ICLR 2025 Papers

As the context limits of Large Language Models (LLMs) increase, the range of possible applications and downstream functions broadens. In many real-world tasks, decisions depend on details scattered across collections of often disparate documents containing mostly irrelevant information. Long-context LLMs appear well-suited to this form of complex information retrieval and reasoning, which has traditionally proven costly and time-consuming. However, although the development of longer context models has seen rapid gains in recent years, our understanding of how effectively LLMs use their context has not kept pace. To address this, we conduct a set of retrieval experiments designed to evaluate the capabilities of 17 leading LLMs, such as their ability to follow threads of information through the context window. Strikingly, we find that many models are remarkably thread- safe: capable of simultaneously following multiple threads without significant loss in performance. Still, for many models, we find the effective context limit is significantly shorter than the supported context length, with accuracy decreasing as the context window grows. Our study also highlights the important point that token counts from different tokenizers should not be directly compared—they often correspond to substantially different numbers of written characters. We release our code and long context experimental data.

In human-centric settings like education or healthcare, model accuracy and model explainability are key factors for user adoption. Towards these two goals, intrinsically interpretable deep learning models have gained popularity, focusing on accurate predictions alongside faithful explanations. However, there exists a gap in the human-centeredness of these approaches, which often produce nuanced and complex explanations that are not easily actionable for downstream users. We present InterpretCC (interpretable conditional computation), a family of intrinsically interpretable neural networks at a unique point in the design space that optimizes for ease of human understanding and explanation faithfulness, while maintaining comparable performance to state-of-the-art models. InterpretCC achieves this through adaptive sparse activation of features before prediction, allowing the model to use a different, minimal set of features for each instance. We extend this idea into an interpretable, global mixture-of-experts (MoE) model that allows users to specify topics of interest, discretely separates the feature space for each data point into topical subnetworks, and adaptively and sparsely activates these topical subnetworks for prediction. We apply InterpretCC for text, time series and tabular data across several real-world datasets, demonstrating comparable performance with non-interpretable baselines and outperforming intrinsically interpretable baselines. Through a user study involving 56 teachers, InterpretCC explanations are found to have higher actionability and usefulness over other intrinsically interpretable approaches.

Uncertainty quantification is an important prerequisite for the deployment of deep learning models in safety-critical areas. Yet, this hinges on the uncertainty estimates being useful to the extent the prediction intervals are well-calibrated and sharp. In the absence of inherent uncertainty estimates (e.g. pretrained models predicting only point estimates), popular approaches that operate post-hoc include Laplace’s method and split conformal prediction (split-CP). However, Laplace’s method can be miscalibrated when the model is misspecified and split-CP requires sample splitting, and thus comes at the expense of statistical efficiency. In this work, we construct prediction intervals for neural network regressors post-hoc without held-out data. This is achieved by approximating the full conformal prediction method (full-CP). Whilst full-CP nominally requires retraining the model for every test point and candidate label, we propose to train just once and locally perturb model parameters using Gauss-Newton influence to approximate the effect of retraining. Coupled with linearization of the network, we express the absolute residual nonconformity score as a piecewise linear function of the candidate label allowing for an efficient procedure that avoids the exhaustive search over the output space. On standard regression benchmarks and bounding box localization, we show the resulting prediction intervals are locally-adaptive and often tighter than those of split-CP.

The weak-to-strong generalization phenomenon is the driver for important machine learning applications including highly data-efficient learning and, most recently, performing superalignment. While decades of research have resulted in numerous algorithms that produce strong empirical performance, understanding what aspects of data enable weak-to-strong generalization has been understudied. We propose a simple data-centric mechanism that characterizes weak-to-strong generalization: the overlap density. Intuitively, generalization tracks the number of points that contain overlaps, i.e., both easy patterns (learnable by a weak model) and challenging patterns (only learnable by a stronger model), as with such points, weak predictions can be used to learn challenging patterns by stronger models. And, we provide a practical overlap detection algorithm to find overlap density from data. Finally, we provide an algorithm to learn, among multiple sources of data, which to query when seeking to maximize overlap density and thereby enhance weak-to-strong generalization. We provide a theoretical result showing that the generalization benefit is a function of the overlap density and a regret bound of our data selection algorithm. Empirically, we validate the mechanism and the overlap detection algorithm on a wide array of settings.

Accurately estimating the informativeness of individual samples in a dataset is an important objective in deep learning, as it can guide sample selection, which can improve model efficiency and accuracy by removing redundant or potentially harmful samples. We propose $\text{\textit{Laplace Sample Information}}$ ($\mathsf{LSI}$) measure of sample informativeness grounded in information theory widely applicable across model architectures and learning settings. $\mathsf{LSI}$ leverages a Bayesian approximation to the weight posterior and the KL divergence to measure the change in the parameter distribution induced by a sample of interest from the dataset. We experimentally show that $\mathsf{LSI}$ is effective in ordering the data with respect to typicality, detecting mislabeled samples, measuring class-wise informativeness, and assessing dataset difficulty. We demonstrate these capabilities of $\mathsf{LSI}$ on image and text data in supervised and unsupervised settings. Moreover, we show that $\mathsf{LSI}$ can be computed efficiently through probes and transfers well to the training of large models.

Global Covariance Pooling (GCP) has been demonstrated to improve the performance of Deep Neural Networks (DNNs) by exploiting second-order statistics of high-level representations. GCP typically performs classification of the covariance matrices by applying matrix function normalization, such as matrix logarithm or power, followed by a Euclidean classifier. However, covariance matrices inherently lie in a Riemannian manifold, known as the Symmetric Positive Definite (SPD) manifold. The current literature does not provide a satisfactory explanation of why Euclidean classifiers can be applied directly to Riemannian features after the normalization of the matrix power. To mitigate this gap, this paper provides a comprehensive and unified understanding of the matrix logarithm and power from a Riemannian geometry perspective. The underlying mechanism of matrix functions in GCP is interpreted from two perspectives: one based on tangent classifiers (Euclidean classifiers on the tangent space) and the other based on Riemannian classifiers. Via theoretical analysis and empirical validation through extensive experiments on fine-grained and large-scale visual classification datasets, we conclude that the working mechanism of the matrix functions should be attributed to the Riemannian classifiers they implicitly respect. The code is available at https://github.com/GitZH-Chen/RiemGCP.git.

The rising interest in Bayesian deep learning (BDL) has led to a plethora of methods for estimating the posterior distribution. However, efficient computation of inferences, such as predictions, has been largely overlooked with Monte Carlo integration remaining the standard. In this work we examine streamlining prediction in BDL through a single forward pass without sampling. For this, we use local linearisation of activation functions and local Gaussian approximations at linear layers. Thus allowing us to analytically compute an approximation of the posterior predictive distribution. We showcase our approach for both MLP and transformers, such as ViT and GPT-2, and assess its performance on regression and classification tasks. Open-source library: https://github.com/AaltoML/SUQ.

Density estimation and reliable prediction regions for outputs are crucial in supervised and unsupervised learning. While conformal prediction effectively generates coverage-guaranteed regions, it struggles with multi-dimensional outputs due to reliance on one-dimensional nonconformity scores. To address this, we introduce CONTRA: CONformal prediction region via normalizing flow TRAnsformation. CONTRA utilizes the latent spaces of normalizing flows to define nonconformity scores based on distances from the center. This allows for the mapping of high-density regions in latent space to sharp prediction regions in the output space, surpassing traditional hyperrectangular or elliptical conformal regions. Further, for scenarios where other predictive models are favored over flow-based models, we extend CONTRA to enhance any such model with a reliable prediction region by training a simple normalizing flow on the residuals. We demonstrate that both CONTRA and its extension maintain guaranteed coverage probability and outperform existing methods in generating accurate prediction regions across various datasets. We conclude that CONTRA is an effective tool for (conditional) density estimation, addressing the under-explored challenge of delivering multi-dimensional prediction regions.

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.

Conformal prediction has been a popular distribution-free framework for uncertainty quantification. In this work, we present a novel conformal prediction method for time-series, which we call Kernel-based Optimally Weighted Conformal Prediction Intervals ($\texttt{KOWCPI}$). Specifically, $\texttt{KOWCPI}$ adapts the classic Reweighted Nadaraya-Watson (RNW) estimator for quantile regression on dependent data and learns optimal data-adaptive weights. Theoretically, we tackle the challenge of establishing a conditional coverage guarantee for non-exchangeable data under strong mixing conditions on the non-conformity scores. We demonstrate the superior performance of $\texttt{KOWCPI}$ on real time-series against state-of-the-art methods, where $\texttt{KOWCPI}$ achieves narrower confidence intervals without losing coverage.

Reinforcement learning (RL) provides an effective means to capture users' evolving preferences, leading to improved recommendation performance over time. However, existing RL approaches primarily rely on standard exploration strategies, which are less effective for a large item space with sparse reward signals given the limited interactions for most users. Therefore, they may not be able to learn the optimal policy that effectively captures user's evolving preferences and achieves the maximum expected reward over the long term. In this paper, we propose a novel evidential conservative Q-learning framework (ECQL) that learns an effective and conservative recommendation policy by integrating evidence-based uncertainty and conservative learning. ECQL conducts evidence-aware explorations to discover items that are located beyond current observations but reflect users' long-term interests. It offers an uncertainty-aware conservative view on policy evaluation to discourage deviating too much from users' current interests. Two central components of ECQL include a uniquely designed sequential state encoder and a novel conservative evidential-actor-critic (CEAC) module. The former generates the current state of the environment by aggregating historical information and a sliding window that contains the current user interactions as well as newly recommended items from RL exploration that may represent short and long-term interests respectively. The latter performs an evidence-based rating prediction by maximizing the conservative evidential Q-value and leverages an uncertainty-aware ranking score to explore the item space for a more diverse and valuable recommendation. Experiments on multiple real-world dynamic datasets demonstrate the state-of-the-art performance of ECQL and its capability to capture users' long-term interests.

Post-translational modifications (PTMs) profoundly expand the complexity and functionality of the proteome, regulating protein attributes and interactions that are crucial for biological processes. Accurately predicting PTM sites and their specific types is therefore essential for elucidating protein function and understanding disease mechanisms. Existing computational approaches predominantly focus on protein sequences to predict PTM sites, driven by the recognition of sequence-dependent motifs. However, these approaches often overlook protein structural contexts. In this work, we first compile a large-scale sequence-structure PTM dataset, which serves as the foundation for fair comparison. We introduce the MeToken model, which tokenizes the micro-environment of each amino acid, integrating both sequence and structural information into unified discrete tokens. This model not only captures the typical sequence motifs associated with PTMs but also leverages the spatial arrangements dictated by protein tertiary structures, thus providing a holistic view of the factors influencing PTM sites. Designed to address the long-tail distribution of PTM types, MeToken employs uniform sub-codebooks that ensure even the rarest PTMs are adequately represented and distinguished. We validate the effectiveness and generalizability of MeToken across multiple datasets, demonstrating its superior performance in accurately identifying PTM types. The results underscore the importance of incorporating structural data and highlight MeToken's potential in facilitating accurate and comprehensive PTM predictions, which could significantly impact proteomics research.

Leveraging machine learning (ML) to predict an initial solution for mixed-integer linear programming (MILP) has gained considerable popularity in recent years. These methods predict a solution and fix a subset of variables to reduce the problem dimension. Then, they solve the reduced problem to obtain the final solutions. However, directly fixing variable values can lead to low-quality solutions or even infeasible reduced problems if the predicted solution is not accurate enough. To address this challenge, we propose an Alternating prediction-correction neural solving framework (Apollo-MILP) that can identify and select accurate and reliable predicted values to fix. In each iteration, Apollo-MILP conducts a prediction step for the unfixed variables, followed by a correction step to obtain an improved solution (called reference solution) through a trust-region search. By incorporating the predicted and reference solutions, we introduce a novel Uncertainty-based Error upper BOund (UEBO) to evaluate the uncertainty of the predicted values and fix those with high confidence. A notable feature of Apollo-MILP is the superior ability for problem reduction while preserving optimality, leading to high-quality final solutions. Experiments on commonly used benchmarks demonstrate that our proposed Apollo-MILP significantly outperforms other ML-based approaches in terms of solution quality, achieving over a 50% reduction in the solution gap.

Conformal prediction (CP) converts any model's output to prediction sets with a guarantee to cover the true label with (adjustable) high probability. Robust CP extends this guarantee to worst-case (adversarial) inputs. Existing baselines achieve robustness by bounding randomly smoothed conformity scores. In practice, they need expensive Monte-Carlo (MC) sampling (e.g. $\sim10^4$ samples per point) to maintain an acceptable set size. We propose a robust conformal prediction that produces smaller sets even with significantly lower MC samples (e.g. 150 for CIFAR10). Our approach binarizes samples with an adjustable (or automatically adjusted) threshold selected to preserve the coverage guarantee. Remarkably, we prove that robustness can be achieved by computing only one binary certificate, unlike previous methods that certify each calibration (or test) point. Thus, our method is faster and returns smaller robust sets. We also eliminate a previous limitation that requires a bounded score function.

Conformal prediction has attracted significant attention as a distribution-free method for uncertainty quantification in black-box models, providing prediction sets with guaranteed coverage. However, its practical utility is often limited when these prediction sets become excessively large, reducing its overall effectiveness. In this paper, we introduce a novel approach to conformal prediction for classification problems, which leverages a multi-dimensional nonconformity score. By extending standard conformal prediction to higher dimensions, we achieve better separation between correct and incorrect labels. Utilizing this we can focus on regions with low concentrations of incorrect labels, leading to smaller, more informative prediction sets. To efficiently generate the multi-dimensional score, we employ a self-ensembling technique that trains multiple diverse classification heads on top of a backbone model. We demonstrate the advantage of our approach compared to baselines across different benchmarks.

Symbolic regression, a task discovering the formula best fitting the given data, is typically based on the heuristical search. These methods usually update candidate formulas to obtain new ones with lower prediction errors iteratively. However, since formulas with similar function shapes may have completely different symbolic forms, the prediction error does not decrease monotonously as the search approaches the target formula, causing the low recovery rate of existing methods. To solve this problem, we propose a novel search objective based on the minimum description length, which reflects the distance from the target and decreases monotonically as the search approaches the correct form of the target formula. To estimate the minimum description length of any input data, we design a neural network, MDLformer, which enables robust and scalable estimation through large-scale training. With the MDLformer's output as the search objective, we implement a symbolic regression method, SR4MDL, that can effectively recover the correct mathematical form of the formula. Extensive experiments illustrate its excellent performance in recovering formulas from data. Our method successfully recovers around 50 formulas across two benchmark datasets comprising 133 problems, outperforming state-of-the-art methods by 43.92%. Experiments on 122 unseen black-box problems further demonstrate its generalization performance. We release our code at https://github.com/tsinghua-fib-lab/SR4MDL .

Low-Rank Adaptation (LoRA) has emerged as a popular technique for fine-tuning large language models (LLMs) to various domains due to its modular design and widespread availability on platforms like Huggingface. This modularity has sparked interest in combining multiple LoRAs to significantly enhance LLM capabilities. However, existing methods for LoRA composition primarily focus on task-specific adaptations that require additional training, and current model merging techniques often fail to fully leverage LoRA's modular nature, leading to parameter interference and performance degradation. In this paper, we explore the possibility of disassembling and reassembling multiple LoRAs at a finer granularity, much like assembling LEGO blocks. We introduce the concept of Minimal Semantic Units (MSUs), where the parameters corresponding to each rank in LoRA function as independent units. These MSUs exhibit properties such as permutation invariance and concatenation-summation equivalence, allowing for flexible combinations to form new LoRAs. Building on these insights, we propose the LoRA-LEGO framework. This framework conducts rank-wise parameter clustering by grouping MSUs from different LoRAs into $k$ clusters. The centroid of each cluster serves as a representative MSU, enabling the assembly of a merged LoRA with an adjusted rank of $k$. Additionally, we apply a dual reweighting strategy to optimize the scale of the merged LoRA. Experiments across various benchmarks demonstrate that our method outperforms existing approaches in LoRA merging.

Immunogenicity prediction is a central topic in reverse vaccinology for finding candidate vaccines that can trigger protective immune responses. Existing approaches typically rely on highly compressed features and simple model architectures, leading to limited prediction accuracy and poor generalizability. To address these challenges, we introduce VenusVaccine, a novel deep learning solution with a dual attention mechanism that integrates pre-trained latent vector representations of protein sequences and structures. We also compile the most comprehensive immunogenicity dataset to date, encompassing over 7000 antigen sequences, structures, and immunogenicity labels from bacteria, viruses, and tumors. Extensive experiments demonstrate that VenusVaccine outperforms existing methods across a wide range of evaluation metrics. Furthermore, we establish a post-hoc validation protocol to assess the practical significance of deep learning models in tackling vaccine design challenges. Our work provides an effective tool for vaccine design and sets valuable benchmarks for future research. The implementation is at \url{https://github.com/songleee/VenusVaccine}.

Visual counterfactual explanations (VCEs) have recently gained immense popularity as a tool for clarifying the decision-making process of image classifiers. This trend is largely motivated by what these explanations promise to deliver -- indicate semantically meaningful factors that change the classifier's decision. However, we argue that current state-of-the-art approaches lack a crucial component -- the region constraint -- whose absence prevents from drawing explicit conclusions, and may even lead to faulty reasoning due to phenomenons like confirmation bias. To address the issue of previous methods, which modify images in a very entangled and widely dispersed manner, we propose region-constrained VCEs (RVCEs), which assume that only a predefined image region can be modified to influence the model's prediction. To effectively sample from this subclass of VCEs, we propose Region-Constrained Counterfactual Schrödinger Bridge (RCSB), an adaptation of a tractable subclass of Schrödinger Bridges to the problem of conditional inpainting, where the conditioning signal originates from the classifier of interest. In addition to setting a new state-of-the-art by a large margin, we extend RCSB to allow for exact counterfactual reasoning, where the predefined region contains only the factor of interest, and incorporating the user to actively interact with the RVCE by predefining the regions manually.