ICLR 2025 Papers

High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to widespread adoption. Machine learning has the potential to guide efficient exploration of the perturbation space and extract novel insights from these data. However, current approaches neglect the semantic richness of the relevant biology, and their objectives are misaligned with downstream biological analyses. In this paper, we hypothesize that large language models (LLMs) present a natural medium for representing complex biological relationships and rationalizing experimental outcomes. We propose PerturbQA, a benchmark for structured reasoning over perturbation experiments. Unlike current benchmarks that primarily interrogate existing knowledge, PerturbQA is inspired by open problems in perturbation modeling: prediction of differential expression and change of direction for unseen perturbations, and gene set enrichment. We evaluate state-of-the-art machine learning and statistical approaches for modeling perturbations, as well as standard LLM reasoning strategies, and we find that current methods perform poorly on PerturbQA. As a proof of feasibility, we introduce Summer (SUMMarize, retrievE, and answeR, a simple, domain-informed LLM framework that matches or exceeds the current state-of-the-art. Our code and data are publicly available at https://github.com/genentech/PerturbQA.

Multi-modal models, such as CLIP, have demonstrated strong performance in aligning visual and textual representations, excelling in tasks like image retrieval and zero-shot classification. Despite this success, the mechanisms by which these models utilize training data, particularly the role of memorization, remain unclear. In uni-modal models, both supervised and self-supervised, memorization has been shown to be essential for generalization. However, it is not well understood how these findings would apply to CLIP, which incorporates elements from both supervised learning via captions that provide a supervisory signal similar to labels, and from self-supervised learning via the contrastive objective. To bridge this gap in understanding, we propose a formal definition of memorization in CLIP (CLIPMem) and use it to quantify memorization in CLIP models. Our results indicate that CLIP’s memorization behavior falls between the supervised and self-supervised paradigms, with "mis-captioned" samples exhibiting highest levels of memorization. Additionally, we find that the text encoder contributes more to memorization than the image encoder, suggesting that mitigation strategies should focus on the text domain. Building on these insights, we propose multiple strategies to reduce memorization while at the same time improving utility---something that had not been shown before for traditional learning paradigms where reducing memorization typically results in utility decrease.

3D maps assembled from planar primitives are compact and expressive in representing man-made environments. In this paper, we present **NeuralPlane**, a novel approach that explores **neural** fields for multi-view 3D **plane** reconstruction. Our method is centered upon the core idea of distilling geometric and semantic cues from inconsistent 2D plane observations into a unified 3D neural representation, which unlocks the full leverage of plane attributes. It is accomplished through several key designs, including: 1) a monocular module that generates geometrically smooth and semantically meaningful segments known as 2D plane observations, 2) a plane-guided training procedure that implicitly learns accurate 3D geometry from the multi-view plane observations, and 3) a self-supervised feature field termed *Neural Coplanarity Field* that enables the modeling of scene semantics alongside the geometry. Without relying on prior plane annotations, our method achieves high-fidelity reconstruction comprising planar primitives that are not only crisp but also well-aligned with the semantic content. Comprehensive experiments on ScanNetv2 and ScanNet++ demonstrate the superiority of our method in both geometry and semantics.

Continual Learning (CL) with foundation models has recently emerged as a promising paradigm to exploit abundant knowledge acquired during pre-training for tackling sequential tasks. However, existing prompt-based and Low-Rank Adaptation-based (LoRA-based) methods often require expanding a prompt/LoRA pool or retaining samples of previous tasks, which poses significant scalability challenges as the number of tasks grows. To address these limitations, we propose Scalable Decoupled LoRA (SD-LoRA) for class incremental learning, which continually separates the learning of the magnitude and direction of LoRA components without rehearsal. Our empirical and theoretical analysis reveals that SD-LoRA tends to follow a low-loss trajectory and converges to an overlapping low-loss region for all learned tasks, resulting in an excellent stability-plasticity trade-off. Building upon these insights, we introduce two variants of SD-LoRA with further improved parameter efficiency. All parameters of SD-LoRAs can be end-to-end optimized for CL objectives. Meanwhile, they support efficient inference by allowing direct evaluation with the finally trained model, obviating the need for component selection. Extensive experiments across multiple CL benchmarks and foundation models consistently validate the effectiveness of SD-LoRA. The code is available at https://github.com/WuYichen-97/SD-Lora-CL.

The ever-increasing size of large language models (LLMs) presents significant challenges for deployment due to their heavy computational and memory requirements. Current model pruning techniques attempt to alleviate these issues by relying heavily on external calibration datasets to determine which parameters to prune or compress, thus limiting their flexibility and scalability across different compression ratios. Moreover, these methods often cause severe performance degradation, particularly in downstream tasks, when subjected to higher compression rates. In this paper, we propose *PruneNet*, a novel model compression method that addresses these limitations by reformulating model pruning as a policy learning process. PruneNet decouples the pruning process from the model architecture, eliminating the need for calibration datasets. It learns a stochastic pruning policy to assess parameter importance solely based on intrinsic model properties while preserving the spectral structure to minimize information loss. PruneNet can compress the LLaMA-2-7B model in just 15 minutes, achieving over 80\% retention of its zero-shot performance with a 30\% compression ratio, outperforming existing methods that retain only 75\% performance. Furthermore, on complex multitask language understanding tasks, PruneNet demonstrates its robustness by preserving up to 80\% performance of the original model, proving itself a superior alternative to conventional structured compression techniques.

The powerful capabilities of Large Language Models (LLMs) have led to their growing use in evaluating human-generated content, particularly in evaluating research ideas within academic settings. Existing solutions primarily rely on prompt-based LLM methods or fine-tuned lightweight language models for idea evaluation. However, these methods are often unstable and struggle to comprehend the complex semantic information embedded in the ideas, impeding their ability to perform high-quality evaluations. To address the above challenges, we propose $\texttt{GraphEval}$, a lightweight graph-based LLM framework for idea evaluation. Our insight is that a complex idea can be broken down into comprehensible viewpoint nodes using prompts from small LLMs. These viewpoint nodes can then be linked together through edges created from LLM-based relation extraction and/or BERT similarity scores. The created viewpoint-graph can be used to conveniently propagate scores across view-nodes to improve the robustness of the idea evaluations. In particular, we propose two lightweight graph-based methods for idea evaluation: (1) GraphEval-LP: a training-free label propagation algorithm that propagates evaluation scores from known view-nodes to unknown nodes; (2) GraphEval-GNN: a Graph Neural Networks (GNN) that is trained to predict the evaluation scores given the observed graph with minimal computation resources. Moreover, to overcome LLM's limitation in objectively assessing the novelty of ideas, we further propose a novelty detection model to GraphEval-GNN to enhance its capability in judging idea novelty. Experiments on two datasets show $\texttt{GraphEval}$ improves F1 scores by at least 14% with low computation and API costs. Additionally, $\texttt{GraphEval}$ can effectively detect plagiarized ideas.

Modular neural networks outperform nonmodular neural networks on tasks ranging from visual question answering to robotics. These performance improvements are thought to be due to modular networks' superior ability to model the compositional and combinatorial structure of real-world problems. However, a theoretical explanation of how modularity improves generalizability, and how to leverage task modularity while training networks remains elusive. Using recent theoretical progress in explaining neural network generalization, we investigate how the amount of training data required to generalize on a task varies with the intrinsic dimensionality of a task's input. We show theoretically that when applied to modularly structured tasks, while nonmodular networks require an exponential number of samples with task dimensionality, modular networks' sample complexity is independent of task dimensionality: modular networks can generalize in high dimensions. We then develop a novel learning rule for modular networks to exploit this advantage and empirically show the improved generalization of the rule, both in- and out-of-distribution, on high-dimensional, modular tasks.

Low-rank adaptation methods are a popular approach for parameter-efficient fine-tuning of large-scale neural networks. However, selecting the optimal rank for each layer remains a challenging problem that significantly affects both performance and efficiency. In this paper, we introduce a novel bilevel optimization strategy that simultaneously trains both matrix and tensor low-rank adapters, dynamically selecting the optimal rank for each layer. Our method avoids the use of implicit differentiation in the computation of the hypergradient, and integrates a stochastic away-step variant of the Frank-Wolfe algorithm, eliminating the need for projection and providing identifiability guarantees of the optimal rank structure. This results in a highly efficient and cost-effective training scheme that adaptively allocates the parameter budget across the network layers. On top of a detailed theoretical analysis of the method, we provide different numerical experiments showcasing its effectiveness.

The rapid increase in textual information means we need more efficient methods to sift through, organize, and understand it all. While retrieval-augmented generation (RAG) models excel in accessing information from large document collections, they struggle with complex tasks that require aggregation and reasoning over information spanning across multiple documents--what we call \textit{holistic reasoning}. Long-context language models (LCLMs) have great potential for managing large-scale documents, but their holistic reasoning capabilities remain unclear. In this work, we introduce HoloBench, a novel framework that brings database reasoning operations into text-based contexts, making it easier to systematically evaluate how LCLMs handle holistic reasoning across large documents. Our approach adjusts key factors such as context length, information density, distribution of information, and query complexity to evaluate LCLMs comprehensively. Our experiments show that the amount of information in the context has a bigger influence on LCLM performance than the actual context length. Furthermore, the complexity of queries affects performance more than the amount of information, particularly for different types of queries. Interestingly, queries that involve finding maximum or minimum values are easier for LCLMs and are less affected by context length, even though they pose challenges for RAG systems. However, tasks requiring the aggregation of multiple pieces of information show a noticeable drop in accuracy as context length increases. Additionally, we find that while grouping relevant information generally improves performance, the optimal positioning varies across models. Our findings surface both the advancements and the ongoing challenges in achieving a holistic understanding of long contexts. These can guide future developments in LCLMs and set the stage for creating more robust language models for real-world applications.

(Partial) differential equations (PDEs) are fundamental tools for describing natural phenomena, making their solution crucial in science and engineering. While traditional methods, such as the finite element method, provide reliable solutions, their accuracy is often tied to the use of computationally intensive fine meshes. Moreover, they do not naturally account for measurements or prior solutions, and any change in the problem parameters requires results to be fully recomputed. Neural network-based approaches, such as physics-informed neural networks and neural operators, offer a mesh-free alternative by directly fitting those models to the PDE solution. They can also integrate prior knowledge and tackle entire families of PDEs by simply aggregating additional training losses. Nevertheless, they are highly sensitive to hyperparameters such as collocation points and the weights associated with each loss. This paper addresses these challenges by developing a science-constrained learning (SCL) framework. It demonstrates that finding a (weak) solution of a PDE is equivalent to solving a constrained learning problem with worst-case losses. This explains the limitations of previous methods that minimize the expected value of aggregated losses. SCL also organically integrates structural constraints (e.g., invariances) and (partial) measurements or known solutions. The resulting constrained learning problems can be tackled using a practical algorithm that yields accurate solutions across a variety of PDEs, neural network architectures, and prior knowledge levels without extensive hyperparameter tuning and sometimes even at a lower computational cost.

The subset selection problem is fundamental in machine learning and other fields of computer science. We introduce a stochastic formulation for the minimum cost subset selection problem in a black box setting, in which only the subset metric value is available. Subsequently, we can handle two-stage schemes, with an outer subset-selection component and an inner subset cost evaluation component. We propose formulating the subset selection problem in a stochastic manner by choosing subsets at random from a distribution whose parameters are learned. Two stochastic formulations are proposed. The first explicitly restricts the subset's cardinality, and the second yields the desired cardinality in expectation. The distribution is parameterized by a decision variable, which we optimize using Stochastic Mirror Descent. Our choice of distributions yields constructive closed-form unbiased stochastic gradient formulas and convergence guarantees, including a rate with favorable dependency on the problem parameters. Empirical evaluation of selecting a subset of layers in transfer learning complements our theoretical findings and demonstrates the potential benefits of our approach.

Federated Graph Learning is rapidly evolving as a privacy-preserving collaborative approach. However, backdoor attacks are increasingly undermining federated systems by injecting carefully designed triggers that lead to the model making incorrect predictions. Trigger structures and injection locations in Federated Graph Learning are more diverse, making traditional federated defense methods less effective. In our work, we propose an effective Federated Graph Backdoor Defense using Topological Graph Energy (FedTGE). At the local client level, it injects distribution knowledge into the local model, assigning low energy to benign samples and high energy to the constructed malicious substitutes, and selects benign clients through clustering. At the global server level, the energy elements uploaded by each client are treated as new nodes to construct a global energy graph for energy propagation, making the selected clients' energy elements more similar and further adjusting the aggregation weights. Our method can handle high data heterogeneity, does not require a validation dataset, and is effective under both small and large malicious proportions. Extensive results on various settings of federated graph scenarios under backdoor attacks validate the effectiveness of this approach.

Spiking neural networks (SNNs) are emerging as a promising energy-efficient alternative to traditional artificial neural networks (ANNs) due to their spike-driven paradigm. However, recent research in the SNN domain has mainly focused on enhancing accuracy by designing large-scale Transformer structures, which typically rely on substantial computational resources, limiting their deployment on resource-constrained devices. To overcome this challenge, we propose a quantized spike-driven Transformer baseline (QSD-Transformer), which achieves reduced resource demands by utilizing a low bit-width parameter. Regrettably, the QSD-Transformer often suffers from severe performance degradation. In this paper, we first conduct empirical analysis and find that the bimodal distribution of quantized spike-driven self-attention (Q-SDSA) leads to spike information distortion (SID) during quantization, causing significant performance degradation. To mitigate this issue, we take inspiration from mutual information entropy and propose a bi-level optimization strategy to rectify the information distribution in Q-SDSA. Specifically, at the lower level, we introduce an information-enhanced LIF to rectify the information distribution in Q-SDSA. At the upper level, we propose a fine-grained distillation scheme for the QSD-Transformer to align the distribution in Q-SDSA with that in the counterpart ANN. By integrating the bi-level optimization strategy, the QSD-Transformer can attain enhanced energy efficiency without sacrificing its high-performance advantage. We validate the QSD-Transformer on various visual tasks, and experimental results indicate that our method achieves state-of-the-art results in the SNN domain. For instance, when compared to the prior SNN benchmark on ImageNet, the QSD-Transformer achieves 80.3\% top-1 accuracy, accompanied by significant reductions of 6.0$\times$ and 8.1$\times$ in power consumption and model size, respectively. Code is available at https://github.com/bollossom/QSD-Transformer.

Sample-efficient online reinforcement learning often uses replay buffers to store experience for reuse when updating the value function. However, uniform replay is inefficient, since certain classes of transitions can be more relevant to learning. While prioritization of more useful samples is helpful, this strategy can also lead to overfitting, as useful samples are likely to be more rare. In this work, we instead propose a prioritized, parametric version of an agent's memory, using generative models to capture online experience. This paradigm enables (1) densification of past experience, with new generations that benefit from the generative model's generalization capacity and (2) guidance via a family of "relevance functions" that push these generations towards more useful parts of an agent's acquired history. We show this recipe can be instantiated using conditional diffusion models and simple relevance functions such as curiosity- or value-based metrics. Our approach consistently improves performance and sample efficiency in both state- and pixel-based domains. We expose the mechanisms underlying these gains, showing how guidance promotes diversity in our generated transitions and reduces overfitting. We also showcase how our approach can train policies with even higher update-to-data ratios than before, opening up avenues to better scale online RL agents. Project page available at: https://pgenreplay.github.io

As AI systems are increasingly deployed in high-stakes applications, ensuring their interpretability is essential. Mechanistic Interpretability (MI) aims to reverse-engineer neural networks by extracting human-understandable algorithms embedded within their structures to explain their behavior. This work systematically examines a fundamental question: for a fixed behavior to explain, and under the criteria that MI sets for itself, are we guaranteed a unique explanation? Drawing an analogy with the concept of identifiability in statistics, which ensures the uniqueness of parameters inferred from data under specific modeling assumptions, we speak about the identifiability of explanations produced by MI. We identify two broad strategies to produce MI explanations: (i) "where-then-what", which first identifies a subset of the network (a circuit) that replicates the model's behavior before deriving its interpretation, and (ii) "what-then-where", which begins with candidate explanatory algorithms and searches in the activation subspaces of the neural model where the candidate algorithm may be implemented, relying on notions of causal alignment between the states of the candidate algorithm and the neural network. We systematically test the identifiability of both strategies using simple tasks (learning Boolean functions) and multi-layer perceptrons small enough to allow a complete enumeration of candidate explanations. Our experiments reveal overwhelming evidence of non-identifiability in all cases: multiple circuits can replicate model behavior, multiple interpretations can exist for a circuit, several algorithms can be causally aligned with the neural network, and a single algorithm can be causally aligned with different subspaces of the network. We discuss whether the unicity intuition is necessary. One could adopt a pragmatic stance, requiring explanations only to meet predictive and/or manipulability standards. However, if unicity is considered essential, e.g., to provide a sense of understanding, we also discuss less permissive criteria. Finally, we also refer to the inner interpretability framework that demands explanations to be validated by multiple complementary criteria. This work aims to contribute constructively to the ongoing effort to formalize what we expect from explanations in AI.

In real-life scenarios, humans seek out objects in the 3D world to fulfill their daily needs or intentions. This inspires us to introduce 3D intention grounding, a new task in 3D object detection employing RGB-D, based on human intention, such as "I want something to support my back." Closely related, 3D visual grounding focuses on understanding human reference. To achieve detection based on human intention, it relies on humans to observe the scene, reason out the target that aligns with their intention ("pillow" in this case), and finally provide a reference to the AI system, such as "A pillow on the couch". Instead, 3D intention grounding challenges AI agents to automatically observe, reason and detect the desired target solely based on human intention. To tackle this challenge, we introduce the new Intent3D dataset, consisting of 44,990 intention texts associated with 209 fine-grained classes from 1,042 scenes of the ScanNet dataset. We also establish several baselines based on different language-based 3D object detection models on our benchmark. Finally, we propose IntentNet, our unique approach, designed to tackle this intention-based detection problem. It focuses on three key aspects: intention understanding, reasoning to identify object candidates, and cascaded adaptive learning that leverages the intrinsic priority logic of different losses for multiple objective optimization.

Recent advances in machine learning for molecules exhibit great potential for facilitating drug discovery from in silico predictions. Most models for molecule generation rely on the decomposition of molecules into frequently occurring substructures (motifs), from which they generate novel compounds. While motif representations greatly aid in learning molecular distributions, such methods fail to represent substructures beyond their known motif set, posing a fundamental limitation for discovering novel compounds. To address this limitation and enhance structural expressivity, we propose to separate structure from features by abstracting motifs to scaffolds and, subsequently, allocating atom and bond types. To this end, we introduce a novel factorisation of the molecules' data distribution that considers the entire molecular context and facilitates learning adequate assignments of atoms and bonds to scaffolds. Complementary to this, we propose MAGNet, the first model to freely learn motifs. Importantly, we demonstrate that MAGNet's improved expressivity leads to molecules with more structural diversity and, at the same time, diverse atom and bond assignments.

To improve the efficiency of reinforcement learning (RL), we propose a novel asynchronous federated reinforcement learning (FedRL) framework termed AFedPG, which constructs a global model through collaboration among $N$ agents using policy gradient (PG) updates. To address the challenge of lagged policies in asynchronous settings, we design a delay-adaptive lookahead technique *specifically for FedRL* that can effectively handle heterogeneous arrival times of policy gradients. We analyze the theoretical global convergence bound of AFedPG, and characterize the advantage of the proposed algorithm in terms of both the sample complexity and time complexity. Specifically, our AFedPG method achieves $\mathcal{O}(\frac{{\epsilon}^{-2.5}}{N})$ sample complexity for global convergence at each agent on average. Compared to the single agent setting with $\mathcal{O}(\epsilon^{-2.5})$ sample complexity, it enjoys a linear speedup with respect to the number of agents. Moreover, compared to synchronous FedPG, AFedPG improves the time complexity from $\mathcal{O}(\frac{t_{\max}}{N})$ to $\mathcal{O}({\sum_{i=1}^{N} \frac{1}{t_{i}}})^{-1}$, where $t_{i}$ denotes the time consumption in each iteration at agent $i$, and $t_{\max}$ is the largest one. The latter complexity $\mathcal{O}({\sum_{i=1}^{N} \frac{1}{t_{i}}})^{-1}$ is always smaller than the former one, and this improvement becomes significant in large-scale federated settings with heterogeneous computing powers ($t_{\max}\gg t_{\min}$). Finally, we empirically verify the improved performance of AFedPG in four widely used MuJoCo environments with varying numbers of agents. We also demonstrate the advantages of AFedPG in various computing heterogeneity scenarios.

The data mixture for large language model pre-training significantly impacts performance, yet how to determine an effective mixture remains unclear. We propose RegMix to automatically identify a high-performing data mixture by formulating it as a regression task. RegMix trains many small models on diverse data mixtures, uses regression to predict performance of unseen mixtures, and applies the best predicted mixture to train a large-scale model with orders of magnitude more compute. To empirically validate RegMix, we train 512 models with 1M parameters for 1B tokens to fit the regression model and predict the best data mixture. Using this mixture we train a 1B parameter model for 25B tokens (i.e. 1000× larger and 25× longer) which we find performs best among 64 candidate 1B parameter models with other mixtures. Furthermore, RegMix consistently outperforms human selection in experiments involving models up to 7B models trained on 100B tokens, while matching or exceeding DoReMi using just 10% of the computational resources. Our experiments also show that (1) Data mixtures significantly impact performance; (2) Web corpora rather than data perceived as high-quality like Wikipedia have the strongest positive correlation with downstream performance; (3) Domains interact in complex ways often contradicting common sense, thus automatic approaches like RegMix are needed; (4) Data mixture effects transcend scaling laws. Our code is available at https://github.com/sail-sg/regmix.