ICLR 2025 论文列表

RNA secondary structure prediction is critical for understanding RNA function but remains challenging due to complex structural elements like pseudoknots and limited training data. We introduce DEPfold, a novel deep learning approach that re-frames RNA secondary structure prediction as a dependency parsing problem. DEPfold presents three key innovations: (1) a biologically motivated transformation of RNA structures into labeled dependency trees, (2) a biaffine attention mechanism for joint prediction of base pairings and their types, and (3) an optimal tree decoding algorithm that enforces valid RNA structural constraints. Unlike traditional energy-based methods, DEPfold learns directly from annotated data and leverages pretrained language models to predict RNA structure. We evaluate DEPfold on both within-family and cross-family RNA datasets, demonstrating significant performance improvements over existing methods. DEPfold shows strong performance in cross-family generalization when trained on data augmented by traditional energy-based models, outperforming existing methods on the bpRNAnew dataset. This demonstrates DEPfold’s ability to effectively learn structural information beyond what traditional methods capture. Our approach bridges natural language processing (NLP) with RNA biology, providing a computationally efficient and adaptable tool for advancing RNA structure prediction and analysis

Human trajectory prediction is fundamental for autonomous driving and service robot. The research community has studied various important aspects of this task and made remarkable progress recently. However, there is an essential perspective which is not well exploited in previous research all along, namely individual feedback. Individual feedback exists in the sequential nature of trajectory prediction, where earlier predictions of a target can be verified over time by his ground-truth trajectories to obtain feedback which provides valuable experience for subsequent predictions on the same agent. In this paper, we show such feedback can reveal the strengths and weaknesses of the model's predictions on a specific target and heuristically guide to deliver better predictions on him. We present an interactive adjustment network to effectively model and leverage the feedback. This network first exploits the feedback from previous predictions to dynamically generate an adjuster which then interactively makes appropriate adjustments to current predictions for more accurate ones. We raise a novel displacement expectation loss to train this interactive architecture. Through experiments on representative prediction methods and widely-used benchmarks, we demonstrate the great value of individual feedback and the superior effectiveness of proposed interactive adjustment network.

Missing values are prevalent across various fields, posing challenges for training and deploying predictive models. In this context, imputation is a common practice, driven by the hope that accurate imputations will enhance predictions. However, recent theoretical and empirical studies indicate that simple constant imputation can be consistent and competitive. This empirical study aims at clarifying *if* and *when* investing in advanced imputation methods yields significantly better predictions. Relating imputation and predictive accuracies across combinations of imputation and predictive models on 19 datasets, we show that imputation accuracy matters less i) when using expressive models, ii) when incorporating missingness indicators as complementary inputs, iii) matters much more for generated linear outcomes than for real-data outcomes. Interestingly, we also show that the use of the missingness indicator is beneficial to the prediction performance, even in MCAR scenarios. Overall, on real-data with powerful models, imputation quality has only a minor effect on prediction performance. Thus, investing in better imputations for improved predictions often offers limited benefits.

Humor is previously regarded as a gift exclusive to humans for the following reasons. Humor is a culturally nuanced aspect of human language, presenting challenges for its understanding and generation. Humor generation necessitates a multi-hop reasoning process, with each hop founded on proper rationales. Although many studies, such as those related to GPT-o1, focus on logical reasoning with reflection and correction, they still fall short in humor generation. Due to the sparsity of the knowledge graph in creative thinking, it is arduous to achieve multi-hop reasoning. Consequently, in this paper, we propose a more robust framework for addressing the humor reasoning task, named LoL. LoL aims to inject external information to mitigate the sparsity of the knowledge graph, thereby enabling multi-hop reasoning. In the first stage of LoL, we put forward an automatic instruction-evolution method to incorporate the deeper and broader thinking processes underlying humor. Judgment-oriented instructions are devised to enhance the model's judgment capability, dynamically supplementing and updating the sparse knowledge graph. Subsequently, through reinforcement learning, the reasoning logic for each online-generated response is extracted using GPT-4o. In this process, external knowledge is re-introduced to aid the model in logical reasoning and the learning of human preferences. Finally, experimental results indicate that the combination of these two processes can enhance both the model's judgment ability and its generative capacity. These findings deepen our comprehension of the creative capabilities of large language models (LLMs) and offer approaches to boost LLMs' creative abilities for cross-domain innovative applications.

Conformal prediction (CP) is an important tool for distribution-free predictive uncertainty quantification. Yet, a major challenge is to balance computational efficiency and prediction accuracy, particularly for multiple predictions. We propose **L**eave-**O**ne-**O**ut **Stab**le **C**onformal **P**rediction (LOO-StabCP), a novel method to speed up full conformal using algorithmic stability without sample splitting. By leveraging *leave-one-out* stability, our method is much faster in handling a large number of prediction requests compared to existing method RO-StabCP based on *replace-one* stability. We derived stability bounds for several popular machine learning tools: regularized loss minimization (RLM) and stochastic gradient descent (SGD), as well as kernel method, neural networks and bagging. Our method is theoretically justified and demonstrates superior numerical performance on synthetic and real-world data. We applied our method to a screening problem, where its effective exploitation of training data led to improved test power compared to state-of-the-art method based on split conformal.

Conformal prediction has emerged as a popular technique for facilitating valid predictive inference across a spectrum of machine learning models, under minimal assumption of exchangeability. Recently, Hoff (2023) showed that full conformal Bayes provides the most efficient prediction sets (smallest by expected volume) among all prediction sets that are valid at the $(1 - \alpha)$ level if the model is correctly specified. However, a critical issue arises when the Bayesian model itself may be mis-specified, resulting in prediction interval that might be suboptimal, even though it still enjoys the frequentist coverage guarantee. To address this limitation, we propose an innovative solution that combines Bayesian model averaging (BMA) with conformal prediction. This hybrid not only leverages the strengths of Bayesian conformal prediction but also introduces a layer of robustness through model averaging. Theoretically, we prove that the resulting prediction interval will converge to the optimal level of efficiency, if the true model is included among the candidate models. This assurance of optimality, even under potential model uncertainty, provides a significant improvement over existing methods, ensuring more reliable and precise uncertainty quantification.

Graph neural networks excel at modeling pairwise interactions, but they cannot flexibly accommodate higher-order interactions and features. Topological deep learning (TDL) has emerged recently as a promising tool for addressing this issue. TDL enables the principled modeling of arbitrary multi-way, hierarchical higher-order interactions by operating on combinatorial topological spaces, such as simplicial or cell complexes, instead of graphs. However, little is known about how to leverage geometric features such as positions and velocities for TDL. This paper introduces E(n)-Equivariant Topological Neural Networks (ETNNs), which are E(n)-equivariant message-passing networks operating on combinatorial complexes, formal objects unifying graphs, hypergraphs, simplicial, path, and cell complexes. ETNNs incorporate geometric node features while respecting rotation, reflection, and translation equivariance. Moreover, being TDL models, ETNNs are natively ready for settings with heterogeneous interactions. We provide a theoretical analysis to show the improved expressiveness of ETNNs over architectures for geometric graphs. We also show how E(n)-equivariant variants of TDL models can be directly derived from our framework. The broad applicability of ETNNs is demonstrated through two tasks of vastly different scales: i) molecular property prediction on the QM9 benchmark and ii) land-use regression for hyper-local estimation of air pollution with multi-resolution irregular geospatial data. The results indicate that ETNNs are an effective tool for learning from diverse types of richly structured data, as they match or surpass SotA equivariant TDL models with a significantly smaller computational burden, thus highlighting the benefits of a principled geometric inductive bias. Our implementation of ETNNs can be found at https://github.com/NSAPH-Projects/topological-equivariant-networks.

Weak gravitational lensing is the slight distortion of galaxy shapes caused primarily by the gravitational effects of dark matter in the universe. In our work, we seek to invert the weak lensing signal from 2D telescope images to reconstruct a 3D map of the universe's dark matter field. While inversion typically yields a 2D projection of the dark matter field, accurate 3D maps of the dark matter distribution are essential for localizing structures of interest and testing theories of our universe. However, 3D inversion poses significant challenges. First, unlike standard 3D reconstruction that relies on multiple viewpoints, in this case, images are only observed from a single viewpoint. This challenge can be partially addressed by observing how galaxy emitters throughout the volume are lensed. However, this leads to the second challenge: the shapes and exact locations of unlensed galaxies are unknown, and can only be estimated with a very large degree of uncertainty. This introduces an overwhelming amount of noise which nearly drowns out the lensing signal completely. Previous approaches tackle this by imposing strong assumptions about the structures in the volume. We instead propose a methodology using a gravitationally-constrained neural field to flexibly model the continuous matter distribution. We take an analysis-by-synthesis approach, optimizing the weights of the neural network through a fully differentiable physical forward model to reproduce the lensing signal present in image measurements. We showcase our method on simulations, including realistic simulated measurements of dark matter distributions that mimic data from upcoming telescope surveys. Our results show that our method can not only outperform previous methods, but importantly is also able to recover potentially surprising dark matter structures.

In recent years, there has been a significant growth in research focusing on minimum $\ell_2$ norm (ridgeless) interpolation least squares estimators. However, the majority of these analyses have been limited to an unrealistic regression error structure, assuming independent and identically distributed errors with zero mean and common variance. In this paper, we explore prediction risk as well as estimation risk under more general regression error assumptions, highlighting the benefits of overparameterization in a more realistic setting that allows for clustered or serial dependence. Notably, we establish that the estimation difficulties associated with the variance components of both risks can be summarized through the trace of the variance-covariance matrix of the regression errors. Our findings suggest that the benefits of overparameterization can extend to time series, panel and grouped data.

General-purpose LLM judges capable of human-level evaluation provide not only a scalable and accurate way of evaluating instruction-following LLMs but also new avenues for supervising and improving their performance. One promising way of leveraging LLM judges for supervision is through Minimum Bayes Risk (MBR) decoding, which uses a reference-based evaluator to select a high-quality output from amongst a set of candidate outputs. In the first part of this work, we explore using MBR decoding as a method for improving the test-time performance of instruction-following LLMs. We find that MBR decoding with reference-based LLM judges substantially improves over greedy decoding, best-of-N decoding with reference-free judges and MBR decoding with lexical and embedding-based metrics on AlpacaEval and MT-Bench. These gains are consistent across LLMs with up to 70B parameters, demonstrating that smaller LLM judges can be used to supervise much larger LLMs. Then, seeking to retain the improvements from MBR decoding while mitigating additional test-time costs, we explore iterative self-training on MBR-decoded outputs. We find that self-training using Direct Preference Optimisation leads to significant performance gains, such that the self-trained models with greedy decoding generally match and sometimes exceed the performance of their base models with MBR decoding.

Examining the alignment of large language models (LLMs) has become increasingly important, e.g., when LLMs fail to operate as intended. This study examines the alignment of LLMs with human values for the domain of politics. Prior research has shown that LLM-generated outputs can include political leanings and mimic the stances of political parties on various issues. However, the extent and conditions under which LLMs deviate from empirical positions are insufficiently examined. To address this gap, we analyze the factors that contribute to LLMs' deviations from empirical positions on political issues, aiming to quantify these deviations and identify the conditions that cause them. Drawing on findings from cognitive science about representativeness heuristics, i.e., situations where humans lean on representative attributes of a target group in a way that leads to exaggerated beliefs, we scrutinize LLM responses through this heuristics' lens. We conduct experiments to determine how LLMs inflate predictions about political parties, which results in stereotyping. We find that while LLMs can mimic certain political parties' positions, they often exaggerate these positions more than human survey respondents do. Also, LLMs tend to overemphasize representativeness more than humans. This study highlights the susceptibility of LLMs to representativeness heuristics, suggesting a potential vulnerability of LLMs that facilitates political stereotyping. We also test prompt-based mitigation strategies, finding that strategies that can mitigate representative heuristics in humans are also effective in reducing the influence of representativeness on LLM-generated responses.

Predictive coding has been established as a promising neuroscientific theory to describe the mechanism of information processing in the retina or cortex. This theory hypothesises that cortex predicts sensory inputs at various levels of abstraction to minimise prediction errors. Inspired by predictive coding, Chen et al. (2024) proposed another theory, temporal prediction hypothesis, to claim that sequence memory residing in hippocampus has emerged through predicting input signals from the past sensory inputs. Specifically, they supposed that the CA3 predictor in hippocampus creates synaptic delay between input signals, which is compensated by the following CA1 predictor. Though recorded neural activities were replicated based on the temporal prediction hypothesis, its validity has not been fully explored. In this work, we aim to explore the temporal prediction hypothesis from the perspective of self-supervised learning (SSL). Specifically, we focus on non-contrastive learning, which generates two augmented views of an input image and predicts one from another. Non-contrastive learning is intimately related to the temporal prediction hypothesis because the synaptic delay is implicitly created by StopGradient. Building upon a popular non-contrastive learner, SimSiam, we propose PhiNet, an extension of SimSiam to have two predictors explicitly corresponding to the CA3 and CA1, respectively. Through studying the PhiNet model, we discover two findings. First, meaningful data representations emerge in PhiNet more stably than in SimSiam. This is initially supported by our learning dynamics analysis: PhiNet is more robust to the representational collapse. Second, PhiNet adapts more quickly to newly incoming patterns in online and continual learning scenarios. For practitioners, we additionally propose an extension called X-PhiNet integrated with a momentum encoder, excelling in continual learning. All in all, our work reveals that the temporal prediction hypothesis is a reasonable model in terms of the robustness and adaptivity.

This paper explores the characterization of equivariant linear layers for representations of permutations and related groups. Unlike traditional approaches, which address these problems using parameter-sharing, we consider an alternative methodology based on irreducible representations and Schur’s lemma. Using this methodology, we obtain an alternative derivation for existing models like DeepSets, 2-IGN graph equivariant networks, and Deep Weight Space (DWS) networks. The derivation for DWS networks is significantly simpler than that of previous results. Next, we extend our approach to unaligned symmetric sets, where equivariance to the wreath product of groups is required. Previous works have addressed this problem in a rather restrictive setting, in which almost all wreath equivariant layers are Siamese. In contrast, we give a full characterization of layers in this case and show that there is a vast number of additional non-Siamese layers in some settings. We also show empirically that these additional non-Siamese layers can improve performance in tasks like graph anomaly detection, weight space alignment, and learning Wasserstein distances.

Conformal prediction has recently emerged as a promising strategy for quantifying the uncertainty of a predictive model; these algorithms modify the model to output sets of labels that are guaranteed to contain the true label with high probability. However, existing conformal prediction algorithms have largely targeted classification and regression settings, where the structure of the prediction set has a simple form as a level set of the scoring function. However, for complex structured outputs such as text generation, these prediction sets might include a large number of labels and therefore be hard for users to interpret. In this paper, we propose a general framework for conformal prediction in the structured prediction setting, that modifies existing conformal prediction algorithms to output structured prediction sets that implicitly represent sets of labels. In addition, we demonstrate how our approach can be applied in domains where the prediction sets can be represented as a set of nodes in a directed acyclic graph; for instance, for hierarchical labels such as image classification, a prediction set might be a small subset of coarse labels implicitly representing the prediction set of all their more fine-descendants. We demonstrate how our algorithm can be used to construct prediction sets that satisfy a desired coverage guarantee in several domains.

Mixture of Experts (MoE) is a widely used technique to expand model sizes for better model quality while maintaining the computation cost constant. In a nutshell, an MoE model consists of multiple experts in each model layer and routes the training tokens to only a fixed number of experts rather than all. In distributed training, as experts are distributed among different GPUs, All-to-All communication is necessary to exchange the training tokens among the GPUs after each time of expert routing. Due to the frequent and voluminous data exchanges, All-to-All communication has become a notable challenge to training efficiency. In this paper, we manage to accelerate All-to-All communication in MoE models from the training sample perspective, which is unexplored so far. In particular, we put forward the observation that tokens in the same training sample have certain levels of locality in expert routing. Motivated by this, we develop NetMoE, which takes such locality into account and dynamically rearranges the placement of training samples to minimize All-to-All communication costs. Specifically, we model the All-to-All communication given the sample placement and formulate an integer programming problem to deduce the optimal placement in polynomial time. Experiments with 32 GPUs show that NetMoE achieves a maximum efficiency improvement of $1.67 \times$ compared with current MoE training frameworks.

Generative models lack rigorous statistical guarantees with respect to their predictions. In this work, we propose Sequential Conformal Prediction for Generative Models (SCOPE-Gen), a sequential conformal prediction method producing prediction sets that satisfy a rigorous statistical guarantee called conformal admissibility control. This guarantee means that the prediction sets contain at least one admissible (or valid) example, with high probability. To this end, our method first samples an initial set of i.i.d. examples from a black box generative model. Then, this set is iteratively pruned via so-called greedy filters. As a consequence of the iterative generation procedure, admissibility of the final prediction set factorizes as a Markov chain, where each factor can be controlled separately, using conformal prediction. In comparison to prior work, our method demonstrates a large reduction in the number of admissibility evaluations during calibration. This is crucial e.g. in safety-critical applications, where these evaluations must be conducted manually by domain experts and are therefore costly and time consuming. We highlight the advantages of our method in terms of admissibility evaluations and cardinality of the prediction set through experiments in natural language generation and molecular graph extension tasks.