ICML 2024 Papers

Denoising diffusion models have become ubiquitous for generative modeling. The core idea is to transport the data distribution to a Gaussian by using a diffusion. Approximate samples from the data distribution are then obtained by estimating the time-reversal of this diffusion using score matching ideas. We follow here a similar strategy to sample from unnormalized probability densities and compute their normalizing constants. However, the time-reversed diffusion is here simulated by using an original iterative particle scheme relying on a novel score matching loss. Contrary to standard denoising diffusion models, the resulting Particle Denoising Diffusion Sampler (PDDS) provides asymptotically consistent estimates under mild assumptions. We demonstrate PDDS on multimodal and high dimensional sampling tasks.

Non-linear mixed-effects models are a powerful tool for studying heterogeneous populations in various fields, including biology, medicine, economics, and engineering. Here, the aim is to find a distribution over the parameters that describe the whole population using a model that can generate simulations for an individual of that population. However, fitting these distributions to data is computationally challenging if the description of individuals is complex and the population is large. To address this issue, we propose a novel machine learning-based approach: We exploit neural density estimation based on conditional normalizing flows to approximate individual-specific posterior distributions in an amortized fashion, thereby allowing for efficient inference of population parameters. Applying this approach to problems from cell biology and pharmacology, we demonstrate its unseen flexibility and scalability to large data sets compared to established methods.

Molecular surfaces imply fingerprints of interaction patterns between proteins. However, non-equivalent efforts have been paid to incorporating the abundant protein surface information for analyzing proteins' biological functions in juxtaposition to amino acid sequences and 3D structures. We propose a novel surface-based unsupervised learning algorithm termed Surface-VQMAE to overcome this obstacle. In light of surface point clouds' sparsity and disorder properties, we first partition them into patches and obtain the sequential arrangement via the Morton curve. Successively, a Transformer-based architecture named SurfFormer was introduced to integrate the surface geometry and capture patch-level relations. At last, we enhance the prevalent masked auto-encoder (MAE) with the vector quantization (VQ) technique, which establishes a surface pattern codebook to enforce a discrete posterior distribution of latent variables and achieve more condensed semantics. Our work is the foremost to implement pretraining purely on molecular surfaces and extensive experiments on diverse real-life scenarios including binding site scoring, binding affinity prediction, and mutant effect estimation demonstrate its effectiveness. The code is available at https://github.com/smiles724/VQMAE.

*How does the internal computation of a machine learning model transform inputs into predictions?* To tackle this question, we introduce a framework called *component modeling* for decomposing a model prediction in terms of its components---architectural "building blocks" such as convolution filters or attention heads. We focus on a special case of this framework, *component attribution*, where the goal is to estimate the counterfactual impact of individual components on a given prediction. We then present COAR, a scalable algorithm for estimating component attributions, and demonstrate its effectiveness across models, datasets and modalities. Finally, we show that COAR directly enables effective model editing. Our code is available at [github.com/MadryLab/modelcomponents]([https://github.com/MadryLab/modelcomponents]).

Although recent advances in higher-order Graph Neural Networks (GNNs) improve the theoretical expressiveness and molecular property predictive performance, they often fall short of the empirical performance of models that explicitly use fragment information as inductive bias. However, for these approaches, there exists no theoretic expressivity study. In this work, we propose the *Fragment-WL* test, an extension to the well-known Weisfeiler & Leman (WL) test, which enables the theoretic analysis of these fragment-biased GNNs. Building on the insights gained from the Fragment-WL test, we develop a new GNN architecture and a fragmentation with infinite vocabulary that significantly boosts expressiveness. We show the effectiveness of our model on synthetic and real-world data where we outperform all GNNs on Peptides and have $12$% lower error than all GNNs on ZINC and $34$% lower error than other fragment-biased models. Furthermore, we show that our model exhibits superior generalization capabilities compared to the latest transformer-based architectures, positioning it as a robust solution for a range of molecular modeling tasks.

In recent years, there has been a surge in the development of 3D structure-based pre-trained protein models, representing a significant advancement over pre-trained protein language models in various downstream tasks. However, most existing structure-based pre-trained models primarily focus on the residue level, i.e., alpha carbon atoms, while ignoring other atoms like side chain atoms. We argue that modeling proteins at both residue and atom levels is important since the side chain atoms can also be crucial for numerous downstream tasks, for example, molecular docking. Nevertheless, we find that naively combining residue and atom information during pre-training typically fails. We identify a key reason is the information leakage caused by the inclusion of atom structure in the input, which renders residue-level pre-training tasks trivial and results in insufficiently expressive residue representations. To address this issue, we introduce a span mask pre-training strategy on 3D protein chains to learn meaningful representations of both residues and atoms. This leads to a simple yet effective approach to learning protein representation suitable for diverse downstream tasks. Extensive experimental results on binding site prediction and function prediction tasks demonstrate our proposed pre-training approach significantly outperforms other methods. Our code will be made public.

A molecule’s 2D representation consists of its atoms, their attributes, and the molecule’s covalent bonds. A 3D (geometric) representation of a molecule is called a conformer and consists of its atom types and Cartesian coordinates. Every conformer has a potential energy, and the lower this energy, the more likely it occurs in nature. Most existing machine learning methods for molecular property prediction consider either 2D molecular graphs or 3D conformer structure representations in isolation. Inspired by recent work on using ensembles of conformers in conjunction with 2D graph representations, we propose E(3)-invariant molecular conformer aggregation networks. The method integrates a molecule’s 2D representation with that of multiple of its conformers. Contrary to prior work, we propose a novel 2D–3D aggregation mechanism based on a differentiable solver for the Fused Gromov-Wasserstein Barycenter problem and the use of an efficient conformer generation method based on distance geometry. We show that the proposed aggregation mechanism is E(3) invariant and propose an efficient GPU implementation. Moreover, we demonstrate that the aggregation mechanism helps to significantly outperform state-of-the-art molecule property prediction methods on established datasets.

Catastrophic forgetting remains a core challenge in continual learning (CL), where the models struggle to retain previous knowledge when learning new tasks. While existing replay-based CL methods have been proposed to tackle this challenge by utilizing a memory buffer to store data from previous tasks, they generally overlook the interdependence between previously learned tasks and fail to encapsulate the optimally integrated knowledge in previous tasks, leading to sub-optimal performance of the previous tasks. Against this issue, we first reformulate replay-based CL methods as a unified hierarchical gradient aggregation framework. We then incorporate the Pareto optimization to capture the interrelationship among previously learned tasks and design a Pareto-Optimized CL algorithm (POCL), which effectively enhances the overall performance of past tasks while ensuring the performance of the current task. Comprehensive empirical results demonstrate that the proposed POCL outperforms current state-of-the-art CL methods across multiple datasets and different settings.

Large-scale sequence modeling has sparked rapid advances that now extend into biology and genomics. However, modeling genomic sequences introduces challenges such as the need to model long-range token interactions, the effects of upstream and downstream regions of the genome, and the reverse complementarity (RC) of DNA. Here, we propose an architecture motivated by these challenges that builds off the long-range Mamba block, and extends it to a BiMamba component that supports bi-directionality, and to a MambaDNA block that additionally supports RC equivariance. We use MambaDNA as the basis of Caduceus, the first family of RC equivariant bi-directional long-range DNA language models, and we introduce pre-training and fine-tuning strategies that yield Caduceus DNA foundation models. Caduceus outperforms previous long-range models on downstream benchmarks; on a challenging long-range variant effect prediction task, Caduceus exceeds the performance of 10x larger models that do not leverage bi-directionality or equivariance. Code to reproduce our experiments is available here: https://github.com/kuleshov-group/caduceus.

As a data-driven paradigm, offline reinforcement learning (RL) has been formulated as sequence modeling that conditions on the hindsight information including returns, goal or future trajectory. Although promising, this supervised paradigm overlooks the core objective of RL that maximizes the return. This overlook directly leads to the lack of trajectory stitching capability that affects the sequence model learning from sub-optimal data. In this work, we introduce the concept of max-return sequence modeling which integrates the goal of maximizing returns into existing sequence models. We propose **Rein*for***ced Trans***for*mer** (**Rein*for*mer**), indicating the sequence model is reinforced by the RL objective. **Rein*for*mer** additionally incorporates the objective of maximizing returns in the training phase, aiming to predict the maximum future return within the distribution. During inference, this in-distribution maximum return will guide the selection of optimal actions. Empirically, **Rein*for*mer** is competitive with classical RL methods on the D4RL benchmark and outperforms state-of-the-art sequence model particularly in trajectory stitching ability. Code is public at https://github.com/Dragon-Zhuang/Reinformer.

In large language model training, input documents are typically concatenated together and then split into sequences of equal length to avoid padding tokens. Despite its efficiency, the concatenation approach compromises data integrity—it inevitably breaks many documents into incomplete pieces, leading to excessive truncations that hinder the model from learning to compose logically coherent and factually consistent content that is grounded on the complete context. To address the issue, we propose Best-fit Packing, a scalable and efficient method that packs documents into training sequences through length-aware combinatorial optimization. Our method completely eliminates unnecessary truncations while retaining the same training efficiency as concatenation. Empirical results from both text and code pre-training show that our method achieves superior performance (e.g., +4.7% on reading comprehension; +16.8% in context following; and +9.2% on program synthesis), and reduces closed-domain hallucination effectively by up to 58.3%.

Autoencoders have become an indispensable tool for generative modeling and representation learning in high dimensions. Imposing structural constraints such as conditional independence in order to capture invariance of latent variables to nuisance information has been attempted through adding *ad hoc* penalties to the loss function mostly in the variational autoencoder (VAE) context, often based on heuristics. This paper demonstrates that Wasserstein autoencoders (WAEs) are highly flexible in embracing such structural constraints. Well-known extensions of VAEs for this purpose are gracefully handled within the framework of WAEs. In particular, given a conditional independence structure of the generative model (decoder), corresponding encoder structure and penalties are derived from the functional constraints that define the WAE. These structural uses of WAEs, termed StrWAEs (“stairways”), open up a principled way of penalizing autoencoders to impose structural constraints. Utilizing these advantages, we present handful of results on semi-supervised classification, conditional generation, and invariant representation tasks.

This paper studies the problem of modeling multi-agent dynamical systems, where agents could interact mutually to influence their behaviors. Recent research predominantly uses geometric graphs to depict these mutual interactions, which are then captured by powerful graph neural networks (GNNs). However, predicting interacting dynamics in challenging scenarios such as out-of-distribution shift and complicated underlying rules remains unsolved. In this paper, we propose a new approach named Prototypical Graph ODE (PGODE) to address the problem. The core of PGODE is to incorporate prototype decomposition from contextual knowledge into a continuous graph ODE framework. Specifically, PGODE employs representation disentanglement and system parameters to extract both object-level and system-level contexts from historical trajectories, which allows us to explicitly model their independent influence and thus enhances the generalization capability under system changes. Then, we integrate these disentangled latent representations into a graph ODE model, which determines a combination of various interacting prototypes for enhanced model expressivity. The entire model is optimized using an end-to-end variational inference framework to maximize the likelihood. Extensive experiments in both in-distribution and out-of-distribution settings validate the superiority of PGODE compared to various baselines.

Deep Gaussian processes (DGPs) provide a robust paradigm in Bayesian deep learning. In DGPs, a set of sparse integration locations called inducing points are selected to approximate the posterior distribution of the model. This is done to reduce computational complexity and improve model efficiency. However, inferring the posterior distribution of inducing points is not straightforward. Traditional variational inference techniques methods to approximate the posterior often leads to significant bias. To address this issue, we propose an alternative named Denoising Diffusion Variational Inference (DDVI) that utilizes a denoising diffusion stochastic differential equation (SDE) for generating posterior samples of inducing variables. We refer to the score matching method in the denoising diffusion model to approximate challenging score functions using a neural network. Furthermore, by combining classical mathematical theory of SDE with the minimization of KL divergence between the approximate and true processes, we propose a novel explicit variational lower bound for the marginal likelihood function of DGP. Through extensive experiments on various datasets and comparisons with baseline methods, we empirically demonstrate the effectiveness of the DDVI method in posterior inference of inducing points for DGP models.

3D molecular representation learning has gained tremendous interest and achieved promising performance in various downstream tasks. A series of recent approaches follow a prevalent framework: an encoder-only model coupled with a coordinate denoising objective. However, through a series of analytical experiments, we prove that the encoder-only model with coordinate denoising objective exhibits inconsistency between pre-training and downstream objectives, as well as issues with disrupted atomic identifiers. To address these two issues, we propose Mol-AE for molecular representation learning, an auto-encoder model using positional encoding as atomic identifiers. We also propose a new training objective named 3D Cloze Test to make the model learn better atom spatial relationships from real molecular substructures. Empirical results demonstrate that Mol-AE achieves a large margin performance gain compared to the current state-of-the-art 3D molecular modeling approach.

Graph transformers typically lack third-order interactions, limiting their geometric understanding which is crucial for tasks like molecular geometry prediction. We propose the Triplet Graph Transformer (TGT) that enables direct communication between pairs within a 3-tuple of nodes via novel triplet attention and aggregation mechanisms. TGT is applied to molecular property prediction by first predicting interatomic distances from 2D graphs and then using these distances for downstream tasks. A novel three-stage training procedure and stochastic inference further improve training efficiency and model performance. Our model achieves new state-of-the-art (SOTA) results on open challenge benchmarks PCQM4Mv2 and OC20 IS2RE. We also obtain SOTA results on QM9, MOLPCBA, and LIT-PCBA molecular property prediction benchmarks via transfer learning. We also demonstrate the generality of TGT with SOTA results on the traveling salesman problem (TSP).

This work introduces reduced models based on Continuous Low Rank Adaptation (CoLoRA) that pre-train neural networks for a given partial differential equation and then continuously adapt low-rank weights in time to rapidly predict the evolution of solution fields at new physics parameters and new initial conditions. The adaptation can be either purely data-driven or via an equation-driven variational approach that provides Galerkin-optimal approximations. Because CoLoRA approximates solution fields locally in time, the rank of the weights can be kept small, which means that only few training trajectories are required offline so that CoLoRA is well suited for data-scarce regimes. Predictions with CoLoRA are orders of magnitude faster than with classical methods and their accuracy and parameter efficiency is higher compared to other neural network approaches.

Masked Image Modeling (MIM) is a promising self-supervised learning approach that enables learning from unlabeled images. Despite its recent success, learning good representations through MIM remains challenging because it requires predicting the right semantic content in accurate locations. For example, given an incomplete picture of a dog, we can guess that there is a tail, but we cannot determine its exact location. In this work, we propose to incorporate location uncertainty to MIM by using stochastic positional embeddings (StoP). Specifically, we condition the model on stochastic masked token positions drawn from a gaussian distribution. We show that using StoP reduces overfitting to location features and guides the model toward learning features that are more robust to location uncertainties. Quantitatively, using StoP improves downstream MIM performance on a variety of downstream tasks. For example, linear probing on ImageNet using ViT-B is improved by $+1.7\%$, and by $2.5\%$ for ViT-H using 1% of the data.

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex molecular structures with fewer examples that are carefully designed using known substructures. We propose a data-efficient and interpretable model for representing and reasoning over such molecules in terms of graph grammars that explicitly describe the hierarchical design space featuring motifs to be the design basis. We present a novel representation in the form of random walks over the design space, which facilitates both molecule generation and property prediction. We demonstrate clear advantages over existing methods in terms of performance, efficiency, and synthesizability of predicted molecules, and we provide detailed insights into the method's chemical interpretability.