ICLR 2025 Papers

Given a collection of neural networks, can we determine which are parent models and which are child models fine-tuned from the parents? In this work, we strive to answer this question via introducing a new task termed as neural phylogeny detection, aimed at identifying the existence and direction of the fine-tuning relationship. Specifically, neural phylogeny detection attempts to identify all parent-child model pairs and determine, within each pair, which model is the parent and which is the child. We present two approaches for neural phylogeny detection: a learning-free method and a learning-based method. First, we propose a metric that leverages the distance from network parameters to a fake initialization to infer fine-tuning directions. By integrating this metric with traditional clustering algorithms, we propose a series of efficient, learning-free neural phylogeny detection methods. Second, we introduce a transformer-based neural phylogeny detector, which significantly enhances detection accuracy through a learning-based manner. Extensive experiments, ranging from shallow fully-connected networks to open-sourced Stable Diffusion and LLaMA models, progressively validate the effectiveness of both methods. The results demonstrate the reliability of both the learning-free and the learning-based approaches across various learning tasks and network architectures, as well as their ability to detect cross-generational phylogeny between ancestor models and their fine-tuned descendants.

Training Data Detection (TDD) is a task aimed at determining whether a specific data instance is used to train a machine learning model. In the computer security literature, TDD is also referred to as Membership Inference Attack (MIA). Given its potential to assess the risks of training data breaches, ensure copyright authentication, and verify model unlearning, TDD has garnered significant attention in recent years, leading to the development of numerous methods. Despite these advancements, there is no comprehensive benchmark to thoroughly evaluate the effectiveness of TDD methods. In this work, we introduce TDDBench, which consists of 13 datasets spanning three data modalities: image, tabular, and text. We benchmark 21 different TDD methods across four detection paradigms and evaluate their performance from five perspectives: average detection performance, best detection performance, memory consumption, and computational efficiency in both time and memory. With TDDBench, researchers can identify bottlenecks and areas for improvement in TDD algorithms, while practitioners can make informed trade-offs between effectiveness and efficiency when selecting TDD algorithms for specific use cases. Our extensive experiments also reveal the generally unsatisfactory performance of TDD algorithms across different datasets. To enhance accessibility and reproducibility, we open-source TDDBench for the research community at https://github.com/zzh9568/TDDBench.

Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods for this task can be categorized into kinase-family-focused and individual kinase-targeted approaches. Individual kinase-targeted methods have gained prominence for their ability to explore a broader protein space and provide more precise target information for kinase inhibitors. However, most existing individual kinase-based approaches focus solely on sequence inputs, neglecting crucial structural information. To address this limitation, we introduce SAGEPhos (Structure-aware kinAse-substrate bio-coupled and bio-auGmented nEtwork for Phosphorylation site prediction), a novel framework that modifies the semantic space of main protein inputs using auxiliary inputs at two distinct modality levels. At the inter-modality level, SAGEPhos introduces a Bio-Coupled Modal Fusion method, distilling essential kinase sequence information to refine task-oriented local substrate feature space, creating a shared semantic space that captures crucial kinase-substrate interaction patterns. Within the substrate's intra-modality domain, it focuses on Bio-Augmented Fusion, emphasizing 2D local sequence information while selectively incorporating 3D spatial information from predicted structures to complement the sequence space. Moreover, to address the lack of structural information in current datasets, we contribute a new, refined phosphorylation site prediction dataset, which incorporates crucial structural elements and will serve as a new benchmark for the field. Experimental results demonstrate that SAGEPhos significantly outperforms baseline methods, notably achieving almost 10\% and 12\% improvements in prediction accuracy and AUC-ROC, respectively. We further demonstrate our algorithm's robustness and generalization through stable results across varied data partitions and significant improvements in zero-shot scenarios. These results underscore the effectiveness of constructing a larger and more precise protein space in advancing the state-of-the-art in phosphorylation site prediction. We release the SAGEPhos models and code at https://github.com/ZhangJJ26/SAGEPhos.

To build safe and reliable graph machine learning systems, unsupervised graph-level anomaly detection (GLAD) and unsupervised graph-level out-of-distribution (OOD) detection (GLOD) have received significant attention in recent years. Though these two lines of research share the same objective, they have been studied independently in the community due to distinct evaluation setups, creating a gap that hinders the application and evaluation of methods from one to the other. To bridge the gap, in this work, we present a Unified Benchmark for unsupervised Graph-level OOD and anomaly Detection (UB-GOLD), a comprehensive evaluation framework that unifies GLAD and GLOD under the concept of generalized graph-level OOD detection. Our benchmark encompasses 35 datasets spanning four practical anomaly and OOD detection scenarios, facilitating the comparison of 18 representative GLAD/GLOD methods. We conduct multi-dimensional analyses to explore the effectiveness, generalizability, robustness, and efficiency of existing methods, shedding light on their strengths and limitations. Furthermore, we provide an open-source codebase of UB-GOLD to foster reproducible research and outline potential directions for future investigations based on our insights.

Out-of-distribution (OOD) detection methods have recently become more prominent, serving as a core element in safety-critical autonomous systems. One major purpose of OOD detection is to reject invalid inputs that could lead to unpredictable errors and compromise safety. Due to the cost of labeled data, recent works have investigated the feasibility of self-supervised learning (SSL) OOD detection, unlabled OOD detection, and zero shot OOD detection. In this work, we identify a set of conditions for a theoretical guarantee of failure in unlabeled OOD detection algorithms from an information-theoretic perspective. These conditions are present in all OOD tasks dealing with real world data: I) we provide theoretical proof of unlabeled OOD detection failure when there exists zero mutual information between the learning objective and the in-distribution labels, a.k.a. ‘label blindness’, II) we define a new OOD task – Adjacent OOD detection – that tests for label blindness and accounts for a previously ignored safety gap in all OOD detection benchmarks, and III) we perform experiments demonstrating that existing unlabeled OOD methods fail under conditions suggested by our label blindness theory and analyze the implications for future research in unlabeled OOD methods.

As latent diffusion models (LDMs) democratize image generation capabilities, there is a growing need to detect fake images. A good detector should focus on the generative model’s fingerprints while ignoring image properties such as semantic content, resolution, file format, etc. Fake image detectors are usually built in a data-driven way, where a model is trained to separate real from fake images. Existing works primarily investigate network architecture choices and training recipes. In this work, we argue that in addition to these algorithmic choices, we also require a well-aligned dataset of real/fake images to train a robust detector. For the family of LDMs, we propose a very simple way to achieve this: we reconstruct all the real images using the LDM's autoencoder, without any denoising operation. We then train a model to separate these real images from their reconstructions. The fakes created this way are extremely similar to the real ones in almost every aspect (e.g., size, aspect ratio, semantic content), which forces the model to look for the LDM decoder's artifacts. We empirically show that this way of creating aligned real/fake datasets, which also sidesteps the computationally expensive denoising process, helps in building a detector that focuses less on spurious correlations, something that a very popular existing method is susceptible to. Finally, to demonstrate the effectivenss of dataset alignment, we build a detector using images that are not natural objects, and present promising results. Overall, our work identifies the subtle but significant issues that arise when training a fake image detector and proposes a simple and inexpensive solution to address these problems.

Partial matching is a kind of graph matching where only part of two graphs can be aligned. This problem is particularly important in computer vision applications, where challenges like point occlusion or annotation errors often occur when labeling key points. Previous work has often conflated point occlusion and annotation errors, despite their distinct underlying causes. We propose two components to address these challenges: (1) a structured universe graph is learned to connect two input graphs $X_{ij} = X_{iu} X_{ju}^\top$, effectively resolving the issue of point occlusion; (2) an energy-based out-of-distribution detection is designed to remove annotation errors from the input graphs before matching. We evaluated our method on the Pascal VOC and Willow Object datasets, focusing on scenarios involving point occlusion and random outliers. The experimental results demonstrate that our approach consistently outperforms state-of-the-art methods across all tested scenarios, highlighting the accuracy and robustness of our method.

The goal of object-centric representation learning is to decompose visual scenes into a structured representation that isolates the entities into individual vectors. Recent successes have shown that object-centric representation learning can be scaled to real-world scenes by utilizing features from pre-trained foundation models like DINO. However, so far, these object-centric methods have mostly been applied in-distribution, with models trained and evaluated on the same dataset. This is in contrast to the underlying foundation models, which have been shown to be applicable to a wide range of data and tasks. Thus, in this work, we answer the question of whether current real-world capable object-centric methods exhibit similar levels of transferability by introducing a benchmark comprising seven different synthetic and real-world datasets. We analyze the factors influencing performance under transfer and find that training on diverse real-world images improves generalization to unseen scenarios. Furthermore, inspired by the success of task-specific fine-tuning in foundation models, we introduce a novel fine-tuning strategy to adapt pre-trained vision encoders for the task of object discovery. We find that the proposed approach results in state-of-the-art performance for unsupervised object discovery, exhibiting strong zero-shot transfer to unseen datasets.

All data modalities are not created equal, even when the signal they measure comes from the same source. In the case of the brain, two of the most important data modalities are the scalp electroencephalogram (EEG), and the intracranial electroencephalogram (iEEG). iEEG benefits from a higher signal-to-noise ratio (SNR), as it measures the electrical activity directly in the brain, while EEG is noisier and has lower spatial and temporal resolutions. Nonetheless, both EEG and iEEG are important sources of data for human neurology, from healthcare to brain–machine interfaces. They are used by human experts, supported by deep learning (DL) models, to accomplish a variety of tasks, such as seizure detection and motor imagery classification. Although the differences between EEG and iEEG are well understood by human experts, the performance of DL models across these two modalities remains under-explored. To help characterize the importance of clean data on the performance of DL models, we propose BrainCodec, a high-fidelity EEG and iEEG neural compressor. We find that training BrainCodec on iEEG and then transferring to EEG yields higher reconstruction quality than training on EEG directly. In addition, we also find that training BrainCodec on both EEG and iEEG improves fidelity when reconstructing EEG. Our work indicates that data sources with higher SNR, such as iEEG, provide better performance across the board also in the medical time-series domain. This finding is consistent with reports coming from natural language processing, where clean data sources appear to have an outsized effect on the performance of the DL model overall. BrainCodec also achieves up to a 64x compression on iEEG and EEG without a notable decrease in quality. BrainCodec markedly surpasses current state-of-the-art compression models both in final compression ratio and in reconstruction fidelity. We also evaluate the fidelity of the compressed signals objectively on a seizure detection and a motor imagery task performed by standard DL models. Here, we find that BrainCodec achieves a reconstruction fidelity high enough to ensure no performance degradation on the downstream tasks. Finally, we collect the subjective assessment of an expert neurologist, that confirms the high reconstruction quality of BrainCodec in a realistic scenario. The code is available at https://github.com/IBM/eeg-ieeg-brain-compressor.

We propose a new task and model for dense video object captioning -- detecting, tracking and captioning trajectories of objects in a video. This task unifies spatial and temporal localization in video, whilst also requiring fine-grained visual understanding that is best described by natural language. We propose a unified model, and demonstrate how our end-to-end approach is more accurate and temporally coherent than a multi-stage pipeline combining state-of-the-art detection, tracking, and captioning models. Moreover, we propose a training strategy based on a mixture of disjoint tasks, which allows us to leverage diverse, large-scale datasets which supervise different parts of our model. Although each pretraining task only provides weak supervision, they are complementary and, when combined, result in noteworthy zero-shot ability and serve as strong initialization for additional finetuning to further improve accuracy. We carefully design new metrics capturing all components of our task, and show how we can repurpose existing video grounding datasets (e.g. VidSTG and VLN) for our new task. We show that our model improves upon a number of strong baselines for this new task. Furthermore, we can apply our model to the task of spatial grounding, outperforming prior state-of-the-art on VidSTG and VLN, without explicitly training for it. Our code is available at https://github.com/google-research/scenic.

Advanced large language models (LLMs) can generate text almost indistinguishable from human-written text, highlighting the importance of LLM-generated text detection. However, current zero-shot techniques face challenges as white-box methods are restricted to use weaker open-source LLMs, and black-box methods are limited by partial observation from stronger proprietary LLMs. It seems impossible to enable white-box methods to use proprietary models because API-level access to the models neither provides full predictive distributions nor inner embeddings. To traverse the divide, we propose **Glimpse**, a probability distribution estimation approach, predicting the full distributions from partial observations. Despite the simplicity of Glimpse, we successfully extend white-box methods like Entropy, Rank, Log-Rank, and Fast-DetectGPT to latest proprietary models. Experiments show that Glimpse with Fast-DetectGPT and GPT-3.5 achieves an average AUROC of about 0.95 in five latest source models, improving the score by 51\% relative to the remaining space of the open source baseline. It demonstrates that the latest LLMs can effectively detect their own outputs, suggesting that advanced LLMs may be the best shield against themselves. We release our code and data at https://github.com/baoguangsheng/glimpse.

Urban time series forecasting is crucial for smart city development and is key to sustainable urban management. Although urban time series models (UTSMs) are effective in general forecasting, they often overlook low-frequency events, such as holidays and extreme weather, leading to degraded performance in practical applications. In this paper, we first investigate how UTSMs handle these infrequent patterns from a neural perspective. Based on our findings, we propose $\textbf{P}$attern $\textbf{N}$euron guided $\textbf{Train}$ing ($\texttt{PN-Train}$), a novel training method that features (i) a $\textit{perturbation-based detector}$ to identify neurons responsible for low-frequency patterns in UTSMs, and (ii) a $\textit{fine-tuning mechanism}$ that enhances these neurons without compromising representation learning on high-frequency patterns. Empirical results demonstrate that $\texttt{PN-Train}$ considerably improves forecasting accuracy for low-frequency events while maintaining high performance for high-frequency events. The code is available at https://github.com/cwang-nus/PN-Train.

The problem of pre-training data detection for large language models (LLMs) has received growing attention due to its implications in critical issues like copyright violation and test data contamination. Despite improved performance, existing methods (including the state-of-the-art, Min-K%) are mostly developed upon simple heuristics and lack solid, reasonable foundations. In this work, we propose a novel and theoretically motivated methodology for pre-training data detection, named Min-K%++. Specifically, we present a key insight that training samples tend to be local maxima of the modeled distribution along each input dimension through maximum likelihood training, which in turn allow us to insightfully translate the problem into identification of local maxima. Then, we design our method accordingly that works under the discrete distribution modeled by LLMs, whose core idea is to determine whether the input forms a mode or has relatively high probability under the conditional categorical distribution. Empirically, the proposed method achieves new SOTA performance across multiple settings (evaluated with 5 families of 10 models and 2 benchmarks). On the WikiMIA benchmark, Min-K%++ outperforms the runner-up by 6.2% to 10.5% in detection AUROC averaged over five models. On the more challenging MIMIR benchmark, it consistently improves upon reference-free methods while performing on par with reference-based method that requires an extra reference model.

Accurate 3D object detection in real-world environments requires a huge amount of annotated data with high quality. Acquiring such data is tedious and expensive, and often needs repeated effort when a new sensor is adopted or when the detector is deployed in a new environment. We investigate a new scenario to construct 3D object detectors: *learning from the predictions of a nearby unit that is equipped with an accurate detector.* For example, when a self-driving car enters a new area, it may learn from other traffic participants whose detectors have been optimized for that area. This setting is label-efficient, sensor-agnostic, and communication-efficient: nearby units only need to share the predictions with the ego agent (e.g., car). Naively using the received predictions as ground-truths to train the detector for the ego car, however, leads to inferior performance. We systematically study the problem and identify viewpoint mismatches and mislocalization (due to synchronization and GPS errors) as the main causes, which unavoidably result in false positives, false negatives, and inaccurate pseudo labels. We propose a distance-based curriculum, first learning from closer units with similar viewpoints and subsequently improving the quality of other units' predictions via self-training. We further demonstrate that an effective pseudo label refinement module can be trained with a handful of annotated data, largely reducing the data quantity necessary to train an object detector. We validate our approach on the recently released real-world collaborative driving dataset, using reference cars' predictions as pseudo labels for the ego car. Extensive experiments including several scenarios (e.g., different sensors, detectors, and domains) demonstrate the effectiveness of our approach toward label-efficient learning of 3D perception from other units' predictions.

LiDAR-based 3D object detection is crucial for various applications but often experiences performance degradation in real-world deployments due to domain shifts. While most studies focus on cross-dataset shifts, such as changes in environments and object geometries, practical corruptions from sensor variations and weather conditions remain underexplored. In this work, we propose a novel online test-time adaptation framework for 3D detectors that effectively tackles these shifts, including a challenging $\textit{cross-corruption}$ scenario where cross-dataset shifts and corruptions co-occur. By leveraging long-term knowledge from previous test batches, our approach mitigates catastrophic forgetting and adapts effectively to diverse shifts. Specifically, we propose a Model Synergy (MOS) strategy that dynamically selects historical checkpoints with diverse knowledge and assembles them to best accommodate the current test batch. This assembly is directed by our proposed Synergy Weights (SW), which perform a weighted averaging of the selected checkpoints, minimizing redundancy in the composite model. The SWs are computed by evaluating the similarity of predicted bounding boxes on the test data and the independence of features between checkpoint pairs in the model bank. To maintain an efficient and informative model bank, we discard checkpoints with the lowest average SW scores, replacing them with newly updated models. Our method was rigorously tested against existing test-time adaptation strategies across three datasets and eight types of corruptions, demonstrating superior adaptability to dynamic scenes and conditions. Notably, it achieved a 67.3% improvement in a challenging cross-corruption scenario, offering a more comprehensive benchmark for adaptation. Source code: https://github.com/zhuoxiao-chen/MOS.

Detecting training data for large language models (LLMs) is receiving growing attention, especially in applications requiring high reliability. While numerous efforts have been made to address this issue, they typically focus on accuracy without ensuring controllable results. To fill this gap, we propose **K**nockoff Inference-based **T**raining data **D**etector (KTD), a novel method that achieves rigorous false discovery rate (FDR) control in training data detection. Specifically, KTD generates synthetic knockoff samples that seamlessly replace original data points without compromising contextual integrity. A novel knockoff statistic, which incorporates multiple knockoff draws, is then calculated to ensure FDR control while maintaining high power. Our theoretical analysis demonstrates KTD's asymptotic optimality in terms of FDR control and power. Empirical experiments on real-world datasets such as WikiMIA, XSum and Real Time BBC News further validate KTD's superior performance compared to existing methods.

Evaluating the contribution of individual data points to a model's prediction is critical for interpreting model predictions and improving model performance. Existing data contribution methods have been applied to various data types, including tabular data, images, and text; however, their primary focus has been on i.i.d. settings. Despite the pressing need for principled approaches tailored to time series datasets, the problem of estimating data contribution in such settings remains under-explored, possibly due to challenges associated with handling inherent temporal dependencies. This paper introduces TimeInf, a model-agnostic data contribution estimation method for time-series datasets. By leveraging influence scores, TimeInf attributes model predictions to individual time points while preserving temporal structures between the time points. Our empirical results show that TimeInf effectively detects time series anomalies and outperforms existing data attribution techniques as well as state-of-the-art anomaly detection methods. Moreover, TimeInf offers interpretable attributions of data values, allowing us to distinguish diverse anomalous patterns through visualizations. We also showcase a potential application of TimeInf in identifying mislabeled anomalies in the ground truth annotations.

The phenomenon of knowledge hallucinations has raised substantial concerns about the security and reliability of deployed large language models (LLMs). Current methods for detecting hallucinations primarily depend on manually designed individual metrics, such as prediction uncertainty and consistency, and fall short in effectively calibrating model predictions, thus constraining their detection accuracy and applicability in practical applications. In response, we propose an advanced framework, termed HaDeMiF, for detecting and mitigating hallucinations in LLMs. Specifically, hallucinations within the output and semantic spaces of LLMs are comprehensively captured through two compact networks—a novel, interpretable tree model known as the Deep Dynamic Decision Tree (D3T) and a Multilayer Perceptron (MLP)—which take as input a set of prediction characteristics and the hidden states of tokens, respectively. The predictions of LLMs are subsequently calibrated using the outputs from the D3T and MLP networks, aiming to mitigate hallucinations and enhance model calibration. HaDeMiF can be applied during both the inference and fine-tuning phases of LLMs, introducing less than 2% of the parameters relative to the LLMs through the training of two small-scale networks. Extensive experiments conclusively demonstrate the effectiveness of our framework in hallucination detection and model calibration across text generation tasks with responses of varying lengths.

DETR-based methods, which use multi-layer transformer decoders to refine object queries iteratively, have shown promising performance in 3D indoor object detection. However, the scene point features in the transformer decoder remain fixed, leading to minimal contributions from later decoder layers, thereby limiting performance improvement. Recently, State Space Models (SSM) have shown efficient context modeling ability with linear complexity through iterative interactions between system states and inputs. Inspired by SSMs, we propose a new 3D object DEtection paradigm with an interactive STate space model (DEST). In the interactive SSM, we design a novel state-dependent SSM parameterization method that enables system states to effectively serve as queries in 3D indoor detection tasks. In addition, we introduce four key designs tailored to the characteristics of point cloud and SSM: The serialization and bidirectional scanning strategies enable bidirectional feature interaction among scene points within the SSM. The inter-state attention mechanism models the relationships between state points, while the gated feed-forward network enhances inter-channel correlations. To the best of our knowledge, this is the first method to model queries as system states and scene points as system inputs, which can simultaneously update scene point features and query features with linear complexity. Extensive experiments on two challenging datasets demonstrate the effectiveness of our DEST-based method. Our method improves the GroupFree baseline in terms of $\text{AP}_{50}$ on ScanNet V2 (+5.3) and SUN RGB-D (+3.2) datasets. Based on the VDETR baseline, Our method sets a new state-of-the-art on the ScanNetV2 and SUN RGB-D datasets.