ICLR 2024 Papers

Most Neural Radiance Fields (NeRFs) exhibit limited generalization capabilities,which restrict their applicability in representing multiple scenes using a single model. To address this problem, existing generalizable NeRF methods simply condition the model on image features. These methods still struggle to learn precise global representations over diverse scenes since they lack an effective mechanism for interacting among different points and views. In this work, we unveil that 3D implicit representation learning can be significantly improved by mask-based modeling. Specifically, we propose **m**asked **r**ay and **v**iew **m**odeling for generalizable **NeRF** (**MRVM-NeRF**), which is a self-supervised pretraining target to predict complete scene representations from partially masked features along each ray. With this pretraining target, MRVM-NeRF enables better use of correlations across different rays and views as the geometry priors, which thereby strengthens the capability of capturing intricate details within the scenes and boosts the generalization capability across different scenes. Extensive experiments demonstrate the effectiveness of our proposed MRVM-NeRF on both synthetic and real-world datasets, qualitatively and quantitatively. Besides, we also conduct experiments to show the compatibility of our proposed method with various backbones and its superiority under few-shot cases.

Advanced generative model (\textit{e.g.}, diffusion model) derived from simplified continuity assumptions of data distribution, though showing promising progress, has been difficult to apply directly to geometry generation applications due to the \textit{multi-modality} and \textit{noise-sensitive} nature of molecule geometry. This work introduces Geometric Bayesian Flow Networks (GeoBFN), which naturally fits molecule geometry by modeling diverse modalities in the differentiable parameter space of distributions. GeoBFN maintains the SE-(3) invariant density modeling property by incorporating equivariant inter-dependency modeling on parameters of distributions and unifying the probabilistic modeling of different modalities. Through optimized training and sampling techniques, we demonstrate that GeoBFN achieves state-of-the-art performance on multiple 3D molecule generation benchmarks in terms of generation quality (90.87\% molecule stability in QM9 and 85.6\% atom stability in GEOM-DRUG\footnote{The scores are reported at 1k sampling steps for fair comparison, and our scores could be further improved if sampling sufficiently longer steps.}). GeoBFN can also conduct sampling with any number of steps to reach an optimal trade-off between efficiency and quality (\textit{e.g.}, 20$\times$ speedup without sacrificing performance).

Language models are currently trained to predict tokens given document prefixes, enabling them to zero shot long form generation and prompting-style tasks which can be reduced to document completion. We instead present IN-CONTEXT PRETRAINING, a new approach where language models are trained on a sequence of related documents, thereby explicitly encouraging them to read and reason across document boundaries. Our approach builds on the fact that current pipelines train by concatenating random sets of shorter documents to create longer context windows; this improves efficiency even though the prior documents provide no signal for predicting the next document. Given this fact, we can do IN-CONTEXT PRETRAINING by simply changing the document ordering so that each context contains related documents, and directly applying existing pretraining pipelines. However, this document sorting problem is challenging. There are billions of documents and we would like the sort to maximize contextual similarity for every document without repeating any data. To do this, we introduce approximate algorithms for finding related documents with efficient nearest neighbor search and constructing coherent batches with a graph cover algorithm. Our experiments show IN-CONTEXT PRETRAINING offers a scalable and simple approach to significantly enhance LM performance: we see notable improvements in tasks that require more complex contextual reasoning, including in-context learning (+8%), reading comprehension (+15%), faithfulness to previous contexts (+16%), long-context reasoning (+5%), and retrieval augmentation (+9%).

Large language models are trained on vast amounts of internet data, prompting concerns that they have memorized public benchmarks. Detecting this type of contamination is challenging because the pretraining data used by proprietary models are often not publicly accessible. We propose a procedure for detecting test set contamination of language models with exact false positive guarantees and without access to pretraining data or model weights. Our approach leverages the fact that when there is no data contamination, all orderings of an exchangeable benchmark should be equally likely. In contrast, the tendency for language models to memorize example order means that a contaminated language model will find certain canonical orderings to be much more likely than others. Our test flags potential contamination whenever the likelihood of a canonically ordered benchmark dataset is significantly higher than the likelihood after shuffling the examples. We demonstrate that our procedure is sensitive enough to reliably detect contamination in challenging situations, including models as small as 1.4 billion parameters, on small test sets only 1000 examples, and datasets that appear only a few times in the pretraining corpus. Finally, we evaluate LLaMA-2 to apply our test in a realistic setting and find our results to be consistent with existing contamination evaluations.

Are camera poses necessary for multi-view 3D modeling? Existing approaches predominantly assume access to accurate camera poses. While this assumption might hold for dense views, accurately estimating camera poses for sparse views is often elusive. Our analysis reveals that noisy estimated poses lead to degraded performance for existing sparse-view 3D modeling methods. To address this issue, we present LEAP, a novel pose-free approach, therefore challenging the prevailing notion that camera poses are indispensable. LEAP discards pose-based operations and learns geometric knowledge from data. LEAP is equipped with a neural volume, which is shared across scenes and is parameterized to encode geometry and texture priors. For each incoming scene, we update the neural volume by aggregating 2D image features in a feature-similarity-driven manner. The updated neural volume is decoded into the radiance field, enabling novel view synthesis from any viewpoint. On both object-centric and bounded scene-level datasets, we show that LEAP significantly outperforms prior methods when they employ predicted poses from state-of-the-art pose estimators. Notably, LEAP performs on par with prior approaches that use ground-truth poses while running $400\times$ faster than PixelNeRF. We show LEAP generalizes to novel object categories and scenes, and learns knowledge closely resembles epipolar geometry.

Recent representation learning approaches enhance neural topic models by optimizing the weighted linear combination of the evidence lower bound (ELBO) of the log-likelihood and the contrastive learning objective that contrasts pairs of input documents. However, document-level contrastive learning might capture low-level mutual information, such as word ratio, which disturbs topic modeling. Moreover, there is a potential conflict between the ELBO loss that memorizes input details for better reconstruction quality, and the contrastive loss which attempts to learn topic representations that generalize among input documents. To address these issues, we first introduce a novel contrastive learning method oriented towards sets of topic vectors to capture useful semantics that are shared among a set of input documents. Secondly, we explicitly cast contrastive topic modeling as a gradient-based multi-objective optimization problem, with the goal of achieving a Pareto stationary solution that balances the trade-off between the ELBO and the contrastive objective. Extensive experiments demonstrate that our framework consistently produces higher-performing neural topic models in terms of topic coherence, topic diversity, and downstream performance.

Diffusion models are powerful generative models that map noise to data using stochastic processes. However, for many applications such as image editing, the model input comes from a distribution that is not random noise. As such, diffusion models must rely on cumbersome methods like guidance or projected sampling to incorporate this information in the generative process. In our work, we propose Denoising Diffusion Bridge Models (DDBMs), a natural alternative to this paradigm based on *diffusion bridges*, a family of processes that interpolate between two paired distributions given as endpoints. Our method learns the score of the diffusion bridge from data and maps from one endpoint distribution to the other by solving a (stochastic) differential equation based on the learned score. Our method naturally unifies several classes of generative models, such as score-based diffusion models and OT-Flow-Matching, allowing us to adapt existing design and architectural choices to our more general problem. Empirically, we apply DDBMs to challenging image datasets in both pixel and latent space. On standard image translation problems, DDBMs achieve significant improvement over baseline methods, and, when we reduce the problem to image generation by setting the source distribution to random noise, DDBMs achieve comparable FID scores to state-of-the-art methods despite being built for a more general task.

Given a set of $K$ probability densities, we consider the multimarginal generative modeling problem of learning a joint distribution that recovers these densities as marginals. The structure of this joint distribution should identify multi-way correspondences among the prescribed marginals. We formalize an approach to this task within a generalization of the stochastic interpolant framework, leading to efficient learning algorithms built upon dynamical transport of measure. Our generative models are defined by velocity and score fields that can be characterized as the minimizers of simple quadratic objectives, and they are defined on a simplex that generalizes the time variable in the usual dynamical transport framework. The resulting transport on the simplex is influenced by all marginals, and we show that multi-way correspondences can be extracted. The identification of such correspondences has applications to style transfer, algorithmic fairness, and data decorruption. In addition, the multimarginal perspective enables an efficient algorithm for optimizing the dynamical transport cost in the ordinary two-marginal setting. We demonstrate these capacities with several numerical examples.

The ground-state conformation of a molecule is often decisive for its properties. However, experimental or computational methods, such as density functional theory (DFT), are time-consuming and labor-intensive for obtaining this conformation. Deep learning (DL) based molecular representation learning (MRL) has made significant advancements in molecular modeling and has achieved remarkable results in various tasks. Consequently, it has emerged as a promising approach for directly predicting the ground-state conformation of molecules. In this regard, we introduce GTMGC, a novel network based on Graph-Transformer (GT) that seamlessly predicts the spatial configuration of molecules in a 3D space from their 2D topological architecture in an end-to-end manner. Moreover, we propose a novel self-attention mechanism called Molecule Structural Residual Self-Attention (MSRSA) for molecular structure modeling. This mechanism not only guarantees high model performance and easy implementation but also lends itself well to other molecular modeling tasks. Our method has been evaluated on the Molecule3D benchmark dataset and the QM9 dataset. Experimental results demonstrate that our approach achieves remarkable performance and outperforms current state-of-the-art methods as well as the widely used open-source software RDkit.

Models trained on different datasets can be merged by a weighted-averaging of their parameters, but why does it work and when can it fail? Here, we connect the inaccuracy of weighted-averaging to mismatches in the gradients and propose a new uncertainty-based scheme to improve the performance by reducing the mismatch. The connection also reveals implicit assumptions in other schemes such as averaging, task arithmetic, and Fisher-weighted averaging. Our new method gives consistent improvements for large language models and vision transformers, both in terms of performance and robustness to hyperparameters.

Molecular docking is critical to structure-based virtual screening, yet the throughput of such workflows is limited by the expensive optimization of scoring functions involved in most docking algorithms. We explore how machine learning can accelerate this process by learning a scoring function with a functional form that allows for more rapid optimization. Specifically, we define the scoring function to be the cross-correlation of multi-channel ligand and protein scalar fields parameterized by equivariant graph neural networks, enabling rapid optimization over rigid-body degrees of freedom with fast Fourier transforms. The runtime of our approach can be amortized at several levels of abstraction, and is particularly favorable for virtual screening settings with a common binding pocket. We benchmark our scoring functions on two simplified docking-related tasks: decoy pose scoring and rigid conformer docking. Our method attains similar but faster performance on crystal structures compared to the widely-used Vina and Gnina scoring functions, and is more robust on computationally predicted structures. Code is available at https://github.com/bjing2016/scalar-fields.

The generation of molecules with desired properties has become increasingly popular, revolutionizing the way scientists design molecular structures and providing valuable support for chemical and drug design. However, despite the potential of language models in molecule generation, they face challenges such as generating syntactically or chemically flawed molecules, having narrow domain focus, and struggling to create diverse and feasible molecules due to limited annotated data or external molecular databases. To tackle these challenges, we introduce MolGen, a pre-trained molecular language model tailored specifically for molecule generation. Through the reconstruction of over 100 million molecular SELFIES, MolGen internalizes structural and grammatical insights. This is further enhanced by domain-agnostic molecular prefix tuning, fostering robust knowledge transfer across diverse domains. Importantly, our chemical feedback paradigm steers the model away from "molecular hallucinations", ensuring alignment between the model's estimated probabilities and real-world chemical preferences. Extensive experiments on well-known benchmarks underscore MolGen's optimization capabilities in properties such as penalized logP, QED, and molecular docking. Additional analyses confirm its proficiency in accurately capturing molecule distributions, discerning intricate structural patterns, and efficiently exploring the chemical space (https://github.com/zjunlp/MolGen).

High-throughput drug screening -- using cell imaging or gene expression measurements as readouts of drug effect -- is a critical tool in biotechnology to assess and understand the relationship between the chemical structure and biological activity of a drug. Since large-scale screens have to be divided into multiple experiments, a key difficulty is dealing with batch effects, which can introduce systematic errors and non-biological associations in the data. We propose InfoCORE, an Information maximization approach for COnfounder REmoval, to effectively deal with batch effects and obtain refined molecular representations. InfoCORE establishes a variational lower bound on the conditional mutual information of the latent representations given a batch identifier. It adaptively reweights samples to equalize their implied batch distribution. Extensive experiments on drug screening data reveal InfoCORE's superior performance in a multitude of tasks including molecular property prediction and molecule-phenotype retrieval. Additionally, we show results for how InfoCORE offers a versatile framework and resolves general distribution shifts and issues of data fairness by minimizing correlation with spurious features or removing sensitive attributes.

Retrosynthesis planning is a fundamental challenge in chemistry which aims at designing multi-step reaction pathways from commercially available starting materials to a target molecule. Each step in multi-step retrosynthesis planning requires accurate prediction of possible precursor molecules given the target molecule and confidence estimates to guide heuristic search algorithms. We model single-step retrosynthesis as a distribution learning problem in a discrete state space. First, we introduce the Markov Bridge Model, a generative framework aimed to approximate the dependency between two intractable discrete distributions accessible via a finite sample of coupled data points. Our framework is based on the concept of a Markov bridge, a Markov process pinned at its endpoints. Unlike diffusion-based methods, our Markov Bridge Model does not need a tractable noise distribution as a sampling proxy and directly operates on the input product molecules as samples from the intractable prior distribution. We then address the retrosynthesis planning problem with our novel framework and introduce RetroBridge, a template-free retrosynthesis modeling approach that achieves state-of-the-art results on standard evaluation benchmarks.

Large-scale protein language models (PLMs), such as the ESM family, have achieved remarkable performance in various downstream tasks related to protein structure and function by undergoing unsupervised training on residue sequences. They have become essential tools for researchers and practitioners in biology. However, a limitation of vanilla PLMs is their lack of explicit consideration for protein structure information, which suggests the potential for further improvement. Motivated by this, we introduce the concept of a ``structure-aware vocabulary" that integrates residue tokens with structure tokens. The structure tokens are derived by encoding the 3D structure of proteins using Foldseek. We then propose SaProt, a large-scale general-purpose PLM trained on an extensive dataset comprising approximately 40 million protein sequences and structures. Through extensive evaluation, our SaProt model surpasses well-established and renowned baselines across 10 significant downstream tasks, demonstrating its exceptional capacity and broad applicability. We have made the code, pre-trained model, and all relevant materials available at https://github.com/westlake-repl/SaProt.

Neural language models are probabilistic models of human text. They are predominantly trained using maximum likelihood estimation (MLE), which is equivalent to minimizing the forward cross-entropy between the empirical data distribution and the model distribution. However, various degeneration phenomena are still widely observed when decoding from the distributions learned by such models. We establish that the forward cross-entropy is suboptimal as a distance metric for aligning human and model distribution due to its (1) recall-prioritization (2) negative diversity ignorance and (3) train-test mismatch. In this paper, we propose Earth Mover Distance Optimization (EMO) for auto-regressive language modeling. EMO capitalizes on the inherent properties of earth mover distance to address the aforementioned challenges. Due to the high complexity of direct computation, we further introduce a feasible upper bound for EMO to ease end-to-end training. Upon extensive evaluation of language models trained using EMO and MLE. We find that EMO demonstrates a consistently better language modeling performance than MLE across domains. Moreover, EMO demonstrates noteworthy enhancements in downstream performance with minimal fine-tuning on merely 25,000 sentences. This highlights the tremendous potential of EMO as a lightweight calibration method for enhancing large-scale pre-trained language models.

Generating a sequence of intermediate steps, \emph{a.k.a.}, a chain of thought (CoT), is a highly effective method to improve the accuracy of large language models (LLMs) on arithmetics and symbolic reasoning tasks. However, the mechanism behind CoT remains unclear. This work provides a theoretical understanding of the power of CoT for decoder-only transformers through the lens of expressiveness. Conceptually, CoT empowers the model with the ability to perform inherently serial computation, which is otherwise lacking in transformers, especially when depth is low. Given input length $n$, previous works have constant-depth transformers with finite precision $\mathsf{poly}(n)$ embedding size can only solve problems in $\mathsf{TC}^0$ without CoT. We first show an even tighter expressiveness upper bound for constant-depth transformers with constant-bit precision, which can only solve problems in $\mathsf{AC}^0$, a proper subset of $ \mathsf{TC}^0$. However, with $T$ steps of CoT, constant-depth transformers using constant-bit precision and $O(\log n)$ embedding size can solve any problem solvable by boolean circuits of size $T$. Empirically, enabling CoT dramatically improves the accuracy for tasks that are hard for parallel computation, including the composition of permutation groups, iterated squaring, and circuit value problems, especially for low-depth transformers.