ICML 2025 Papers

International Conference on Machine Learning

Decision breakdown

3,342papers

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

  • Oral
    1213.6%
  • Spotlight
    2256.7%
  • Poster
    2,99689.6%

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P(all-atom) Is Unlocking New Path For Protein Design

Wei Qu, Jiawei Guan, Rui Ma, kezhai, Weikun.Wu, Haobo Wang

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We introduce Pallatom, an innovative protein generation model capable of producing protein structures with all-atom coordinates. Pallatom directly learns and models the joint distribution $P(\textit{structure}, \textit{seq})$ by focusing on $P(\textit{all-atom})$, effectively addressing the interdependence between sequence and structure in protein generation. To achieve this, we propose a novel network architecture specifically designed for all-atom protein generation. Our model employs a dual-track framework that tokenizes proteins into token-level and atomic-level representations, integrating them through a multi-layer decoding process with "traversing" representations and recycling mechanism. We also introduce the $\texttt{atom14}$ representation method, which unifies the description of unknown side-chain coordinates, ensuring high fidelity between the generated all-atom conformation and its physical structure. Experimental results demonstrate that Pallatom excels in key metrics of protein design, including designability, diversity, and novelty, showing significant improvements across the board. Our model not only enhances the accuracy of protein generation but also exhibits excellent sampling efficiency, paving the way for future applications in larger and more complex systems.

Spotlight
Principal-Agent Bandit Games with Self-Interested and Exploratory Learning Agents

Junyan Liu, Lillian J. Ratliff

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We study the repeated principal-agent bandit game, where the principal indirectly explores an unknown environment by incentivizing an agent to play arms. Unlike prior work that assumes a greedy agent with full knowledge of reward means, we consider a self-interested learning agent who iteratively updates reward estimates and may explore arbitrarily with some probability. As a warm-up, we first consider a self-interested learning agent without exploration. We propose algorithms for both i.i.d. and linear reward settings with bandit feedback in a finite horizon $T$, achieving regret bounds of $\widetilde{O}(\sqrt{T})$ and $\widetilde{O}(T^{\frac{2}{3}})$, respectively. Specifically, these algorithms rely on a novel elimination framework coupled with new search algorithms which accommodate the uncertainty from the agent's learning behavior. We then extend the framework to handle an exploratory learning agent and develop an algorithm to achieve a $\widetilde{O}(T^{\frac{2}{3}})$ regret bound in i.i.d. reward setup by enhancing the robustness of our elimination framework to the potential agent exploration. Finally, when our agent model reduces to that in (Dogan et al., 2023a), we propose an algorithm based on our robust framework, which achieves a $\widetilde{O}(\sqrt{T})$ regret bound, significantly improving upon their $\widetilde{O}(T^{\frac{11}{12}})$ bound.

Poster
Heads up! Large Language Models Can Perform Tasks Without Your Instruction via Selective Attention Head Masking

Senyu Han, Hongchuan Zeng, Kai Yu, Lu Chen

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Large language models (LLMs) consist of numerous Transformer modules, and while the models can perform various functions, it remains an open question of how these modules are combined to elicit distinct inherent functionalities. In this paper, we investigate the modules inside LLMs and demonstrate that, by simply masking or retaining specific attention heads during inference, LLMs can exhibit specific task functionalities without requiring explicit instructions or modifications to the model parameters. Experiments across various models and tasks reveal that LLMs inherently encode ``functional pathways'', the structured groups of interdependent attention heads that are crucial for executing specific tasks. These pathways not only govern the model's functional behaviors but also enhance parameter efficiency, as suppressing attention heads outside the pathway can improve task performance. The code is available in this repository: [https://github.com/OpenDFM/HeadsUp](https://github.com/OpenDFM/HeadsUp).

Poster
Distributionally Robust Active Learning for Gaussian Process Regression

Shion Takeno, Yoshito Okura, Yu Inatsu, Aoyama Tatsuya, Tomonari Tanaka, Akahane Satoshi, Hiroyuki Hanada, Noriaki Hashimoto, Taro Murayama, Hanju Lee, Shinya Kojima, Ichiro Takeuchi

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Gaussian process regression (GPR) or kernel ridge regression is a widely used and powerful tool for nonlinear prediction. Therefore, active learning (AL) for GPR, which actively collects data labels to achieve an accurate prediction with fewer data labels, is an important problem. However, existing AL methods do not theoretically guarantee prediction accuracy for target distribution. Furthermore, as discussed in the distributionally robust learning literature, specifying the target distribution is often difficult. Thus, this paper proposes two AL methods that effectively reduce the worst-case expected error for GPR, which is the worst-case expectation in target distribution candidates. We show an upper bound of the worst-case expected squared error, which suggests that the error will be arbitrarily small by a finite number of data labels under mild conditions. Finally, we demonstrate the effectiveness of the proposed methods through synthetic and real-world datasets.

Poster
Simplifying DINO via Coding Rate Regularization

Ziyang Wu, Jingyuan Zhang, Druv Pai, Xudong Wang, Chandan Singh, Jianwei Yang, Jianfeng Gao, Yi Ma

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DINO and DINOv2 are two model families being widely used to learn representations from unlabeled imagery data at large scales. Their learned representations often enable state-of-the-art performance for downstream tasks, such as image classification and segmentation. However, they employ many empirically motivated design choices and their training pipelines are highly complex and unstable --- many hyperparameters need to be carefully tuned to ensure that the representations do not collapse --- which poses considerable difficulty to improving them or adapting them to new domains. In this work, we posit that we can remove most such-motivated idiosyncrasies in the pre-training pipelines, and only need to add an explicit coding rate term in the loss function to avoid collapse of the representations. As a result, we obtain highly simplified variants of the DINO and DINOv2 which we call SimDINO and SimDINOv2, respectively. Remarkably, these simplified models are more robust to different design choices, such as network architecture and hyperparameters, and they learn even higher-quality representations, measured by performance on downstream tasks, offering a Pareto improvement over the corresponding DINO and DINOv2 models. This work highlights the potential of using simplifying design principles to improve the empirical practice of deep learning. Code and model checkpoints are available at https://github.com/RobinWu218/SimDINO.

Poster
Mind the Gap: a Spectral Analysis of Rank Collapse and Signal Propagation in Attention Layers

Thiziri Nait Saada, Alireza Naderi, Jared Tanner

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Attention layers are the core component of transformers, the current state-of-the-art neural network architecture. Alternatives to softmax-based attention are being explored due to its tendency to hinder effective information flow. Even *at initialisation*, it remains poorly understood why the propagation of signals and gradients through these random networks can be pathological, resulting in issues known as (i) vanishing/exploding gradients and (ii) rank collapse *in depth*, i.e. when all tokens converge to a single representation along layers. While rank collapse in depth naturally arises from repeated matrix multiplications---a common pattern across various architectures---we identify an additional and previously unknown challenge unique to softmax attention layers: (iii) rank collapse *in width*, which occurs as the context length increases. Using Random Matrix Theory, we conduct a rigorous analysis that uncovers a spectral gap between the two largest singular values of the attention matrix as the cause of (iii), which in turn exacerbates (i) and (ii). Building on this insight, we propose a novel yet simple practical solution to mitigate rank collapse in width by removing the outlier eigenvalue(s). Our theoretical framework offers a fresh perspective on recent practical studies, such as (Ye et al., 2024; Ali et al., 2023), whose ad hoc solutions can now be interpreted as implicit efforts to address the spectral gap issue. This work provides valuable theoretical support for ongoing large-scale empirical research, bringing theory and practice one step closer in the understanding of transformers.

Poster
Policy Design for Two-sided Platforms with Participation Dynamics

Haruka Kiyohara, Fan Yao, Sarah Dean

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In two-sided platforms (e.g., video streaming or e-commerce), viewers and providers engage in interactive dynamics: viewers benefit from increases in provider populations, while providers benefit from increases in viewer population. Despite the importance of such “population effects” on long-term platform health, recommendation policies do not generally take the participation dynamics into account. This paper thus studies the dynamics and recommender policy design on two-sided platforms under the population effects for the first time. Our control- and game-theoretic findings warn against the use of the standard “myopic-greedy” policy and shed light on the importance of provider-side considerations (i.e., effectively distributing exposure among provider groups) to improve social welfare via population growth. We also present a simple algorithm to optimize long-term social welfare by taking the population effects into account, and demonstrate its effectiveness in synthetic and real-data experiments. Our experiment code is available at https://github.com/sdean-group/dynamics-two-sided-market.

Poster
R*: Efficient Reward Design via Reward Structure Evolution and Parameter Alignment Optimization with Large Language Models

Pengyi Li, Jianye Hao, Hongyao Tang, Yifu Yuan, Jinbin Qiao, Zibin Dong, Yan Zheng

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Reward functions are crucial for policy learning. Large Language Models (LLMs), with strong coding capabilities and valuable domain knowledge, provide an automated solution for high-quality reward design. However, code-based reward functions require precise guiding logic and parameter configurations within a vast design space, leading to low optimization efficiency. To address the challenges, we propose an efficient automated reward design framework, called R*, which decomposes reward design into two parts: reward structure evolution and parameter alignment optimization. To design high-quality reward structures, R* maintains a reward function population and modularizes the functional components. LLMs are employed as the mutation operator, and module-level crossover is proposed to facilitate efficient exploration and exploitation. To design more efficient reward parameters, R* first leverages LLMs to generate multiple critic functions for trajectory comparison and annotation. Based on these critics, a voting mechanism is employed to collect the trajectory segments with high-confidence labels. These labeled segments are then used to refine the reward function parameters through preference learning. Experiments on diverse robotic control tasks demonstrate that R* outperforms strong baselines in both reward design efficiency and quality, surpassing human-designed reward functions.

Poster
Simple Randomized Rounding for Max-Min Eigenvalue Augmentation

Jourdain Lamperski, Haeseong Yang, Oleg Prokopyev

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We consider the *max-min eigenvalue augmentation* problem: given $n \times n$ symmetric positive semidefinite matrices $M,A_1,\ldots, A_m$ and a positive integer $k < m$, the goal is to choose a subset $I \subset \{1,\ldots,m\}$ of cardinality at most $k$ that maximizes the minimum eigenvalue of the matrix $M + \sum_{i \in I} A_i$. The problem captures both the *Bayesian E-optimal design* and *maximum algebraic connectivity augmentation* problems. In contrast to the existing work, we do not assume that the *augmentation matrices* are rank-one matrices, and we focus on the setting in which $k < n$. We show that a *simple* randomized rounding method provides a constant-factor approximation if the *optimal increase* is sufficiently large, specifically, if $\mathrm{OPT} - \lambda_{\mathrm{min}}(M) = \Omega(R \ln k)$, where $\mathrm{OPT}$ is the optimal value, and $R$ is the maximum trace of an augmentation matrix. To establish the guarantee, we derive a matrix concentration inequality that is of independent interest. The inequality can be interpreted as an *intrinsic dimension* analog of the matrix Chernoff inequality for the minimum eigenvalue of a sum of independent random positive semidefinite matrices; such an inequality has already been established for the maximum eigenvalue, but not for the minimum eigenvalue.

Poster
MxMoE: Mixed-precision Quantization for MoE with Accuracy and Performance Co-Design

Haojie Duanmu, Xiuhong Li, Zhihang Yuan, Size Zheng, Jiangfei Duan, Xingcheng Zhang, Dahua Lin

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Mixture-of-Experts (MoE) models face deployment challenges due to their large parameter counts and computational demands. We explore quantization for MoE models and highlight two key insights: 1) linear blocks exhibit varying quantization sensitivity, and 2) divergent expert activation frequencies create heterogeneous computational characteristics. Based on these observations, we introduce MxMoE, a mixed-precision optimization framework for MoE models that considers both algorithmic and system perspectives. MxMoE navigates the design space defined by parameter sensitivity, expert activation dynamics, and hardware resources to derive efficient mixed-precision configurations. Additionally, MxMoE automatically generates optimized mixed-precision GroupGEMM kernels, enabling parallel execution of GEMMs with different precisions. Evaluations show that MxMoE outperforms existing methods, achieving 2.4 lower Wikitext-2 perplexity than GPTQ at 2.25-bit and delivering up to 3.4x speedup over full precision, as well as up to 29.4% speedup over uniform quantization at equivalent accuracy with 5-bit weight-activation quantization. Our code is available at https://github.com/cat538/MxMoE.

Poster
Data-driven Design of Randomized Control Trials with Guaranteed Treatment Effects

Santiago Cortes-Gomez, Naveen Janaki Raman, Aarti Singh, Bryan Wilder

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Randomized controlled trials (RCTs) generate guarantees for treatment effects. However, RCTs often spend unnecessary resources exploring sub-optimal treatments, which can reduce the power of treatment guarantees. To address this, we propose a two-stage RCT design. In the first stage, a data-driven screening procedure prunes low-impact treatments, while the second stage focuses on developing high-probability lower bounds for the best-performing treatment effect. Unlike existing adaptive RCT frameworks, our method is simple enough to be implemented in scenarios with limited adaptivity. We derive optimal designs for two-stage RCTs and demonstrate how such designs can be implemented through sample splitting. Empirically, we demonstrate that two-stage designs improve upon single-stage approaches, especially for scenarios where domain knowledge is available through a prior. Our work is thus, a simple yet effective design for RCTs, optimizing for the ability to certify with high probability the largest possible treatment effect for at least one of the arms studied.

Poster
Diversity By Design: Leveraging Distribution Matching for Offline Model-Based Optimization

Michael S Yao, James Gee, Osbert Bastani

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The goal of offline model-based optimization (MBO) is to propose new designs that maximize a reward function given only an offline dataset. However, an important desiderata is to also propose a *diverse* set of final candidates that capture many optimal and near-optimal design configurations. We propose **D**iversit**y** I**n** **A**dversarial **M**odel-based **O**ptimization (**DynAMO**) as a novel method to introduce design diversity as an explicit objective into any MBO problem. Our key insight is to formulate diversity as a *distribution matching problem* where the distribution of generated designs captures the inherent diversity contained within the offline dataset. Extensive experiments spanning multiple scientific domains show that DynAMO can be used with common optimization methods to significantly improve the diversity of proposed designs while still discovering high-quality candidates.

Poster
Reliable Algorithm Selection for Machine Learning-Guided Design

Clara Fannjiang, Ji Won Park

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Algorithms for machine learning-guided design, or *design algorithms*, use machine learning-based predictions to propose novel objects with desired property values. Given a new design task—for example, to design novel proteins with high binding affinity to a therapeutic target—one must choose a design algorithm and specify any hyperparameters and predictive and/or generative models involved. How can these decisions be made such that the resulting designs are successful? This paper proposes a method for *design algorithm selection*, which aims to select design algorithms that will produce a distribution of design labels satisfying a user-specified success criterion—for example, that at least ten percent of designs’ labels exceed a threshold. It does so by combining designs’ predicted property values with held-out labeled data to reliably forecast characteristics of the label distributions produced by different design algorithms, building upon techniques from prediction-powered inference (Angelopoulos et al., 2023). The method is guaranteed with high probability to return design algorithms that yield successful label distributions (or the null set if none exist), if the density ratios between the design and labeled data distributions are known. We demonstrate the method’s effectiveness in simulated protein and RNA design tasks, in settings with either known or estimated density ratios.

Poster
Procurement Auctions via Approximately Optimal Submodular Optimization

Yuan Deng, amin karbasi, Vahab Mirrokni, Renato Paes Leme, Grigoris Velegkas, Song Zuo

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We study the problem of procurement auctions, in which an auctioneer seeks to acquire services from a group of strategic sellers with private costs. The quality of the services is measured through some submodular function that is known to the auctioneer. Our goal is to design computationally efficient procurement auctions that (approximately) maximize the difference between the quality of the acquired services and the total cost of the sellers, in a way that is incentive compatible (IC) and individual rational (IR) for the sellers, and generates non-negative surplus (NAS) for the auctioneer. {Our contribution is twofold: \textbf{i)} we provide an improved analysis of existing algorithms for non-positive submodular function maximization and \textbf{ii)} we design computationally efficient frameworks that transform submodular function optimization algorithms to mechanisms that are IC and IR for the sellers, NAS for the auctioneer, and approximation-preserving.} Our frameworks are general and work both in the offline setting where the auctioneer can observe the bids and the services of all the sellers simultaneously, and in the online setting where the sellers arrive in an adversarial order and the auctioneer has to make an irrevocable decision whether to purchase their service or not. We further investigate whether it is possible to convert state-of-art submodular optimization algorithms into descending auctions. We focus on the adversarial setting, meaning that the schedule of the descending prices is determined by an adversary. We show that a submodular optimization algorithm satisfying bi-criteria $(1/2,1)$-approximation in welfare can be effectively converted to a descending auction in this setting. We further establish a connection between descending auctions and online submodular optimization. Finally, we demonstrate the practical applications of our frameworks by instantiating them with different state-of-the-art submodular optimization algorithms and comparing their welfare performance through empirical experiments on publicly available datasets that consist of thousands of sellers.

Spotlight
Domain-Adapted Diffusion Model for PROTAC Linker Design Through the Lens of Density Ratio in Chemical Space

Zixing Song, Ziqiao Meng, José Miguel Hernández-Lobato

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Proteolysis-targeting chimeras (PROTACs) are a groundbreaking technology for targeted protein degradation, but designing effective linkers that connect two molecular fragments to form a drug-candidate PROTAC molecule remains a key challenge. While diffusion models show promise in molecular generation, current diffusion models for PROTAC linker design are typically trained on small molecule datasets, introducing distribution mismatches in the chemical space between small molecules and target PROTACs. Direct fine-tuning on limited PROTAC datasets often results in overfitting and poor generalization. In this work, we propose DAD-PROTAC, a domain-adapted diffusion model for PROTAC linker design, which addresses this distribution mismatch in chemical space through density ratio estimation to bridge the gap between small-molecule and PROTAC domains. By decomposing the target score estimator into a pre-trained score function and a lightweight score correction term, DAD-PROTAC achieves efficient fine-tuning without full retraining. Experimental results demonstrate its superior ability to generate high-quality PROTAC linkers.

Poster
Elucidating the Design Space of Multimodal Protein Language Models

Cheng-Yen Hsieh, Xinyou Wang, Daiheng Zhang, Dongyu Xue, Fei YE, Shujian Huang, Zaixiang Zheng, Quanquan Gu

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Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models. Project page and code: https://bytedance.github.io/dplm/dplm-2.1.

Spotlight
DeepCrossAttention: Supercharging Transformer Residual Connections

Mike Heddes, Adel Javanmard, Kyriakos Axiotis, Gang Fu, Mohammadhossein Bateni, Vahab Mirrokni

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Transformer networks have achieved remarkable success across diverse domains, leveraging a variety of architectural innovations, including residual connections. However, traditional residual connections, which simply sum the outputs of previous layers, can dilute crucial information. This work introduces DeepCrossAttention (DCA), an approach that enhances residual learning in transformers. DCA employs learnable, input-dependent weights to dynamically combine layer outputs, enabling the model to selectively focus on the most relevant information in any of the previous layers. Furthermore, DCA incorporates depth-wise cross-attention, allowing for richer interactions between layers at different depths. Our language modeling experiments show that DCA achieves improved perplexity for a given training time. Moreover, DCA obtains the same model quality up to 3x faster while adding a negligible number of parameters (e.g., 0.2\%). Theoretical analysis confirms that DCA provides an improved trade-off between accuracy and model size when the ratio of collective layer ranks to the ambient dimension falls below a critical threshold.

Poster
Safely Learning Optimal Auctions: A Testable Learning Framework for Mechanism Design

Vikram Kher, Manolis Zampetakis

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When can the distributional assumptions of theorems and learning algorithms be trusted? Inspired by this question, Rubinfeld and Vasilyan (2023) initiated the study of testable learning. In this schema, we always learn one of the following two things: either we have achieved the desired accuracy regardless of whether the distributional assumptions are satisfied, or the input distribution does not satisfy the original distributional assumptions. Motivated by the challenge of relying on strong distributional assumptions in many theorems in mechanism design, we develop a testable learning framework for mechanism design. Traditional models in mechanism design assume that value distributions satisfy some notion of regularity. Unfortunately, testing regularity is not possible in the original testable learning framework as we show. To bypass this impossibility, we propose a regularized version of the testable learning framework. Under this framework, we always learn one of the following two things: either we achieve high revenue compared to the best possible revenue of any regular distribution close to the input distribution, or the input distribution does not satisfy regularity. We then use this framework to provide: 1) a tester-learner pair for revenue optimal mechanisms, 2) a tester for whether the fundamental Bulow-Klemperer Theorem (Bulow and Klemperer 1996) is applicable to a given dataset, and 3) a tester to confirm the existence of an anonymous reserve price that results in the anonymous price auction securing a constant fraction of the optimal revenue.

Poster
Fraud-Proof Revenue Division on Subscription Platforms

Abheek Ghosh, Tzeh Yuan Neoh, Nicholas Teh, Giannis Tyrovolas

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We study a model of subscription-based platforms where users pay a fixed fee for unlimited access to content, and creators receive a share of the revenue. Existing approaches to detecting fraud predominantly rely on machine learning methods, engaging in an ongoing arms race with bad actors. We explore revenue division mechanisms that inherently disincentivize manipulation. We formalize three types of manipulation-resistance axioms and examine which existing rules satisfy these. We show that a mechanism widely used by streaming platforms, not only fails to prevent fraud, but also makes detecting manipulation computationally intractable. We also introduce a novel rule, ScaledUserProp, that satisfies all three manipulation-resistance axioms. Finally, experiments with both real-world and synthetic streaming data support ScaledUserProp as a fairer alternative compared to existing rules.

Poster
Understanding the Skill Gap in Recurrent Language Models: The Role of the Gather-and-Aggregate Mechanism

Aviv Bick, Eric P. Xing, Albert Gu

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State-space models (SSMs) offer efficient alternatives to Transformers for long sequences, but their fixed-size recurrent state limits capability on algorithmic tasks, such as retrieving past context. In this work, we examine how in-context retrieval operates in Transformer- and SSM-based language models and find that both rely on a Gather-and-Aggregate (G&A) mechanism: a Gather Head extracts relevant information from context, which an Aggregate Head integrates into representation. In both architectures, G&A concentrates in a few heads, forming bottlenecks even for simple retrieval. For example, disabling a single Gather or Aggregate Head in a pruned Llama-3.1-8B impairs retrieving the correct answer letter in MMLU, reducing its accuracy from 66% to 25%. Moreover, this retrieval bottleneck can obscure knowledge demands of tasks as the pruned model succeeds on MMLU with functioning G&A heads yet fails on other knowledge benchmarks. The bottleneck similarly extends to tasks where SSMs typically underperform, like GSM8K, BBH, and dialogue. We show that SSMs' retrieval challenges manifest in these heads, creating smoother attention patterns instead of the sharp transitions effective G&A requires. Thus, the Transformer-SSM retrieval gap exists in just a few heads, rather than the entire language model. % Result 3: Analyzing Hybrid models This suggests a unified explanation for Transformer vs. SSM performance gap while showing how to merge their strengths. We find that pretrained hybrid models, where SSMs are combined with attention layers, delegate the role of Aggregate Heads to attention. Similarly, replacing a single G&A head in a pretrained SSM with an attention variant boosts retrieval and benchmark scores.

Poster