ICML 2023 Papers

Learning shared structures across changing environments enables an agent to efficiently retain obtained knowledge and transfer it between environments. A skill is a promising concept to represent shared structures. Several recent works proposed unsupervised skill discovery algorithms that can discover useful skills without a reward function. However, they focused on discovering skills in stationary environments or assumed that a skill being trained is fixed within an episode, which is insufficient to learn and represent shared structures. In this paper, we introduce a new unsupervised skill discovery algorithm that discovers a set of skills that can represent shared structures across changing environments. Our algorithm trains incremental skills and encourages a new skill to expand state coverage obtained with compositions of previously learned skills. We also introduce a skill evaluation process to prevent our skills from containing redundant skills, a common issue in previous work. Our experimental results show that our algorithm acquires skills that represent shared structures across changing maze navigation and locomotion environments. Furthermore, we demonstrate that our skills are more useful than baselines on downstream tasks.

Activity and property prediction models are the central workhorses in drug discovery and materials sciences, but currently, they have to be trained or fine-tuned for new tasks. Without training or fine-tuning, scientific language models could be used for such low-data tasks through their announced zero- and few-shot capabilities. However, their predictive quality at activity prediction is lacking. In this work, we envision a novel type of activity prediction model that is able to adapt to new prediction tasks at inference time, via understanding textual information describing the task. To this end, we propose a new architecture with separate modules for chemical and natural language inputs, and a contrastive pretraining objective on data from large biochemical databases. In extensive experiments, we show that our method CLAMP yields improved predictive performance on few-shot learning benchmarks and zero-shot problems in drug discovery. We attribute the advances of our method to the modularized architecture and to our pre-training objective.

Molecule pretraining has quickly become the go-to schema to boost the performance of AI-based drug discovery. Naturally, molecules can be represented as 2D topological graphs or 3D geometric point clouds. Although most existing pertaining methods focus on merely the single modality, recent research has shown that maximizing the mutual information (MI) between such two modalities enhances the molecule representation ability. Meanwhile, existing molecule multi-modal pretraining approaches approximate MI based on the representation space encoded from the topology and geometry, thus resulting in the loss of critical structural information of molecules. To address this issue, we propose MoleculeSDE. MoleculeSDE leverages group symmetric (e.g., SE(3)-equivariant and reflection-antisymmetric) stochastic differential equation models to generate the 3D geometries from 2D topologies, and vice versa, directly in the input space. It not only obtains tighter MI bound but also enables prosperous downstream tasks than the previous work. By comparing with 17 pretraining baselines, we empirically verify that MoleculeSDE can learn an expressive representation with state-of-the-art performance on 26 out of 32 downstream tasks.

The discovery of therapeutics to treat genetically-driven pathologies relies on identifying genes involved in the underlying disease mechanism. Existing approaches search over the billions of potential interventions to maximize the expected influence on the target phenotype. However, to reduce the risk of failure in future stages of trials, practical experiment design aims to find a set of interventions that maximally change a target phenotype via diverse mechanisms. We propose DiscoBAX - a sample-efficient method for maximizing the rate of significant discoveries per experiment while simultaneously probing for a wide range of diverse mechanisms during a genomic experiment campaign. We provide theoretical guarantees of optimality under standard assumptions, and conduct a comprehensive experimental evaluation covering both synthetic as well as real-world experimental design tasks. DiscoBAX outperforms existing state-of-the-art methods for experimental design, selecting effective and diverse perturbations in biological systems.

We study the autonomous exploration (AX) problem proposed by Lim & Auer (2012). In this setting, the objective is to discover a set of $\epsilon$-optimal policies reaching a set $\mathcal{S}\_L^{\rightarrow}$ of incrementally $L$-controllable states. We introduce a novel layered decomposition of the set of incrementally $L$-controllable states that is based on the iterative application of a state-expansion operator. We leverage these results to design Layered Autonomous Exploration (LAE), a novel algorithm for AX that attains a sample complexity of $\tilde{\mathcal{O}}(LS^{\rightarrow}\_{L(1+\epsilon)}\Gamma\_{L(1+\epsilon)} A \ln^{12}(S^{\rightarrow}\_{L(1+\epsilon)})/\epsilon^2)$, where $S^{\rightarrow}\_{L(1+\epsilon)}$ is the number of states that are incrementally $L(1+\epsilon)$-controllable, $A$ is the number of actions, and $\Gamma\_{L(1+\epsilon)}$ is the branching factor of the transitions over such states. LAE improves over the algorithm of Tarbouriech et al. (2020a) by a factor of $L^2$ and it is the first algorithm for AX that works in a countably-infinite state space. Moreover, we show that, under a certain identifiability assumption, LAE achieves minimax-optimal sample complexity of $\tilde{\mathcal{O}}(LS^{\rightarrow}\_{L}A\ln^{12}(S^{\rightarrow}\_{L})/\epsilon^2)$, outperforming existing algorithms and matching for the first time the lower bound proved by Cai et al. (2022) up to logarithmic factors.

Generating molecules with high binding affinities to target proteins (a.k.a. structure-based drug design) is a fundamental and challenging task in drug discovery. Recently, deep generative models have achieved remarkable success in generating 3D molecules conditioned on the protein pocket. However, most existing methods consider molecular generation for protein pockets independently while neglecting the underlying connections such as subpocket-level similarities. Subpockets are the local protein environments of ligand fragments and pockets with similar subpockets may bind the same molecular fragment (motif) even though their overall structures are different. Therefore, the trained models can hardly generalize to unseen protein pockets in real-world applications. In this paper, we propose a novel method DrugGPS for generalizable structure-based drug design. With the biochemical priors, we propose to learn subpocket prototypes and construct a global interaction graph to model the interactions between subpocket prototypes and molecular motifs. Moreover, a hierarchical graph transformer encoder and motif-based 3D molecule generation scheme are used to improve the model's performance. The experimental results show that our model consistently outperforms baselines in generating realistic drug candidates with high affinities in challenging out-of-distribution settings.

We present a constraint-based algorithm for learning causal structures from observational time-series data, in the presence of latent confounders. We assume a discrete-time, stationary structural vector autoregressive process, with both temporal and contemporaneous causal relations. One may ask if temporal and contemporaneous relations should be treated differently. The presented algorithm gradually refines a causal graph by learning long-term temporal relations before short-term ones, where contemporaneous relations are learned last. This ordering of causal relations to be learnt leads to a reduction in the required number of statistical tests. We validate this reduction empirically and demonstrate that it leads to higher accuracy for synthetic data and more plausible causal graphs for real-world data compared to state-of-the-art algorithms.

Machine learning-driven human behavior analysis is gaining attention in behavioral/mental healthcare, due to its potential to identify behavioral patterns that cannot be recognized by traditional assessments. Real-life applications, such as digital behavioral biomarker identification, often require the discovery of complex spatiotemporal patterns in multimodal data, which is largely under-explored. To fill this gap, we propose a novel model that integrates uniquely designed Deep Temporal Sets (DTS) with Evidential Reinforced Attentions (ERA). DTS captures complex temporal relationships in the input and generates a set-based representation, while ERA captures the policy network's uncertainty and conducts evidence-aware exploration to locate attentive regions in behavioral data. Using child-computer interaction data as a testing platform, we demonstrate the effectiveness of DTS-ERA in differentiating children with Autism Spectrum Disorder and typically developing children based on sequential multimodal visual and touch behaviors. Comparisons with baseline methods show that our model achieves superior performance and has the potential to provide objective, quantitative, and precise analysis of complex human behaviors.

Automatically discovering composable abstractions from raw perceptual data is a long-standing challenge in machine learning. Recent slot-based neural networks that learn about objects in a self-supervised manner have made exciting progress in this direction. However, they typically fall short at adequately capturing spatial symmetries present in the visual world, which leads to sample inefficiency, such as when entangling object appearance and pose. In this paper, we present a simple yet highly effective method for incorporating spatial symmetries via slot-centric reference frames. We incorporate equivariance to per-object pose transformations into the attention and generation mechanism of Slot Attention by translating, scaling, and rotating position encodings. These changes result in little computational overhead, are easy to implement, and can result in large gains in terms of data efficiency and overall improvements to object discovery. We evaluate our method on a wide range of synthetic object discovery benchmarks namely CLEVR, Tetrominoes, CLEVRTex, Objects Room and MultiShapeNet, and show promising improvements on the challenging real-world Waymo Open dataset.

Causal discovery, the task of discovering the causal graph over a set of observed variables $X_1,\ldots,X_m$, is a challenging problem. One of the cornerstone assumptions is that of causal sufficiency: that *all* common causes of *all* measured variables have been observed. When it does not hold, causal discovery algorithms making this assumption return networks with many spurious edges. In this paper, we propose a nonlinear causal model involving hidden confounders. We show that it is identifiable from only the observed data and propose an efficient method for recovering this causal model. At the heart of our approach is a variational autoencoder which parametrizes both the causal interactions between observed variables as well as the influence of the unobserved confounders. Empirically we show that it outperforms other state-of-the-art methods for causal discovery under latent confounding on synthetic and real-world data.

Evaluating the performance of machine learning models under distribution shifts is challenging, especially when we only have unlabeled data from the shifted (target) domain, along with labeled data from the original (source) domain. Recent work suggests that the notion of *disagreement*, the degree to which two models trained with different randomness differ on the same input, is a key to tackling this problem. Experimentally, disagreement and prediction error have been shown to be strongly connected, which has been used to estimate model performance. Experiments have led to the discovery of the *disagreement-on-the-line* phenomenon, whereby the classification error under the target domain is often a linear function of the classification error under the source domain; and whenever this property holds, disagreement under the source and target domain follow the same linear relation. In this work, we develop a theoretical foundation for analyzing disagreement in high-dimensional random features regression; and study under what conditions the disagreement-on-the-line phenomenon occurs in our setting. Experiments on CIFAR-10-C, Tiny ImageNet-C, and Camelyon17 are consistent with our theory and support the universality of the theoretical findings.

Adversarial poisoning attacks pose huge threats to various machine learning applications. Especially, the recent accumulative poisoning attacks show that it is possible to achieve irreparable harm on models via a sequence of imperceptible attacks followed by a trigger batch. Due to the limited data-level discrepancy in real-time data streaming, current defensive methods are indiscriminate in handling the poison and clean samples. In this paper, we dive into the perspective of model dynamics and propose a novel information measure, namely, Memorization Discrepancy, to explore the defense via the model-level information. By implicitly transferring the changes in the data manipulation to that in the model outputs, Memorization Discrepancy can discover the imperceptible poison samples based on their distinct dynamics from the clean samples. We thoroughly explore its properties and propose Discrepancy-aware Sample Correction (DSC) to defend against accumulative poisoning attacks. Extensive experiments comprehensively characterized Memorization Discrepancy and verified its effectiveness. The code is publicly available at: https://github.com/tmlr-group/Memorization-Discrepancy.

Causal discovery with latent confounders is an important but challenging task in many scientific areas. Despite the success of some overcomplete independent component analysis (OICA) based methods in certain domains, they are computationally expensive and can easily get stuck into local optima. We notice that interestingly, by making use of higher-order cumulants, there exists a closed-form solution to OICA in specific cases, e.g., when the mixing procedure follows the One-Latent-Component structure. In light of the power of the closed-form solution to OICA corresponding to the One-Latent-Component structure, we formulate a way to estimate the mixing matrix using the higher-order cumulants, and further propose the testable One-Latent-Component condition to identify the latent variables and determine causal orders. By iteratively removing the share identified latent components, we successfully extend the results on the One-Latent-Component structure to the Multi-Latent-Component structure and finally provide a practical and asymptotically correct algorithm to learn the causal structure with latent variables. Experimental results illustrate the asymptotic correctness and effectiveness of the proposed method.

Antibodies are Y-shaped proteins that neutralize pathogens and constitute the core of our adaptive immune system. De novo generation of new antibodies that target specific antigens holds the key to accelerating vaccine discovery. However, this co-design of the amino acid sequence and the 3D structure subsumes and accentuates, some central challenges from multiple tasks including protein folding (sequence to structure), inverse folding (structure to sequence), and docking (binding). We strive to surmount these challenges with a new generative model AbODE that extends graph PDEs to accommodate both contextual information and external interactions. Unlike existing approaches, AbODE uses a single round of full-shot decoding, and elicits continuous differential attention that encapsulates, and evolves with, latent interactions within the antibody as well as those involving the antigen. We unravel fundamental connections between AbODE and temporal networks as well as graph-matching networks. The proposed model significantly outperforms existing methods on standard metrics across benchmarks.

One of the key capabilities of intelligent agents is the ability to discover useful skills without external supervision. However, the current unsupervised skill discovery methods are often limited to acquiring simple, easy-to-learn skills due to the lack of incentives to discover more complex, challenging behaviors. We introduce a novel unsupervised skill discovery method, Controllability-aware Skill Discovery (CSD), which actively seeks complex, hard-to-control skills without supervision. The key component of CSD is a controllability-aware distance function, which assigns larger values to state transitions that are harder to achieve with the current skills. Combined with distance-maximizing skill discovery, CSD progressively learns more challenging skills over the course of training as our jointly trained distance function reduces rewards for easy-to-achieve skills. Our experimental results in six robotic manipulation and locomotion environments demonstrate that CSD can discover diverse complex skills including object manipulation and locomotion skills with no supervision, significantly outperforming prior unsupervised skill discovery methods. Videos and code are available at https://seohong.me/projects/csd/

Accelerating the discovery of novel and more effective therapeutics is an important pharmaceutical problem in which deep learning is playing an increasingly significant role. However, real-world drug discovery tasks are often characterized by a scarcity of labeled data and significant covariate shift---a setting that poses a challenge to standard deep learning methods. In this paper, we present Q-SAVI, a probabilistic model able to address these challenges by encoding explicit prior knowledge of the data-generating process into a prior distribution over functions, presenting researchers with a transparent and probabilistically principled way to encode data-driven modeling preferences. Building on a novel, gold-standard bioactivity dataset that facilitates a meaningful comparison of models in an extrapolative regime, we explore different approaches to induce data shift and construct a challenging evaluation setup. We then demonstrate that using Q-SAVI to integrate contextualized prior knowledge of drug-like chemical space into the modeling process affords substantial gains in predictive accuracy and calibration, outperforming a broad range of state-of-the-art self-supervised pre-training and domain adaptation techniques.

Designing 3D ligands within a target binding site is a fundamental task in drug discovery. Existing structured-based drug design methods treat all ligand atoms equally, which ignores different roles of atoms in the ligand for drug design and can be less efficient for exploring the large drug-like molecule space. In this paper, inspired by the convention in pharmaceutical practice, we decompose the ligand molecule into two parts, namely arms and scaffold, and propose a new diffusion model, DecompDiff, with decomposed priors over arms and scaffold. In order to facilitate the decomposed generation and improve the properties of the generated molecules, we incorporate both bond diffusion in the model and additional validity guidance in the sampling phase. Extensive experiments on CrossDocked2020 show that our approach achieves state-of-the-art performance in generating high-affinity molecules while maintaining proper molecular properties and conformational stability, with up to $-8.39$ Avg. Vina Dock score and $24.5\%$ Success Rate. The code is provided at https://github.com/bytedance/DecompDiff

Designing protein sequences with desired biological function is crucial in biology and chemistry. Recent machine learning methods use a surrogate sequence-function model to replace the expensive wet-lab validation. How can we efficiently generate diverse and novel protein sequences with high fitness? In this paper, we propose IsEM-Pro, an approach to generate protein sequences towards a given fitness criterion. At its core, IsEM-Pro is a latent generative model, augmented by combinatorial structure features from a separately learned Markov random fields (MRFs). We develop an Monte Carlo Expectation-Maximization method (MCEM) to learn the model. During inference, sampling from its latent space enhances diversity while its MRFs features guide the exploration in high fitness regions. Experiments on eight protein sequence design tasks show that our IsEM-Pro outperforms the previous best methods by at least 55% on average fitness score and generates more diverse and novel protein sequences.

Despite the success of equivariant neural networks in scientific applications, they require knowing the symmetry group a priori. However, it may be difficult to know which symmetry to use as an inductive bias in practice. Enforcing the wrong symmetry could even hurt the performance. In this paper, we propose a framework, LieGAN, to *automatically discover equivariances* from a dataset using a paradigm akin to generative adversarial training. Specifically, a generator learns a group of transformations applied to the data, which preserve the original distribution and fool the discriminator. LieGAN represents symmetry as interpretable Lie algebra basis and can discover various symmetries such as the rotation group $\mathrm{SO}(n)$, restricted Lorentz group $\mathrm{SO}(1,3)^+$ in trajectory prediction and top-quark tagging tasks. The learned symmetry can also be readily used in several existing equivariant neural networks to improve accuracy and generalization in prediction.