our hierarchical autoencoder operates on unordered sets of vectors. Each level of the autoencoder controls different geometric levels of detail. We show that the model can be used to represent a wide range of 3D models while faithfully representing high-resolution geometry details. The training of the new architecture takes 0.70x time and 0.58x memory compared to the baseline. We also explore how the new representation can be used for generative modeling. Specifically, we propose a cascaded diffusion framework where each stage is conditioned on the previous stage. Our design extends existing cascaded designs for image and volume grids to vector sets.

Recently, scaling images to high resolution has received much attention in multimodal large language models (MLLMs). Most existing practices adopt a sliding-window-style cropping strategy to adapt to resolution increase. Such a cropping strategy, however, can easily cut off objects and connected regions, which introduces semantic discontinuity and therefore impedes MLLMs from recognizing small or irregularly shaped objects or text, leading to a phenomenon we call the semantic sawtooth effect. This effect is particularly evident in lightweight MLLMs. To address this issue, we introduce a Complementary Image Pyramid (CIP), a simple, effective, and plug-and-play solution designed to mitigate semantic discontinuity during high-resolution image processing. In particular, CIP dynamically constructs an image pyramid to provide complementary semantic information for the cropping-based MLLMs, enabling it rich acquire semantics at all levels. Furthermore, we introduce a Scale Compression Mechanism (SCM) to reduce the additional computational overhead by compressing the redundant visual tokens. Our experiments demonstrate that CIP can consistently enhance the performance across diverse architectures (e.g., MiniCPM-V-2, InternVL2, and LLaVA-OneVision), various model capacity (1B$\rightarrow$8B), and different usage configurations (training-free and fine-tuning). Leveraging the proposed CIP and SCM, we introduce a lightweight MLLM, Mini-Monkey, which achieves remarkable performance in both general multimodal understanding and document understanding. On the OCRBench, the 2B-version Mini-Monkey even surpasses the 8B model InternVL2-8B by 12 score. Additionally, training Mini-Monkey is cheap, requiring only eight RTX 3090 GPUs. Code and models are available at https://github.com/Yuliang-Liu/Monkey.

The advancements of language language models (LLMs) have piqued growing interest in developing LLM-based language agents to automate scientific discovery end-to-end, which has sparked both excitement and skepticism about the true capabilities of such agents. In this work, we argue that for an agent to fully automate scientific discovery, it must be able to complete all essential tasks in the workflow. Thus, we call for rigorous assessment of agents on individual tasks in a scientific workflow before making bold claims on end-to-end automation. To this end, we present ScienceAgentBench, a new benchmark for evaluating language agents for data-driven scientific discovery. To ensure the scientific authenticity and real-world relevance of our benchmark, we extract 102 tasks from 44 peer-reviewed publications in four disciplines and engage nine subject matter experts to validate them. We unify the target output for every task to a self-contained Python program file and employ an array of evaluation metrics to examine the generated programs, execution results, and costs. Each task goes through multiple rounds of manual validation by annotators and subject matter experts to ensure its annotation quality and scientific plausibility. We also propose two effective strategies to mitigate data contamination concerns. Using our benchmark, we evaluate five open-weight and proprietary LLMs, each with three frameworks: direct prompting, OpenHands, and self-debug. Given three attempts for each task, the best-performing agent can only solve 32.4% of the tasks independently and 34.3% with expert-provided knowledge. These results underscore the limited capacities of current language agents in generating code for data-driven discovery, let alone end-to-end automation for scientific research.

Episodic memory -- the ability to recall specific events grounded in time and space -- is a cornerstone of human cognition, enabling not only coherent storytelling, but also planning and decision-making. Despite their remarkable capabilities, Large Language Models (LLMs) lack a robust mechanism for episodic memory: we argue that integrating episodic memory capabilities into LLM is essential for advancing AI towards human-like cognition, increasing their potential to reason consistently and ground their output in real-world episodic events, hence avoiding confabulations. To address this challenge, we introduce a comprehensive framework to model and evaluate LLM episodic memory capabilities. Drawing inspiration from cognitive science, we develop a structured approach to represent episodic events, encapsulating temporal and spatial contexts, involved entities, and detailed descriptions. We synthesize a unique episodic memory benchmark, free from contamination, and release open source code and datasets to assess LLM performance across various recall and episodic reasoning tasks. Our evaluation of state-of-the-art models, including GPT-4 and Claude variants, Llama 3.1, and o1-mini, reveals that even the most advanced LLMs struggle with episodic memory tasks, particularly when dealing with multiple related events or complex spatio-temporal relationships -- even in contexts as short as 10k-100k tokens.

Mixed Integer Linear Programming (MILP) is essential for modeling complex decision-making problems but faces challenges in computational tractability and interpretability. Current deep learning approaches for MILP focus on specific problem classes and do not generalize to unseen classes. To address this shortcoming, we take a foundation model training approach, where we train a single deep learning model on a diverse set of MILP problems to generalize across problem classes. As existing datasets for MILP lack diversity and volume, we introduce MILP-Evolve, a novel LLM-based evolutionary framework that is capable of generating a large set of diverse MILP classes with an unlimited amount of instances. We study our methodology on three key learning tasks that capture diverse aspects of MILP: (1) integrality gap prediction, (2) learning to branch, and (3) a new task of aligning MILP instances with natural language descriptions. Our empirical results show that models trained on the data generated by MILP-Evolve achieve significant improvements on unseen problems, including MIPLIB benchmarks. Our work highlights the potential of moving towards a foundation model approach for MILP that can generalize to a broad range of MILP problem classes. Our code and data are publicly available at https://github.com/microsoft/OptiGuide.

Multiple Instance Learning (MIL) in digital pathology Whole Slide Image (WSI) analysis has shown significant progress. However, due to data bias and unobservable confounders, this paradigm still faces challenges in terms of performance and interpretability. Existing MIL methods might identify patches that do not have true diagnostic significance, leading to false correlations, and experience difficulties in integrating multi-scale features and handling unobservable confounders. To address these issues, we propose a new Multi-Scale Frequency Domain Causal framework (MFC). This framework employs an adaptive memory module to estimate the overall data distribution through multi-scale frequency-domain information during training and simulates causal interventions based on this distribution to mitigate confounders in pathological diagnosis tasks. The framework integrates the Multi-scale Spatial Representation Module (MSRM), Frequency Domain Structure Representation Module (FSRM), and Causal Memory Intervention Module (CMIM) to enhance the model's performance and interpretability. Furthermore, the plug-and-play nature of this framework allows it to be broadly applied across various models. Experimental results on Camelyon16 and TCGA-NSCLC dataset show that, compared to previous work, our method has significantly improved accuracy and generalization ability, providing a new theoretical perspective for medical image analysis and potentially advancing the field further. The code will be released at https://github.com/WissingChen/MFC-MIL.

Prompt tuning vision-language models like CLIP has shown great potential in learning transferable representations for various downstream tasks. The main issue is how to mitigate the over-fitting problem on downstream tasks with limited training samples. While knowledge-guided context optimization has been proposed by constructing consistency constraints to handle catastrophic forgetting in the pre-trained backbone, it also introduces a bias toward pre-training. This paper proposes a novel and simple Divergence-enhanced Knowledge-guided Prompt Tuning (DeKg) method to address this issue. The key insight is that the bias toward pre-training can be alleviated by encouraging the independence between the learnable and the crafted prompt. Specifically, DeKg employs the Hilbert-Schmidt Independence Criterion (HSIC) to regularize the learnable prompts, thereby reducing their dependence on prior general knowledge, and enabling divergence induced by target knowledge. Comprehensive evaluations demonstrate that DeKg serves as a plug-and-play module can seamlessly integrate with existing knowledge-guided context optimization methods and achieves superior performance in three challenging benchmarks. We make our code available at https://github.com/cnunlp/DeKg.

Computationally intensive decoding procedures---including search, reranking, and self-critique---can improve the quality of language model (LM) outputs in problems spanning code generation, numerical reasoning, and dialog. Existing work typically applies the same decoding procedure for every input to an LM. But not all inputs require the same amount of computation to process. Can we allocate decoding computation adaptively, using more resources to answer questions whose answers will be harder to compute? We present an approach that predicts the distribution of rewards given an input and computation budget, then allocates additional computation to inputs for which it is predicted to be most useful. We apply this approach in two decoding procedures: first, an adaptive best-of-$k$ procedure that dynamically selects the number of samples to generate as input to a reranker; second, a routing procedure that dynamically responds to a query using a decoding procedure that is expensive but accurate, or one that is cheaper but less capable. Across a suite of programming, mathematics, and dialog tasks, we show that accurate computation-allocation procedures can be learned, and reduce computation by up to 50% at no cost to quality.

Negative Prompting (NP) is widely utilized in diffusion models, particularly in text-to-image applications, to prevent the generation of undesired features. In this paper, we show that conventional NP is limited by the assumption of a constant guidance scale, which may lead to highly suboptimal results, or even complete failure, due to the non-stationarity and state-dependence of the reverse process. Based on this analysis, we derive a principled technique called ***D**ynamic **N**egative **G**uidance*, which relies on a near-optimal time and state dependent modulation of the guidance without requiring additional training. Unlike NP, negative guidance requires estimating the posterior class probability during the denoising process, which is achieved with limited additional computational overhead by tracking the discrete Markov Chain during the generative process. We evaluate the performance of DNG class-removal on MNIST and CIFAR10, where we show that DNG leads to higher safety, preservation of class balance and image quality when compared with baseline methods. Furthermore, we show that it is possible to use DNG with Stable Diffusion to obtain more accurate and less invasive guidance than NP.

State-of-the-art methods for forecasting irregularly sampled time series with missing values predominantly rely on just four datasets and a few small toy examples for evaluation. While ordinary differential equations (ODE) are the prevalent models in science and engineering, a baseline model that forecasts a constant value outperforms ODE-based models from the last five years on three of these existing datasets. This unintuitive finding hampers further research on ODE-based models, a more plausible model family. In this paper, we develop a methodology to generate irregularly sampled multivariate time series (IMTS) datasets from ordinary differential equations and to select challenging instances via rejection sampling. Using this methodology, we create Physiome-ODE, a large and sophisticated benchmark of IMTS datasets consisting of 50 individual datasets, derived from real-world ordinary differential equations from research in biology. Physiome-ODE is the first benchmark for IMTS forecasting that we are aware of and an order of magnitude larger than the current evaluation setting of four datasets. Using our benchmark Physiome-ODE, we show qualitatively completely different results than those derived from the current four datasets: on Physiome-ODE ODE-based models can play to their strength and our benchmark can differentiate in a meaningful way between different IMTS forecasting models. This way, we expect to give a new impulse to research on ODE-based time series modeling.

Label smoothing (LS) is a popular regularisation method for training neural networks as it is effective in improving test accuracy and is simple to implement. ''Hard'' one-hot labels are ''smoothed'' by uniformly distributing probability mass to other classes, reducing overfitting. Prior work has shown that in some cases *LS can degrade selective classification (SC)* -- where the aim is to reject misclassifications using a model's uncertainty. In this work, we first demonstrate empirically across an extended range of large-scale tasks and architectures that LS *consistently* degrades SC. We then address a gap in existing knowledge, providing an *explanation* for this behaviour by analysing logit-level gradients: LS degrades the uncertainty rank ordering of correct vs incorrect predictions by regularising the max logit *more* when a prediction is likely to be correct, and *less* when it is likely to be wrong. This elucidates previously reported experimental results where strong classifiers underperform in SC. We then demonstrate the empirical effectiveness of post-hoc *logit normalisation* for recovering lost SC performance caused by LS. Furthermore, linking back to our gradient analysis, we again provide an explanation for why such normalisation is effective.

Learning effective graph similarities is crucial for tasks like clustering, yet selecting the optimal kernel to evaluate such similarities in unsupervised settings remains a major challenge. Despite the development of various graph kernels, determining the most appropriate one for a specific task is particularly difficult in the absence of labeled data. Existing methods often struggle to handle the complex structure of graph data and rely on heuristic approaches that fail to adequately capture the global relationships between graphs. To overcome these limitations, we propose Unsupervised Multiple Kernel Learning for Graphs (UMKL-G), a model that combines multiple graph kernels without requiring labels or predefined local neighbors. Our approach preserves the topology of the data by maintaining ordinal relationships among graphs through a probability simplex, allowing for a unified and adaptive kernel learning process. We provide theoretical guarantees on the stability, robustness, and generalization of our method. Empirical results demonstrate that UMKL-G outperforms individual kernels and other state-of-the-art methods, offering a robust solution for unsupervised graph analysis.

Dataset ownership verification, the process of determining if a dataset is used in a model's training data, is necessary for detecting unauthorized data usage and data contamination. Existing approaches, such as backdoor watermarking, rely on inducing a detectable behavior into the trained model on a part of the data distribution. However, these approaches have limitations, as they can be harmful to the model's performances or require unpractical access to the model's internals. Most importantly, previous approaches lack guarantee against false positives.\ This paper introduces *data taggants*, a novel non-backdoor dataset ownership verification technique. Our method uses pairs of out-of-distribution samples and random labels as secret *keys*, and leverages clean-label targeted data poisoning to subtly alter a dataset, so that models trained on it respond to the key samples with the corresponding key labels. The keys are built as to allow for statistical certificates with black-box access only to the model.\ We validate our approach through comprehensive and realistic experiments on ImageNet1k using ViT and ResNet models with state-of-the-art training recipes. Our findings demonstrate that data taggants can reliably detect models trained on the protected dataset with high confidence, without compromising validation accuracy, and show their superiority over backdoor watermarking. We demonstrate the stealthiness and robustness of our method % shows to be stealthy and robust against various defense mechanisms.

Recent progress in text-guided image inpainting, based on the unprecedented success of text-to-image diffusion models, has led to exceptionally realistic and visually plausible results. However, there is still significant potential for improvement in current text-to-image inpainting models, particularly in better aligning the inpainted area with user prompts. Therefore, we introduce $\textit{HD-Painter}$, a $\textbf{training-free}$ approach that $\textbf{accurately follows prompts}$. To this end, we design the $\textit{Prompt-Aware Introverted Attention (PAIntA)}$ layer enhancing self-attention scores by prompt information resulting in better text aligned generations. To further improve the prompt coherence we introduce the $\textit{Reweighting Attention Score Guidance (RASG)}$ mechanism seamlessly integrating a post-hoc sampling strategy into the general form of DDIM to prevent out-of-distribution latent shifts. Our experiments demonstrate that HD-Painter surpasses existing state-of-the-art approaches quantitatively and qualitatively across multiple metrics and a user study. Code is publicly available at: [https://github.com/Picsart-AI-Research/HD-Painter](https://github.com/Picsart-AI-Research/HD-Painter)