ICLR 2025 Papers

International Conference on Learning Representations

Decision breakdown

3,703papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Oral
    2135.8%
  • Spotlight
    38010.3%
  • Poster
    3,11084.0%

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Retri3D: 3D Neural Graphics Representation Retrieval

Yushi Guan, Daniel Kwan, Jean Sebastien Dandurand, Xi Yan, Ruofan Liang, Yuxuan Zhang, Nilesh Jain, Nilesh Ahuja, Selvakumar Panneer, Nandita Vijaykumar

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Learnable 3D Neural Graphics Representations (3DNGR) have emerged as promising 3D representations for reconstructing 3D scenes from 2D images. Numerous works, including Neural Radiance Fields (NeRF), 3D Gaussian Splatting (3DGS), and their variants, have significantly enhanced the quality of these representations. The ease of construction from 2D images, suitability for online viewing/sharing, and applications in game/art design downstream tasks make it a vital 3D representation, with potential creation of large numbers of such 3D models. This necessitates large data stores, local or online, to save 3D visual data in these formats. However, no existing framework enables accurate retrieval of stored 3DNGRs. In this work, we propose, Retri3D, a framework that enables accurate and efficient retrieval of 3D scenes represented as NGRs from large data stores using text queries. We introduce a novel Neural Field Artifact Analysis technique, combined with a Smart Camera Movement Module, to select clean views and navigate pre-trained 3DNGRs. These techniques enable accurate retrieval by selecting the best viewing directions in the 3D scene for high-quality visual feature embeddings. We demonstrate that Retri3D is compatible with any NGR representation. On the LERF and ScanNet++ datasets, we show significant improvement in retrieval accuracy compared to existing techniques, while being orders of magnitude faster and storage efficient.

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CLoSD: Closing the Loop between Simulation and Diffusion for multi-task character control

Guy Tevet, Sigal Raab, Setareh Cohan, Daniele Reda, Zhengyi Luo, Xue Bin Peng, Amit Haim Bermano, Michiel van de Panne

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Motion diffusion models and Reinforcement Learning (RL) based control for physics-based simulations have complementary strengths for human motion generation. The former is capable of generating a wide variety of motions, adhering to intuitive control such as text, while the latter offers physically plausible motion and direct interaction with the environment. In this work, we present a method that combines their respective strengths. CLoSD is a text-driven RL physics-based controller, guided by diffusion generation for various tasks. Our key insight is that motion diffusion can serve as an on-the-fly universal planner for a robust RL controller. To this end, CLoSD maintains a closed-loop interaction between two modules — a Diffusion Planner (DiP), and a tracking controller. DiP is a fast-responding autoregressive diffusion model, controlled by textual prompts and target locations, and the controller is a simple and robust motion imitator that continuously receives motion plans from DiP and provides feedback from the environment. CLoSD is capable of seamlessly performing a sequence of different tasks, including navigation to a goal location, striking an object with a hand or foot as specified in a text prompt, sitting down, and getting up.

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Scalable Decision-Making in Stochastic Environments through Learned Temporal Abstraction

Baiting Luo, Ava Pettet, Aron Laszka, Abhishek Dubey, Ayan Mukhopadhyay

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Sequential decision-making in high-dimensional continuous action spaces, particularly in stochastic environments, faces significant computational challenges. We explore this challenge in the traditional offline RL setting, where an agent must learn how to make decisions based on data collected through a stochastic behavior policy. We present \textit{Latent Macro Action Planner} (L-MAP), which addresses this challenge by learning a set of temporally extended macro-actions through a state-conditional Vector Quantized Variational Autoencoder (VQ-VAE), effectively reducing action dimensionality. L-MAP employs a (separate) learned prior model that acts as a latent transition model and allows efficient sampling of plausible actions. During planning, our approach accounts for stochasticity in both the environment and the behavior policy by using Monte Carlo tree search (MCTS). In offline RL settings, including stochastic continuous control tasks, L-MAP efficiently searches over discrete latent actions to yield high expected returns. Empirical results demonstrate that L-MAP maintains low decision latency despite increased action dimensionality. Notably, across tasks ranging from continuous control with inherently stochastic dynamics to high-dimensional robotic hand manipulation, L-MAP significantly outperforms existing model-based methods and performs on par with strong model-free actor-critic baselines, highlighting the effectiveness of the proposed approach in planning in complex and stochastic environments with high-dimensional action spaces.

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Scalable and Certifiable Graph Unlearning: Overcoming the Approximation Error Barrier

Lu Yi, Zhewei Wei

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Graph unlearning has emerged as a pivotal research area for ensuring privacy protection, given the widespread adoption of Graph Neural Networks (GNNs) in applications involving sensitive user data. Among existing studies, certified graph unlearning is distinguished by providing robust privacy guarantees. However, current certified graph unlearning methods are impractical for large-scale graphs because they necessitate the costly re-computation of graph propagation for each unlearning request. Although numerous scalable techniques have been developed to accelerate graph propagation for GNNs, their integration into certified graph unlearning remains uncertain as these scalable approaches introduce approximation errors into node embeddings. In contrast, certified graph unlearning demands bounded model error on exact node embeddings to maintain its certified guarantee. To address this challenge, we present ScaleGUN, the first approach to scale certified graph unlearning to billion-edge graphs. ScaleGUN integrates the approximate graph propagation technique into certified graph unlearning, offering certified guarantees for three unlearning scenarios: node feature, edge and node unlearning. Extensive experiments on real-world datasets demonstrate the efficiency and unlearning efficacy of ScaleGUN. Remarkably, ScaleGUN accomplishes $(\epsilon,\delta)=(1,10^{-4})$ certified unlearning on the billion-edge graph ogbn-papers100M in 20 seconds for a 5,000 random edge removal request -- of which only 5 seconds are required for updating the node embeddings -- compared to 1.91 hours for retraining and 1.89 hours for re-propagation. Our code is available at https://github.com/luyi256/ScaleGUN.

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Control-oriented Clustering of Visual Latent Representation

Han Qi, Haocheng Yin, Heng Yang

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We initiate a study of the geometry of the visual representation space ---the information channel from the vision encoder to the action decoder--- in an image-based control pipeline learned from behavior cloning. Inspired by the phenomenon of *neural collapse* (NC) in image classification, we empirically demonstrate the prevalent emergence of a similar *law of clustering* in the visual representation space. Specifically, - In discrete image-based control (e.g., Lunar Lander), the visual representations cluster according to the natural discrete action labels; - In continuous image-based control (e.g., Planar Pushing and Block Stacking), the clustering emerges according to ``control-oriented'' classes that are based on (a) the relative pose between the object and the target in the input or (b) the relative pose of the object induced by expert actions in the output. Each of the classes corresponds to one relative pose orthant (REPO). Beyond empirical observation, we show such a law of clustering can be leveraged as an algorithmic tool to improve test-time performance when training a policy with limited expert demonstrations. Particularly, we pretrain the vision encoder using NC as a regularization to encourage control-oriented clustering of the visual features. Surprisingly, such an NC-pretrained vision encoder, when finetuned end-to-end with the action decoder, boosts the test-time performance by 10% to 35%. Real-world vision-based planar pushing experiments confirmed the surprising advantage of control-oriented visual representation pretraining.

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No Need to Talk: Asynchronous Mixture of Language Models

Anastasiia Filippova, Angelos Katharopoulos, David Grangier, Ronan Collobert

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We introduce SMALLTALK LM, an innovative method for training a mixture of language models in an almost asynchronous manner. Each model of the mixture specializes in distinct parts of the data distribution, without the need of high-bandwidth communication between the nodes training each model. At inference, a lightweight router directs a given sequence to a single expert, according to a short prefix. This inference scheme naturally uses a fraction of the parameters from the overall mixture model. Unlike prior works on asynchronous LLM training, our routing method does not rely on full corpus clustering or access to metadata, making it more suitable for real-world applications. Our experiments on language modeling demonstrate that SMALLTALK LM achieves significantly lower perplexity than dense model baselines for the same total training FLOPs and an almost identical inference cost. Finally, in our downstream evaluations we outperform the dense baseline on 75% of the tasks.

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Exploring Local Memorization in Diffusion Models via Bright Ending Attention

Chen Chen, Daochang Liu, Mubarak Shah, Chang Xu

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Text-to-image diffusion models have achieved unprecedented proficiency in generating realistic images. However, their inherent tendency to memorize and replicate training data during inference raises significant concerns, including potential copyright infringement. In response, various methods have been proposed to evaluate, detect, and mitigate memorization. Our analysis reveals that existing approaches significantly underperform in handling local memorization, where only specific image regions are memorized, compared to global memorization, where the entire image is replicated. Also, they cannot locate the local memorization regions, making it hard to investigate locally. To address these, we identify a novel "bright ending" (BE) anomaly in diffusion models prone to memorizing training images. BE refers to a distinct cross-attention pattern observed in text-to-image diffusion models, where memorized image patches exhibit significantly greater attention to the final text token during the last inference step than non-memorized patches. This pattern highlights regions where the generated image replicates training data and enables efficient localization of memorized regions. Equipped with this, we propose a simple yet effective method to integrate BE into existing frameworks, significantly improving their performance by narrowing the performance gap caused by local memorization. Our results not only validate the successful execution of the new localization task but also establish new state-of-the-art performance across all existing tasks, underscoring the significance of the BE phenomenon.

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Provably Reliable Conformal Prediction Sets in the Presence of Data Poisoning

Yan Scholten, Stephan Günnemann

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Conformal prediction provides model-agnostic and distribution-free uncertainty quantification through prediction sets that are guaranteed to include the ground truth with any user-specified probability. Yet, conformal prediction is not reliable under poisoning attacks where adversaries manipulate both training and calibration data, which can significantly alter prediction sets in practice. As a solution, we propose reliable prediction sets (RPS): the first efficient method for constructing conformal prediction sets with provable reliability guarantees under poisoning. To ensure reliability under training poisoning, we introduce smoothed score functions that reliably aggregate predictions of classifiers trained on distinct partitions of the training data. To ensure reliability under calibration poisoning, we construct multiple prediction sets, each calibrated on distinct subsets of the calibration data. We then aggregate them into a majority prediction set, which includes a class only if it appears in a majority of the individual sets. Both proposed aggregations mitigate the influence of datapoints in the training and calibration data on the final prediction set. We experimentally validate our approach on image classification tasks, achieving strong reliability while maintaining utility and preserving coverage on clean data. Overall, our approach represents an important step towards more trustworthy uncertainty quantification in the presence of data poisoning.

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LLaVA-Interleave: Tackling Multi-image, Video, and 3D in Large Multimodal Models

Feng Li, Renrui Zhang, Hao Zhang, Yuanhan Zhang, Bo Li, Wei Li, Zejun MA, Chunyuan Li

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Visual instruction tuning has made considerable strides in enhancing the capabilities of Large Multimodal Models (LMMs). However, existing open LMMs largely focus on single-image tasks, their applications to multi-image scenarios remains less explored. Additionally, prior LMM research separately tackles different scenarios, leaving it impossible to generalize cross scenarios with new emerging capabilities. To this end, we introduce LLaVA-Interleave, which simultaneously tackles Multi-image, Multi-frame (video), Multi-view (3D), and Multi-patch (single-image) scenarios in LMMs. To enable these capabilities, we regard the interleaved data format as a general template and compile the M4-Instruct dataset with 1,177.6k samples, spanning 4 primary domains with 14 tasks and 41 datasets. We also curate the LLaVA-Interleave Bench to comprehensively evaluate the multi-image performance of LMMs. Through extensive experiments, LLaVA-Interleave achieves leading results in multi-image, video, and 3D benchmarks, while maintaining the performance of single-image tasks. Besides, our model also exhibits several emerging capabilities, e.g., transferring tasks across different settings and modalities.

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TokenFormer: Rethinking Transformer Scaling with Tokenized Model Parameters

Haiyang Wang, Yue Fan, Muhammad Ferjad Naeem, Yongqin Xian, Jan Eric Lenssen, Liwei Wang, Federico Tombari, Bernt Schiele

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Transformers have become the predominant architecture in foundation models due to their excellent performance across various domains. However, the substantial cost of scaling these models remains a significant concern. This problem arises primarily from their dependence on a fixed number of parameters within linear projections. When architectural modifications (e.g., channel dimensions) are introduced, the entire model typically requires retraining from scratch. As model sizes continue growing, this strategy results in increasingly high computational costs and becomes unsustainable. To overcome this problem, we introduce Tokenformer, a natively scalable architecture that leverages the attention mechanism not only for computations among input tokens but also for interactions between tokens and model parameters, thereby enhancing architectural flexibility. By treating model parameters as tokens, we replace all the linear projections in Transformers with our token-parameter attention layer, where input tokens act as queries and model parameters as keys and values. This reformulation allows for progressive and efficient scaling without necessitating retraining from scratch. Our model scales from 124M to 1.4B parameters by incrementally adding new key-value parameter pairs, achieving performance comparable to Transformers trained from scratch while greatly reducing training costs. Code and models are available at {\color{red}\url{https://github.com/Haiyang-W/TokenFormer.git}}

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Not All LLM-Generated Data Are Equal: Rethinking Data Weighting in Text Classification

Hsun-Yu Kuo, Yin-Hsiang Liao, Yu-Chieh Chao, Wei-Yun Ma, Pu-Jen Cheng

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Synthetic data augmentation via Large Language Models (LLMs) allows researchers to leverage additional training data, thus enhancing the performance of downstream tasks, especially when real-world data is scarce. However, the generated data can deviate from the real-world data, and this misalignment can bring about deficient results while applying the trained model to applications. Therefore, we proposed efficient weighted-loss approaches to align synthetic data with real-world distribution by emphasizing high-quality and diversified data generated by LLMs using merely a tiny amount of real-world data. We empirically assessed the effectiveness of our methods on multiple text classification tasks, and the results showed that leveraging our approaches on a BERT-level model robustly outperformed standard cross-entropy and other data weighting approaches, providing potential solutions to effectively leveraging synthetic data from any suitable data generator.

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ZAPBench: A Benchmark for Whole-Brain Activity Prediction in Zebrafish

Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen, Peter H. Li, Mariela D Petkova, Nirmala A Iyer, Luuk Willem Hesselink, Aparna Dev, Gudrun Ihrke, Woohyun Park, Alyson Petruncio, Aubrey Weigel, Wyatt Korff, Florian Engert, Jeff Lichtman, Misha Ahrens, Michal Januszewski, Viren Jain

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Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Prediction Benchmark (ZAPBench) to measure progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain. The benchmark is based on a novel dataset containing 4d light-sheet microscopy recordings of over 70,000 neurons in a larval zebrafish brain, along with motion stabilized and voxel-level cell segmentations of these data that facilitate development of a variety of forecasting methods. Initial results from a selection of time series and volumetric video modeling approaches achieve better performance than naive baseline methods, but also show room for further improvement. The specific brain used in the activity recording is also undergoing synaptic-level anatomical mapping, which will enable future integration of detailed structural information into forecasting methods.

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Internet of Agents: Weaving a Web of Heterogeneous Agents for Collaborative Intelligence

Weize Chen, Ziming You, Ran Li, yitong guan, Chen Qian, Chenyang Zhao, Cheng Yang, Ruobing Xie, Zhiyuan Liu, Maosong Sun

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The rapid advancement of large language models (LLMs) has paved the way for the development of highly capable autonomous agents. However, existing multi-agent frameworks often struggle with integrating diverse capable third-party agents due to reliance on agents defined within their own ecosystems. They also face challenges in simulating distributed environments, as most frameworks are limited to single-device setups. Furthermore, these frameworks often rely on hard-coded communication pipelines, limiting their adaptability to dynamic task requirements. Inspired by the concept of the Internet, we propose the Internet of Agents (IoA), a novel framework that addresses these limitations by providing a flexible and scalable platform for LLM-based multi-agent collaboration. IoA introduces an agent integration protocol, an instant-messaging-like architecture design, and dynamic mechanisms for agent teaming and conversation flow control. Through extensive experiments on general assistant tasks, embodied AI tasks, and retrieval-augmented generation benchmarks, we demonstrate that IoA consistently outperforms state-of-the-art baselines, showcasing its ability to facilitate effective collaboration among heterogeneous agents. IoA represents a step towards linking diverse agents in an Internet-like environment, where agents can seamlessly collaborate to achieve greater intelligence and capabilities. We will release our code to facilitate further research.

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Large-scale and Fine-grained Vision-language Pre-training for Enhanced CT Image Understanding

Zhongyi Shui, Jianpeng Zhang, Weiwei Cao, Sinuo Wang, Ruizhe Guo, Le Lu, Lin Yang, Xianghua Ye, Tingbo Liang, Qi Zhang, Ling Zhang

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Artificial intelligence (AI) shows great potential in assisting radiologists to improve the efficiency and accuracy of medical image interpretation and diagnosis. However, a versatile AI model requires large-scale data and comprehensive annotations, which are often impractical in medical settings. Recent studies leverage radiology reports as a naturally high-quality supervision for medical images, using contrastive language-image pre-training (CLIP) to develop language-informed models for radiological image interpretation. Nonetheless, these approaches typically contrast entire images with reports, neglecting the local associations between imaging regions and report sentences, which may undermine model performance and interoperability. In this paper, we propose a fine-grained vision-language model (fVLM) for anatomy-level CT image interpretation. Specifically, we explicitly match anatomical regions of CT images with corresponding descriptions in radiology reports and perform contrastive pre-training for each anatomy individually. Fine-grained alignment, however, faces considerable false-negative challenges, mainly from the abundance of anatomy-level healthy samples and similarly diseased abnormalities, leading to ambiguous patient-level pairings. To tackle this issue, we propose identifying false negatives of both normal and abnormal samples and calibrating contrastive learning from patient-level to disease-aware pairing. We curated the largest CT dataset to date, comprising imaging and report data from 69,086 patients, and conducted a comprehensive evaluation of 54 major and important disease (including several most deadly cancers) diagnosis tasks across 15 main anatomies. Experimental results demonstrate the substantial potential of fVLM in versatile medical image interpretation. In the zero-shot classification task, we achieved an average AUC of 81.3% on 54 diagnosis tasks, surpassing CLIP and supervised methods by 12.9% and 8.0%, respectively. Additionally, on the publicly available CT-RATE and Rad-ChestCT benchmarks, our fVLM outperformed the current state-of-the-art methods with absolute AUC gains of 7.4% and 4.8%, respectively.

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Vision-RWKV: Efficient and Scalable Visual Perception with RWKV-Like Architectures

Yuchen Duan, Weiyun Wang, Zhe Chen, Xizhou Zhu, Lewei Lu, Tong Lu, Yu Qiao, Hongsheng Li, Jifeng Dai, Wenhai Wang

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Transformers have revolutionized computer vision and natural language processing, but their high computational complexity limits their application in high-resolution image processing and long-context analysis. This paper introduces Vision-RWKV (VRWKV), a model that builds upon the RWKV architecture from the NLP field with key modifications tailored specifically for vision tasks. Similar to the Vision Transformer (ViT), our model demonstrates robust global processing capabilities, efficiently handles sparse inputs like masked images, and can scale up to accommodate both large-scale parameters and extensive datasets. Its distinctive advantage is its reduced spatial aggregation complexity, enabling seamless processing of high-resolution images without the need for window operations. Our evaluations demonstrate that VRWKV surpasses ViT's performance in image classification and has significantly faster speeds and lower memory usage processing high-resolution inputs. In dense prediction tasks, it outperforms window-based models, maintaining comparable speeds. These results highlight VRWKV's potential as a more efficient alternative for visual perception tasks. Code and models are available at~\url{https://github.com/OpenGVLab/Vision-RWKV}.

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OS-ATLAS: Foundation Action Model for Generalist GUI Agents

Zhiyong Wu, Zhenyu Wu, Fangzhi Xu, Yian Wang, Qiushi Sun, Chengyou Jia, Kanzhi Cheng, Zichen Ding, Liheng Chen, Paul Pu Liang, Yu Qiao

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Existing efforts in building GUI agents heavily rely on the availability of robust commercial Vision-Language Models (VLMs) such as GPT-4o and GeminiProVision. Practitioners are often reluctant to use open-source VLMs due to their significant performance lag compared to their closed-source counterparts, particularly in GUI grounding and Out-Of-Distribution (OOD) scenarios. To facilitate future research in this area, we developed OS-Atlas—a foundational GUI action model that excels at GUI grounding and OOD agentic tasks through innovations in both data and modeling. We have invested significant engineering effort in developing an open-source toolkit for synthesizing GUI grounding data across multiple platforms, including Windows, Linux, MacOS, Android, and the web. Leveraging this toolkit, we are releasing the largest open-source cross-platform GUI grounding corpus to date, which contains over 13 million GUI elements. This dataset, combined with innovations in model training, provides a solid foundation for OS-Atlas to understand GUI screenshots and generalize to unseen interfaces. Through extensive evaluation across six benchmarks spanning three different platforms (mobile, desktop, and web), OS-Atlas demonstrates significant performance improvements over previous state-of-the-art models. Our evaluation also uncovers valuable insights into continuously improving and scaling the agentic capabilities of open-source VLMs.

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ThinK: Thinner Key Cache by Query-Driven Pruning

Yuhui Xu, Zhanming Jie, Hanze Dong, Lei Wang, Xudong Lu, Aojun Zhou, Amrita Saha, Caiming Xiong, Doyen Sahoo

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Large Language Models (LLMs) have revolutionized the field of natural language processing, achieving unprecedented performance across a variety of applications. However, their increased computational and memory demands present significant challenges, especially when handling long sequences. This paper focuses on the long-context scenario, addressing the inefficiencies in KV cache memory consumption during inference. Unlike existing approaches that optimize the memory based on the sequence length, we identify substantial redundancy in the channel dimension of the KV cache, as indicated by an uneven magnitude distribution and a low-rank structure in the attention weights. In response, we propose ThinK, a novel query-dependent KV cache pruning method designed to minimize attention weight loss while selectively pruning the least significant channels. Our approach not only maintains or enhances model accuracy but also achieves a reduction in KV cache memory costs by over 20\% compared with vanilla KV cache eviction and quantization methods. For instance, ThinK integrated with KIVI can achieve $2.8\times$ peak memory reduction while maintaining nearly the same quality, enabling a batch size increase from 4$\times$ (with KIVI alone) to 5$\times$ when using a single GPU. Extensive evaluations on the LLaMA and Mistral models across various long-sequence datasets verified the efficiency of ThinK. Our code has been made available at https://github.com/SalesforceAIResearch/ThinK.

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Correlated Proxies: A New Definition and Improved Mitigation for Reward Hacking

Cassidy Laidlaw, Shivam Singhal, Anca Dragan

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Because it is difficult to precisely specify complex objectives, reinforcement learning policies are often optimized using proxy reward functions that only approximate the true goal. However, optimizing proxy rewards frequently leads to reward hacking: the optimized reward function ceases to be a good proxy and the resulting policy performs poorly with respect to the unspecified true reward. Principled solutions to reward hacking have been impeded by the lack of a good definition for the problem. To address this gap, we introduce a definition of reward hacking based on the correlation between proxy and true rewards for states and actions seen by a “reference policy” that breaks down under optimization. We show that this definition captures reward hacking behavior across several realistic settings, including in reinforcement learning from human feedback (RLHF). Using our formulation, we show theoretically that regularization to the reference policy can effectively prevent reward hacking. While the current practice in RLHF applies a KL penalty between action distributions for this purpose, our theory suggests regularizing the χ2 divergence between the policies’ occupancy measures can be more effective. We intuitively show the benefits of this type of regularization and demonstrate that it better mitigates reward hacking in practice across four realistic settings, including RLHF. Our code is available at https://github.com/cassidylaidlaw/orpo.

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Probabilistic Geometric Principal Component Analysis with application to neural data

Han-Lin Hsieh, Maryam Shanechi

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Dimensionality reduction is critical across various domains of science including neuroscience. Probabilistic Principal Component Analysis (PPCA) is a prominent dimensionality reduction method that provides a probabilistic approach unlike the deterministic approach of PCA and serves as a connection between PCA and Factor Analysis (FA). Despite their power, PPCA and its extensions are mainly based on linear models and can only describe the data in a Euclidean coordinate system around the mean of data. However, in many neuroscience applications, data may be distributed around a nonlinear geometry (i.e., manifold) rather than lying in the Euclidean space around the mean. We develop Probabilistic Geometric Principal Component Analysis (PGPCA) for such datasets as a new dimensionality reduction algorithm that can explicitly incorporate knowledge about a given nonlinear manifold that is first fitted from these data. Further, we show how in addition to the Euclidean coordinate system, a geometric coordinate system can be derived for the manifold to capture the deviations of data from the manifold and noise. We also derive a data-driven EM algorithm for learning the PGPCA model parameters. As such, PGPCA generalizes PPCA to better describe data distributions by incorporating a nonlinear manifold geometry. In simulations and brain data analyses, we show that PGPCA can effectively model the data distribution around various given manifolds and outperforms PPCA for such data. Moreover, PGPCA provides the capability to test whether the new geometric coordinate system better describes the data than the Euclidean one. Finally, PGPCA can perform dimensionality reduction and learn the data distribution both around and on the manifold. These capabilities make PGPCA valuable for enhancing the efficacy of dimensionality reduction for analysis of high-dimensional data that exhibit noise and are distributed around a nonlinear manifold, especially for neural data.

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CBGBench: Fill in the Blank of Protein-Molecule Complex Binding Graph

Haitao Lin, Guojiang Zhao, Odin Zhang, Yufei Huang, Lirong Wu, Cheng Tan, Zicheng Liu, Zhifeng Gao, Stan Z. Li

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Structure-based drug design (SBDD) aims to generate potential drugs that can bind to a target protein and is greatly expedited by the aid of AI techniques in generative models. However, a lack of systematic understanding persists due to the diverse settings, complex implementation, difficult reproducibility, and task singularity. Firstly, the absence of standardization can lead to unfair comparisons and inconclusive insights. To address this dilemma, we propose CBGBench, a comprehensive benchmark for SBDD, that unifies the task as a generative graph completion, analogous to fill-in-the-blank of the 3D complex binding graph. By categorizing existing methods based on their attributes, CBGBench facilitates a modular and extensible framework that implements cutting-edge methods. Secondly, a single de novo molecule generation task can hardly reflect their capabilities. To broaden the scope, we adapt these models to a range of tasks essential in drug design, considered sub-tasks within the graph fill-in-the-blank tasks. These tasks include the generative designation of de novo molecules, linkers, fragments, scaffolds, and sidechains, all conditioned on the structures of protein pockets. Our evaluations are conducted with fairness, encompassing comprehensive perspectives on interaction, chemical properties, geometry authenticity, and substructure validity. We further provide insights with analysis from empirical studies. Our results indicate that there is potential for further improvements on many tasks, with optimization in network architectures, and effective incorporation of chemical prior knowledge. Finally, to lower the barrier to entry and facilitate further developments in the field, we also provide a single [codebase](https://github.com/EDAPINENUT/CBGBench) that unifies the discussed models, data pre-processing, training, sampling, and evaluation.

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