ICLR 2025 Papers

Optimizing black-box functions is a fundamental problem in science and engineering. To solve this problem, many approaches learn a surrogate function that estimates the underlying objective from limited historical evaluations. Large Language Models (LLMs), with their strong pattern-matching capabilities via pretraining on vast amounts of data, stand out as a potential candidate for surrogate modeling. However, directly prompting a pretrained language model to produce predictions is not feasible in many scientific domains due to the scarcity of domain-specific data in the pretraining corpora and the challenges of articulating complex problems in natural language. In this work, we introduce LICO, a general-purpose model that extends arbitrary base LLMs for black-box optimization, with a particular application to the molecular domain. To achieve this, we equip the language model with a separate embedding layer and prediction layer, and train the model to perform in-context predictions on a diverse set of functions defined over the domain. Once trained, LICO can generalize to unseen molecule properties simply via in-context prompting. LICO performs competitively on PMO, a challenging molecular optimization benchmark comprising 23 objective functions, and achieves state-of-the-art performance on its low-budget version PMO-1K.

Denoising learning of 3D molecules learns molecular representations by imposing noises into the equilibrium conformation and predicting the added noises to recover the equilibrium conformation, which essentially captures the information of molecular force fields. Due to the specificity of Potential Energy Surfaces, the probabilities of physically reasonable noises for each atom in different molecules are different. However, existing methods apply the shared heuristic hand-crafted noise sampling strategy to all molecules, resulting in inaccurate force field learning. In this paper, we propose a novel 3D molecular pre-training method, namely DenoiseVAE, which employs a Noise Generator to acquire atom-specific noise distributions for different molecules. It utilizes the stochastic reparameterization technique to sample noisy conformations from the generated distributions, which are inputted into a Denoising Module for denoising. The Noise Generator and the Denoising Module are jointly learned in a manner conforming with the paradigm of Variational Auto Encoder. Consequently, the sampled noisy conformations can be more diverse, adaptive, and informative, and thus DenoiseVAE can learn representations that better reveal the molecular force fields. Extensive experiments show that DenoiseVAE outperforms the current state-of-the-art methods on various molecular property prediction tasks, demonstrating the effectiveness of it.

Understanding protein dynamics are essential for deciphering protein functional mechanisms and developing molecular therapies. However, the complex high-dimensional dynamics and interatomic interactions of biological processes pose significant challenge for existing computational techniques. In this paper, we approach this problem for the first time by introducing Deep Signature, a novel computationally tractable framework that characterizes complex dynamics and interatomic interactions based on their evolving trajectories. Specifically, our approach incorporates soft spectral clustering that locally aggregates cooperative dynamics to reduce the size of the system, as well as signature transform that collects iterated integrals to provide a global characterization of the non-smooth interactive dynamics. Theoretical analysis demonstrates that Deep Signature exhibits several desirable properties, including invariance to translation, near invariance to rotation, equivariance to permutation of atomic coordinates, and invariance under time reparameterization. Furthermore, experimental results on three benchmarks of biological processes verify that our approach can achieve superior performance compared to baseline methods.

Establishing the relationship between 3D structures and the energy states of molecular systems has proven to be a promising approach for learning 3D molecular representations. However, existing methods are limited to modeling the molecular energy states from classical mechanics. This limitation results in a significant oversight of quantum mechanical effects, such as quantized (discrete) energy level structures, which offer a more accurate estimation of molecular energy and can be experimentally measured through energy spectra. In this paper, we propose to utilize the energy spectra to enhance the pre-training of 3D molecular representations (MolSpectra), thereby infusing the knowledge of quantum mechanics into the molecular representations. Specifically, we propose SpecFormer, a multi-spectrum encoder for encoding molecular spectra via masked patch reconstruction. By further aligning outputs from the 3D encoder and spectrum encoder using a contrastive objective, we enhance the 3D encoder's understanding of molecules. Evaluations on public benchmarks reveal that our pre-trained representations surpass existing methods in predicting molecular properties and modeling dynamics.

Large language models (LLMs) have demonstrated remarkable capabilities across a range of text-generation tasks. However, LLMs still struggle with problems requiring multi-step decision-making and environmental feedback, such as online shopping, scientific reasoning, and mathematical problem-solving. Unlike pure text data, collecting large-scale decision-making data is challenging. Moreover, many powerful LLMs are only accessible through APIs, which hinders their fine-tuning for agent tasks due to cost and complexity. To address LLM agents' limitations, we propose a framework that can automatically learn a reward model from the environment without human annotations. This model can be used to evaluate the action trajectories of LLM agents and provide heuristics for task planning. Specifically, our approach involves employing one LLM-based agent to navigate an environment randomly, generating diverse action trajectories. Subsequently, a separate LLM is leveraged to assign a task intent and synthesize a negative response alongside the correct response for each trajectory. These triplets (task intent, positive response, and negative response) are then utilized as training data to optimize a reward model capable of scoring action trajectories. This reward model can be integrated with LLM-based agents and various planning algorithms to enhance task-solving performance. The effectiveness and generalizability of our framework are demonstrated through evaluations conducted on different agent benchmarks. In conclusion, our proposed framework represents a significant advancement in enhancing LLM agents' decision-making capabilities. By automating the learning of reward models, we overcome the challenges of data scarcity and API limitations, potentially revolutionizing the application of LLMs in complex and interactive environments. This research paves the way for more sophisticated AI agents capable of tackling a wide range of real-world problems requiring multi-step decision-making.

Electron-multiplying charge-coupled device (EMCCD) has been instrumental in sensitive observations under low-light situations including astronomy, material science, and biology. Despite its ingenious designs to enhance target signals overcoming read-out circuit noises, produced images are not completely noise free, which could still cast a cloud on desired experiment outcomes, especially in fluorescence microscopy. Existing studies on EMCCD's noise model have been focusing on statistical characteristics in theory, yet unable to incorporate latest advancements in the field of computational photography, where physics-based noise models are utilized to guide deep learning processes, creating adaptive denoising algorithms for ordinary image sensors. Still, those models are not directly applicable to EMCCD. In this paper, we intend to pioneer EMCCD denoising by introducing a systematic study on physics-based noise model calibration procedures for an EMCCD camera, accurately estimating statistical features of observable noise components in experiments, which are then utilized to generate substantial amount of authentic training samples for one of the most recent neural networks. A first real-world test image dataset for EMCCD is captured, containing both images of ordinary daily scenes and those of microscopic contents. Benchmarking upon the testset and authentic microscopic images, we demonstrate distinct advantages of our model against previous methods for EMCCD and physics-based noise modeling, forging a promising new path for EMCCD denoising.

Transporting between arbitrary distributions is a fundamental goal in generative modeling. Recently proposed diffusion bridge models provide a potential solution, but they rely on a joint distribution that is difficult to obtain in practice. Furthermore, formulations based on continuous domains limit their applicability to discrete domains such as graphs. To overcome these limitations, we propose Discrete Diffusion Schrödinger Bridge Matching (DDSBM), a novel framework that utilizes continuous-time Markov chains to solve the SB problem in a high-dimensional discrete state space. Our approach extends Iterative Markovian Fitting to discrete domains, and we have proved its convergence to the SB. Furthermore, we adapt our framework for the graph transformation, and show that our design choice of underlying dynamics characterized by independent modifications of nodes and edges can be interpreted as the entropy-regularized version of optimal transport with a cost function described by the graph edit distance. To demonstrate the effectiveness of our framework, we have applied DDSBM to molecular optimization in the field of chemistry. Experimental results demonstrate that DDSBM effectively optimizes molecules' property-of-interest with minimal graph transformation, successfully retaining other features. Source code is available [here](https://github.com/junhkim1226/DDSBM).

Discrete diffusion models with absorbing processes have shown promise in language modeling. The key quantities to be estimated are the ratios between the marginal probabilities of two transitive states at all timesteps, called the concrete score. In this paper, we reveal that the concrete score in absorbing diffusion can be expressed as conditional probabilities of clean data, multiplied by a time-dependent scalar in an analytic form. Motivated by this finding, we propose reparameterized absorbing discrete diffusion (RADD), a dedicated diffusion model without time-condition that characterizes the time-independent conditional probabilities. Besides its simplicity, RADD can reduce the number of function evaluations (NFEs) by caching the output of the time-independent network when the noisy sample remains unchanged in a sampling interval, which enables sampling acceleration. Built upon the new perspective of conditional distributions, we further unify absorbing discrete diffusion and any-order autoregressive models (AO-ARMs), showing that the upper bound on the negative log-likelihood for the diffusion model can be interpreted as an expected negative log-likelihood for AO-ARMs. Further, our RADD models achieve SOTA performance among diffusion models on 5 zero-shot language modeling benchmarks (measured by perplexity) at the GPT-2 scale. Our code is available at \url{https://github.com/ML-GSAI/RADD}.

We study the discriminative probabilistic modeling on a continuous domain for the data prediction task of (multimodal) self-supervised representation learning. To address the challenge of computing the integral in the partition function for each anchor data, we leverage the multiple importance sampling (MIS) technique for robust Monte Carlo integration, which can recover InfoNCE-based contrastive loss as a special case. Within this probabilistic modeling framework, we conduct generalization error analysis to reveal the limitation of current InfoNCE-based contrastive loss for self-supervised representation learning and derive insights for developing better approaches by reducing the error of Monte Carlo integration. To this end, we propose a novel non-parametric method for approximating the sum of conditional probability densities required by MIS through convex optimization, yielding a new contrastive objective for self-supervised representation learning. Moreover, we design an efficient algorithm for solving the proposed objective. We empirically compare our algorithm to representative baselines on the contrastive image-language pretraining task. Experimental results on the CC3M and CC12M datasets demonstrate the superior overall performance of our algorithm. Our code is available at https://github.com/bokun-wang/NUCLR.

The Bradley-Terry (BT) model is a common and successful practice in reward modeling for Large Language Model (LLM) alignment. However, it remains unclear *why* this model --- originally developed for multi-player stochastic game matching --- can be adopted to convert pairwise response comparisons to reward values and make predictions. Especially given the fact that only a limited number of prompt-response pairs are sparsely compared with others. In this paper, we first establish the convergence rate of BT reward models based on deep neural networks using embeddings, providing a theoretical foundation for their use. Despite theoretically sound, we argue that the BT model is not a necessary choice from the perspective of downstream optimization, this is because a reward model only needs to preserve the correct ranking predictions through a monotonic transformation of the true reward. We highlight the critical concept of *order consistency* in reward modeling and demonstrate that the BT model possesses this property. Moreover, we propose a simple and straightforward upper-bound algorithm, compatible with off-the-shelf binary classifiers, as an alternative order-consistent reward modeling objective. To offer practical insights, we empirically evaluate the performance of these different reward modeling approaches across more than 12,000 experimental setups, using $6$ base LLMs, $2$ datasets, and diverse annotation designs that vary in quantity, quality, and pairing choices in preference annotations.

While large language models (LLMs) have integrated images, adapting them to graphs remains challenging, limiting their applications in materials and drug design. This difficulty stems from the need for coherent autoregressive generation across texts and graphs. To address this, we introduce Llamole, the first multimodal LLM capable of interleaved text and graph generation, enabling molecular inverse design with retrosynthetic planning. Llamole integrates a base LLM with the Graph Diffusion Transformer and Graph Neural Networks for multi-conditional molecular generation and reaction inference within texts, while the LLM, with enhanced molecular understanding, flexibly controls activation among the different graph modules. Additionally, Llamole integrates A* search with LLM-based cost functions for efficient retrosynthetic planning. We create benchmarking datasets and conduct extensive experiments to evaluate Llamole against in-context learning and supervised fine-tuning. Llamole significantly outperforms 14 adapted LLMs across 12 metrics for controllable molecular design and retrosynthetic planning. Code and model at https://github.com/liugangcode/Llamole.

An essential component of modern recurrent sequence models is the forget gate. While Transformers do not have an explicit recurrent form, we show that a forget gate can be naturally incorporated into Transformers by down-weighting the unnormalized attention scores in a data-dependent way. We name this attention mechanism Forgetting Attention and the resulting model the Forgetting Transformer (FoX). We show that FoX outperforms the Transformer on long-context language modeling, length extrapolation, and short-context downstream tasks, while performing on par with the Transformer on long-context downstream tasks. Moreover, it is compatible with the FlashAttention algorithm and does not require any positional embeddings. Several analyses, including the needle-in-the-haystack test, show that FoX also retains the Transformer's superior long-context capabilities over recurrent sequence models such as Mamba-2, HGRN2, and DeltaNet. We also introduce a "Pro" block design that incorporates some common architectural components in recurrent sequence models and find it significantly improves the performance of both FoX and the Transformer. Our code is available at [`https://github.com/zhixuan-lin/forgetting-transformer`](https://github.com/zhixuan-lin/forgetting-transformer).

Longitudinal biomedical studies monitor individuals over time to capture dynamics in brain development, disease progression, and treatment effects. However, estimating trajectories of brain biomarkers is challenging due to biological variability, inconsistencies in measurement protocols (e.g., differences in MRI scanners) as well as scarcity and irregularity in longitudinal measurements. Herein, we introduce a novel personalized deep kernel regression framework for forecasting brain biomarkers, with application to regional volumetric measurements. Our approach integrates two key components: a population model that captures brain trajectories from a large and diverse cohort, and a subject-specific model that captures individual trajectories. To optimally combine these, we propose Adaptive Shrinkage Estimation, which effectively balances population and subject-specific models. We assess our model’s performance through predictive accuracy metrics, uncertainty quantification, and validation against external clinical studies. Benchmarking against state-of-the-art statistical and machine learning models—including linear mixed effects models, generalized additive models, and deep learning methods—demonstrates the superior predictive performance of our approach. Additionally, we apply our method to predict trajectories of composite neuroimaging biomarkers, which highlights the versatility of our approach in modeling the progression of longitudinal neuroimaging biomarkers. Furthermore, validation on three external neuroimaging studies confirms the robustness of our method across different clinical contexts. We make the code available at https://github.com/vatass/AdaptiveShrinkageDKGP.

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100\% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26\% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13\% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

Estimating an individual's potential outcomes under counterfactual treatments is a challenging task for traditional causal inference and supervised learning approaches when the outcome is high-dimensional (e.g. gene expressions, facial images) and covariates are relatively limited. In this case, to predict one's outcomes under counterfactual treatments, it is crucial to leverage individual information contained in the observed outcome in addition to the covariates. Prior works using variational inference in counterfactual generative modeling have been focusing on neural adaptations and model variants within the conditional variational autoencoder formulation, which we argue is fundamentally ill-suited to the notion of counterfactual in causal inference. In this work, we present a novel variational Bayesian causal inference framework and its theoretical backings to properly handle counterfactual generative modeling tasks, through which we are able to conduct counterfactual supervision end-to-end during training without any counterfactual samples, and encourage disentangled exogenous noise abduction that aids the correct identification of causal effect in counterfactual generations. In experiments, we demonstrate the advantage of our framework compared to state-of-the-art models in counterfactual generative modeling on multiple benchmarks.

Data-driven techniques have emerged as a promising alternative to traditional numerical methods for solving PDEs. For time-dependent PDEs, many approaches are Markovian---the evolution of the trained system only depends on the current state, and not the past states. In this work, we investigate the benefits of using memory for modeling time-dependent PDEs: that is, when past states are explicitly used to predict the future. Motivated by the Mori-Zwanzig theory of model reduction, we theoretically exhibit examples of simple (even linear) PDEs, in which a solution that uses memory is arbitrarily better than a Markovian solution. Additionally, we introduce Memory Neural Operator (MemNO), a neural operator architecture that combines recent state space models (specifically, S4) and Fourier Neural Operators (FNOs) to effectively model memory. We empirically demonstrate that when the PDEs are supplied in low resolution or contain observation noise at train and test time, MemNO significantly outperforms the baselines without memory---with up to $6 \times$ reduction in test error. Furthermore, we show that this benefit is particularly pronounced when the PDE solutions have significant high-frequency Fourier modes (e.g., low-viscosity fluid dynamics) and we construct a challenging benchmark dataset consisting of such PDEs.

We introduce Chunk-Distilled Language Modeling (CD-LM), an approach to text generation that addresses two challenges in current large language models (LLMs): the inefficiency of token-level generation, and the difficulty of adapting to new data and knowledge. Our method combines deep network-based LLMs with a straightforward retrieval module, which allows the generation of multi-token text chunks at a single decoding step. Our retrieval framework enables flexible construction of model- or domain-specific datastores, either leveraging the internal knowledge of existing models, or incorporating expert insights from human-annotated corpora. This adaptability allows for enhanced control over the language model's distribution without necessitating additional training. We present the CD-LM formulation along with performance metrics demonstrating its ability to improve language model performance and efficiency across a diverse set of downstream applications. Code and data will be made publicly available.

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.

Obtaining the desired effect of drugs is highly dependent on their molecular geometries. Thus, the current prevailing paradigm focuses on 3D point-cloud atom representations, utilizing graph neural network (GNN) parametrizations, with rotational symmetries baked in via E(3) invariant layers. We prove that such models must necessarily disregard chirality, a geometric property of the molecules that cannot be superimposed on their mirror image by rotation and translation. Chirality plays a key role in determining drug safety and potency. To address this glaring issue, we introduce a novel field-based representation, proposing reference rotations that replace rotational symmetry constraints. The proposed model captures all molecular geometries including chirality, while still achieving highly competitive performance with E(3)-based methods across standard benchmarking metrics.