ICLR 2024 Papers

Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration shows that improvements to explainability and sample efficiency for molecular design can be made synergistic.

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.

Solving partial differential equations (PDEs) is a central task in scientific computing. Recently, neural network approximation of PDEs has received increasing attention due to its flexible meshless discretization and its potential for high-dimensional problems. One fundamental numerical difficulty is that random samples in the training set introduce statistical errors into the discretization of the loss functional which may become the dominant error in the final approximation, and therefore overshadow the modeling capability of the neural network. In this work, we propose a new minmax formulation to optimize simultaneously the approximate solution, given by a neural network model, and the random samples in the training set, provided by a deep generative model. The key idea is to use a deep generative model to adjust the random samples in the training set such that the residual induced by the neural network model can maintain a smooth profile in the training process. Such an idea is achieved by implicitly embedding the Wasserstein distance between the residual-induced distribution and the uniform distribution into the loss, which is then minimized together with the residual. A nearly uniform residual profile means that its variance is small for any normalized weight function such that the Monte Carlo approximation error of the loss functional is reduced significantly for a certain sample size. The adversarial adaptive sampling (AAS) approach proposed in this work is the first attempt to formulate two essential components, minimizing the residual and seeking the optimal training set, into one minmax objective functional for the neural network approximation of PDEs.

In recent years, Artificial Intelligence has undergone a paradigm shift with the rise of foundation models, which are trained on large amounts of data, typically in a self-supervised way, and can then be adapted to a wide range of downstream tasks. In this work, we propose the first foundation model for Error Correction Codes. This model is trained on multiple codes and can then be applied to an unseen code. To enable this, we extend the Transformer architecture in multiple ways: (1) a code-invariant initial embedding, which is also position- and length-invariant, (2) a learned modulation of the attention maps that is conditioned on the Tanner graph, and (3) a length-invariant code-aware noise prediction module that is based on the parity-check matrix. The proposed architecture is trained on multiple short- and medium-length codes and is able to generalize to unseen codes. Its performance on these codes matches and even outperforms the state of the art, despite having a smaller capacity than the leading code-specific transformers. The suggested framework therefore demonstrates, for the first time, the benefits of learning a universal decoder rather than a neural decoder optimized for a given code.

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.

We present ImplicitSLIM, a novel unsupervised learning approach for sparse high-dimensional data, with applications to collaborative filtering. Sparse linear methods (SLIM) and their variations show outstanding performance, but they are memory-intensive and hard to scale. ImplicitSLIM improves embedding-based models by extracting embeddings from SLIM-like models in a computationally cheap and memory-efficient way, without explicit learning of heavy SLIM-like models. We show that ImplicitSLIM improves performance and speeds up convergence for both state of the art and classical collaborative filtering methods. The source code for ImplicitSLIM, related models, and applications is available at https://github.com/ilya-shenbin/ImplicitSLIM.

Modern techniques for physical simulations rely on numerical schemes and mesh-refinement methods to address trade-offs between precision and complexity, but these handcrafted solutions are tedious and require high computational power. Data-driven methods based on large-scale machine learning promise high adaptivity by integrating long-range dependencies more directly and efficiently. In this work, we focus on computational fluid dynamics and address the shortcomings of a large part of the literature, which are based on fixed support for computations and predictions in the form of regular or irregular grids. We propose a novel setup to perform predictions in a continuous spatial and temporal domain while being trained on sparse observations. We formulate the task as a double observation problem and propose a solution with two interlinked dynamical systems defined on, respectively, the sparse positions and the continuous domain, which allows to forecast and interpolate a solution from the initial condition. Our practical implementation involves recurrent GNNs and a spatio-temporal attention observer capable of interpolating the solution at arbitrary locations. Our model not only generalizes to new initial conditions (as standard auto-regressive models do) but also performs evaluation at arbitrary space and time locations. We evaluate on three standard datasets in fluid dynamics and compare to strong baselines, which are outperformed in classical settings and the extended new task requiring continuous predictions.

The behavior of neural networks still remains opaque, and a recently widely noted phenomenon is that networks often achieve similar performance when initialized with different random parameters. This phenomenon has attracted significant attention in measuring the similarity between features learned by distinct networks. However, feature similarity could be vague in describing the same feature since equivalent features hardly exist. In this paper, we expand the concept of equivalent feature and provide the definition of what we call *functionally equivalent features*. These features produce equivalent output under certain transformations. Using this definition, we aim to derive a more intrinsic metric for the so-called *feature complexity* regarding the redundancy of features learned by a neural network at each layer. We offer a formal interpretation of our approach through the lens of category theory, a well-developed area in mathematics. To quantify the feature complexity, we further propose an efficient algorithm named Iterative Feature Merging. Our experimental results validate our ideas and theories from various perspectives. We empirically demonstrate that the functionally equivalence widely exists among different features learned by the same neural network and we could reduce the number of parameters of the network without affecting the performance. We have also drawn several interesting empirical findings, including: 1) the larger the network, the more redundant features it learns; 2) in particular, we show how to prune the networks based on our finding using direct equivalent feature merging, without fine-tuning which is often needed in peer network pruning methods; 3) same structured networks with higher feature complexity achieve better performance; 4) through the layers of a neural network, the feature complexity first increase then decrease; 5) for the image classification task, a group of functionally equivalent features may correspond to a specific semantic meaning. Source code will be made publicly available.

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.

Structure prediction of large protein complexes (a.k.a., protein multimer mod- elling, PMM) can be achieved through the one-by-one assembly using provided dimer structures and predicted docking paths. However, existing PMM methods struggle with vast search spaces and generalization challenges: (1) The assembly of a N -chain multimer can be depicted using graph structured data, with each chain represented as a node and assembly actions as edges. Thus the assembly graph can be arbitrary acyclic undirected connected graph, leading to the com- binatorial optimization space of N^(N −2) for the PMM problem. (2) Knowledge transfer in the PMM task is non-trivial. The gradually limited data availability as the chain number increases necessitates PMM models that can generalize across multimers of various chains. To address these challenges, we propose GAPN, a Generative Adversarial Policy Network powered by domain-specific rewards and adversarial loss through policy gradient for automatic PMM prediction. Specifi- cally, GAPN learns to efficiently search through the immense assembly space and optimize the direct docking reward through policy gradient. Importantly, we de- sign a adversarial reward function to enhance the receptive field of our model. In this way, GAPN will simultaneously focus on a specific batch of multimers and the global assembly rules learned from multimers with varying chain numbers. Empirically, we have achieved both significant accuracy (measured by RMSD and TM-Score) and efficiency improvements compared to leading complex mod- eling software. GAPN outperforms the state-of-the-art method (MoLPC) with up to 27% improvement in TM-Score, with a speed-up of 600×.

The optimal transport problem for measures supported on non-Euclidean spaces has recently gained ample interest in diverse applications involving representation learning. In this paper, we focus on circular probability measures, i.e., probability measures supported on the unit circle, and introduce a new computationally efficient metric for these measures, denoted as Linear Circular Optimal Transport (LCOT). The proposed metric comes with an explicit linear embedding that allows one to apply Machine Learning (ML) algorithms to the embedded measures and seamlessly modify the underlying metric for the ML algorithm to LCOT. We show that the proposed metric is rooted in the Circular Optimal Transport (COT) and can be considered the linearization of the COT metric with respect to a fixed reference measure. We provide a theoretical analysis of the proposed metric and derive the computational complexities for pairwise comparison of circular probability measures. Lastly, through a set of numerical experiments, we demonstrate the benefits of LCOT in learning representations from circular measures.

This paper presents a framework for learning state and action abstractions in sequential decision-making domains. Our framework, planning abstraction from language (PARL), utilizes language-annotated demonstrations to automatically discover a symbolic and abstract action space and induce a latent state abstraction based on it. PARL consists of three stages: 1) recovering object-level and action concepts, 2) learning state abstractions, abstract action feasibility, and transition models, and 3) applying low-level policies for abstract actions. During inference, given the task description, PARL first makes abstract action plans using the latent transition and feasibility functions, then refines the high-level plan using low-level policies. PARL generalizes across scenarios involving novel object instances and environments, unseen concept compositions, and tasks that require longer planning horizons than settings it is trained on.

Self-supervised heterogeneous graph learning has achieved promising results in various real applications, but it still suffers from the following issues: (i) meta-paths can be employed to capture the homophily in the heterogeneous graph, but meta-paths are human-defined, requiring substantial expert knowledge and computational costs; and (ii) the heterogeneity in the heterogeneous graph is usually underutilized, leading to the loss of task-related information. To solve these issues, this paper proposes to capture both homophily and heterogeneity in the heterogeneous graph without pre-defined meta-paths. Specifically, we propose to learn a self-expressive matrix to capture the homophily from the subspace and nearby neighbors. Meanwhile, we propose to capture the heterogeneity by aggregating the information of nodes from different types. We further design a consistency loss and a specificity loss, respectively, to extract the consistent information between homophily and heterogeneity and to preserve their specific task-related information. We theoretically analyze that the learned homophilous representations exhibit the grouping effect to capture the homophily, and considering both homophily and heterogeneity introduces more task-related information. Extensive experimental results verify the superiority of the proposed method on different downstream tasks.

Neural networks (NNs) that exploit strong inductive biases based on physical laws and symmetries have shown remarkable success in learning the dynamics of physical systems directly from their trajectory. However, these works focus only on the systems that follow deterministic dynamics, such as Newtonian or Hamiltonian. Here, we propose a framework, namely Brownian graph neural networks (BroGNet), combining stochastic differential equations (SDEs) and GNNs to learn Brownian dynamics directly from the trajectory. We modify the architecture of BroGNet to enforce linear momentum conservation of the system, which, in turn, provides superior performance on learning dynamics as revealed empirically. We demonstrate this approach on several systems, namely, linear spring, linear spring with binary particle types, and non-linear spring systems, all following Brownian dynamics at finite temperatures. We show that BroGNet significantly outperforms proposed baselines across all the benchmarked Brownian systems. In addition, we demonstrate zero-shot generalizability of BroGNet to simulate unseen system sizes that are two orders of magnitude larger and to different temperatures than those used during training. Finally, we show that BroGNet conserves the momentum of the system resulting in superior performance and data efficiency. Altogether, our study contributes to advancing the understanding of the intricate dynamics of Brownian motion and demonstrates the effectiveness of graph neural networks in modeling such complex systems.

We present Neural Spectral Methods, a technique to solve parametric Partial Differential Equations (PDEs), grounded in classical spectral methods. Our method uses orthogonal bases to learn PDE solutions as mappings between spectral coefficients, instantiating a spectral-based neural operator. In contrast to current machine learning approaches which enforce PDE constraints by minimizing the numerical quadrature of the residuals in the spatiotemporal domain, we leverage Parseval's identity and introduce a new training strategy through a spectral loss. Our spectral loss enables more efficient differentiation through the neural network, and substantially reduces training complexity. At inference time, the computational cost of our method remains constant, regardless of the spatiotemporal resolution of the domain. Our experimental results demonstrate that our method significantly outperforms previous machine learning approaches in terms of speed and accuracy by one to two orders of magnitude on multiple different problems, including reaction-diffusion, and forced and unforced Navier-Stokes equations. When compared to numerical solvers of the same accuracy, our method demonstrates a $10\times$ increase in performance speed. Our source code is publicly available at https://github.com/ASK-Berkeley/Neural-Spectral-Methods.

Current evaluation protocols predominantly assess physical reasoning in stationary scenes, creating a gap in evaluating agents' abilities to interact with dynamic events. While contemporary methods allow agents to modify initial scene configurations and observe consequences, they lack the capability to interact with events in real time. To address this, we introduce I-PHYRE, a framework that challenges agents to simultaneously exhibit intuitive physical reasoning, multi-step planning, and in-situ intervention. Here, intuitive physical reasoning refers to a quick, approximate understanding of physics to address complex problems; multi-step denotes the need for extensive sequence planning in I-PHYRE, considering each intervention can significantly alter subsequent choices; and in-situ implies the necessity for timely object manipulation within a scene, where minor timing deviations can result in task failure. We formulate four game splits to scrutinize agents' learning and generalization of essential principles of interactive physical reasoning, fostering learning through interaction with representative scenarios. Our exploration involves three planning strategies and examines several supervised and reinforcement agents' zero-shot generalization proficiency on I-PHYRE. The outcomes highlight a notable gap between existing learning algorithms and human performance, emphasizing the imperative for more research in enhancing agents with interactive physical reasoning capabilities. The environment and baselines will be made publicly available.

Decision-makers are often experts of their domain and take actions based on their domain knowledge. Doctors, for instance, may prescribe treatments by predicting the likely outcome of each available treatment. Actions of an expert thus naturally encode part of their domain knowledge, and can help make inferences within the same domain: Knowing doctors try to prescribe the best treatment for their patients, we can tell treatments prescribed more frequently are likely to be more effective. Yet in machine learning, the fact that most decision-makers are experts is often overlooked, and “expertise” is seldom leveraged as an inductive bias. This is especially true for the literature on treatment effect estimation, where often the only assumption made about actions is that of overlap. In this paper, we argue that expertise—particularly the type of expertise the decision-makers of a domain are likely to have—can be informative in designing and selecting methods for treatment effect estimation. We formally define two types of expertise, predictive and prognostic, and demonstrate empirically that: (i) the prominent type of expertise in a domain significantly influences the performance of different methods in treatment effect estimation, and (ii) it is possible to predict the type of expertise present in a dataset, which can provide a quantitative basis for model selection.

Recent years have seen growing interest in developing and applying perceptual similarity metrics. Research has shown the superiority of perceptual metrics over pixel-wise metrics in aligning with human perception and serving as a proxy for the human visual system. On the other hand, as perceptual metrics rely on neural networks, there is a growing concern regarding their resilience, given the established vulnerability of neural networks to adversarial attacks. It is indeed logical to infer that perceptual metrics may inherit both the strengths and shortcomings of neural networks. In this work, we demonstrate the vulnerability of state-of-the-art perceptual similarity metrics based on an ensemble of ViT-based feature extractors to adversarial attacks. We then propose a framework to train a robust perceptual similarity metric called LipSim (Lipschitz Similarity Metric) with provable guarantees. By leveraging 1-Lipschitz neural networks as the backbone, LipSim provides guarded areas around each data point and certificates for all perturbations within an $\ell_2$ ball. Finally, a comprehensive set of experiments shows the performance of LipSim in terms of natural and certified scores and on the image retrieval application.

Metal-organic frameworks (MOFs) are of immense interest in applications such as gas storage and carbon capture due to their exceptional porosity and tunable chemistry. Their modular nature has enabled the use of template-based methods to generate hypothetical MOFs by combining molecular building blocks in accordance with known network topologies. However, the ability of these methods to identify top-performing MOFs is often hindered by the limited diversity of the resulting chemical space. In this work, we propose MOFDiff: a coarse-grained (CG) diffusion model that generates CG MOF structures through a denoising diffusion process over the coordinates and identities of the building blocks. The all-atom MOF structure is then determined through a novel assembly algorithm. As the diffusion model generates 3D MOF structures by predicting scores in E(3), we employ equivariant graph neural networks that respect the permutational and roto-translational symmetries. We comprehensively evaluate our model's capability to generate valid and novel MOF structures and its effectiveness in designing outstanding MOF materials for carbon capture applications with molecular simulations.