ICML 2024 论文列表

The development of deep learning architectures is a resource-demanding process, due to a vast design space, long prototyping times, and high compute costs associated with at-scale model training and evaluation. We set out to simplify this process by grounding it in an end-to-end mechanistic architecture design (MAD) pipeline, encompassing small-scale capability unit tests predictive of scaling laws. Through a suite of synthetic token manipulation tasks such as compression and recall, designed to probe capabilities, we identify and test new hybrid architectures constructed from a variety of computational primitives. We experimentally validate the resulting architectures via an extensive compute-optimal and a new state-optimal scaling law analysis, training over 500 language models between 70M to 7B parameters. Surprisingly, we find MAD synthetics to correlate with compute-optimal perplexity, enabling accurate evaluation of new architectures via isolated proxy tasks. The new architectures found via MAD, based on simple ideas such as hybridization and sparsity, outperform state-of-the-art Transformer, convolutional, and recurrent architectures (Transformer++, Hyena, Mamba) in scaling, both at compute-optimal budgets and in overtrained regimes. Overall, these results provide evidence that performance on curated synthetic tasks can be predictive of scaling laws, and that an optimal architecture should leverage specialized layers via a hybrid topology.

De novo protein design aims to create novel protein structures and sequences unseen in nature. Recent structure-oriented design methods typically employ a two-stage strategy, where structure design and sequence design modules are trained separately, and the backbone structures and sequences are generated sequentially in inference. While diffusion-based generative models like RFdiffusion show great promise in structure design, they face inherent limitations within the two-stage framework. First, the sequence design module risks overfitting, as the accuracy of the generated structures may not align with that of the crystal structures used for training. Second, the sequence design module lacks interaction with the structure design module to further optimize the generated structures. To address these challenges, we propose CarbonNovo, a unified energy-based model for jointly generating protein structure and sequence. Specifically, we leverage a score-based generative model and Markov Random Fields for describing the energy landscape of protein structure and sequence. In CarbonNovo, the structure and sequence design module communicates at each diffusion step, encouraging the generation of more coherent structure-sequence pairs. Moreover, the unified framework allows for incorporating the protein language models as evolutionary constraints for generated proteins. The rigorous evaluation demonstrates that CarbonNovo outperforms two-stage methods across various metrics, including designability, novelty, sequence plausibility, and Rosetta Energy.

Interpretable graph neural networks (XGNNs ) are widely adopted in various scientific applications involving graph-structured data. Existing XGNNs predominantly adopt the attention-based mechanism to learn edge or node importance for extracting and making predictions with the interpretable subgraph. However, the representational properties and limitations of these methods remain inadequately explored. In this work, we present a theoretical framework that formulates interpretable subgraph learning with the multilinear extension of the subgraph distribution, coined as subgraph multilinear extension (SubMT). Extracting the desired interpretable subgraph requires an accurate approximation of SubMT, yet we find that the existing XGNNs can have a huge gap in fitting SubMT. Consequently, the SubMT approximation failure will lead to the degenerated interpretability of the extracted subgraphs. To mitigate the issue, we design a new XGNN architecture called Graph Multilinear neT (GMT), which is provably more powerful in approximating SubMT. We empirically validate our theoretical findings on a number of graph classification benchmarks. The results demonstrate that GMT outperforms the state-of-the-art up to 10% in terms of both interpretability and generalizability across 12 regular and geometric graph benchmarks.

We study contextual bandits with low-rank structure where, in each round, if the (context, arm) pair $(i,j)\in [m]\times [n]$ is selected, the learner observes a noisy sample of the $(i,j)$-th entry of an unknown low-rank reward matrix. Successive contexts are generated randomly in an i.i.d. manner and are revealed to the learner. For such bandits, we present efficient algorithms for policy evaluation, best policy identification and regret minimization. For policy evaluation and best policy identification, we show that our algorithms are nearly minimax optimal. For instance, the number of samples required to return an $\varepsilon$-optimal policy with probability at least $1-\delta$ typically scales as $\frac{m+n}{\varepsilon^2}\log(1/\delta)$. Our regret minimization algorithm enjoys minimax guarantees typically scaling as $r^{5/4}(m+n)^{3/4}\sqrt{T}$, which improves over existing algorithms. All the proposed algorithms consist of two phases: they first leverage spectral methods to estimate the left and right singular subspaces of the low-rank reward matrix. We show that these estimates enjoy tight error guarantees in the two-to-infinity norm. This in turn allows us to reformulate our problems as a misspecified linear bandit problem with dimension roughly $r(m+n)$ and misspecification controlled by the subspace recovery error, as well as to design the second phase of our algorithms efficiently.

We provide an efficient replicable algorithm for the problem of learning large-margin halfspaces. Our results improve upon the algorithms provided by Impagliazzo, Lei, Pitassi, and Sorrell (STOC, 2022). We design the first dimension-independent replicable algorithm for this task which runs in polynomial time, is proper, and has strictly improved sample complexity compared to the one achieved by Impagliazzo et al. (STOC, 2022) with respect to all the relevant parameters. Moreover, our algorithm has sample complexity that is optimal with respect to the accuracy parameter $\epsilon$. Departing from the requirement of polynomial time algorithms, using the DP-to-Replicability reduction of Bun et al. (STOC 2023), we show how to obtain a replicable algorithm for large-margin halfspaces with improved sample complexity with respect to the margin parameter $\tau$, but running time doubly exponential in $1/\tau^2$ and worse sample complexity dependence on $\epsilon$ than our previous algorithm. We then design an improved algorithm with better sample complexity than both of our previous algorithms and running time exponential in $1/\tau^{2}.$

Heuristics are widely used for dealing with complex search and optimization problems. However, manual design of heuristics can be often very labour extensive and requires rich working experience and knowledge. This paper proposes Evolution of Heuristic (EoH), a novel evolutionary paradigm that leverages both Large Language Models (LLMs) and Evolutionary Computation (EC) methods for Automatic Heuristic Design (AHD). EoH represents the ideas of heuristics in natural language, termed thoughts. They are then translated into executable codes by LLMs. The evolution of both thoughts and codes in an evolutionary search framework makes it very effective and efficient for generating high-performance heuristics. Experiments on three widely studied combinatorial optimization benchmark problems demonstrate that EoH outperforms commonly used handcrafted heuristics and other recent AHD methods including FunSearch. Particularly, the heuristic produced by EoH with a low computational budget (in terms of the number of queries to LLMs) significantly outperforms widely-used human hand-crafted baseline algorithms for the online bin packing problem.

Learning a reward function from demonstrations suffers from low sample-efficiency. Even with abundant data, current inverse reinforcement learning methods that focus on learning from a single environment can fail to handle slight changes in the environment dynamics. We tackle these challenges through adaptive environment design. In our framework, the learner repeatedly interacts with the expert, with the former selecting environments to identify the reward function as quickly as possible from the expert’s demonstrations in said environments. This results in improvements in both sample-efficiency and robustness, as we show experimentally, for both exact and approximate inference.

Enzymes are genetically encoded biocatalysts capable of accelerating chemical reactions. How can we automatically design functional enzymes? In this paper, we propose EnzyGen, an approach to learn a unified model to design enzymes across all functional families. Our key idea is to generate an enzyme's amino acid sequence and their three-dimensional (3D) coordinates based on functionally important sites and substrates corresponding to a desired catalytic function. These sites are automatically mined from enzyme databases. EnzyGen consists of a novel interleaving network of attention and neighborhood equivariant layers, which captures both long-range correlation in an entire protein sequence and local influence from nearest amino acids in 3D space. To learn the generative model, we devise a joint training objective, including a sequence generation loss, a position prediction loss and an enzyme-substrate interaction loss. We further construct EnzyBench, a dataset with 3157 enzyme families, covering all available enzymes within the protein data bank (PDB). Experimental results show that our EnzyGen consistently achieves the best performance across all 323 testing families, surpassing the best baseline by 10.79% in terms of substrate binding affinity. These findings demonstrate EnzyGen's superior capability in designing well-folded and effective enzymes binding to specific substrates with high affinities. Our code, model and dataset are provided at https://github.com/LeiLiLab/EnzyGen.

Neural networks extract features from data using stochastic gradient descent (SGD). In particular, higher-order input cumulants (HOCs) are crucial for their performance. However, extracting information from the $p$th cumulant of $d$-dimensional inputs is computationally hard: the number of samples required to recover a single direction from an order-$p$ tensor (tensor PCA) using SGD grows as $d^{p−1}$, which is prohibitive for high-dimensional inputs. This result raises the question of how neural networks extract relevant directions from the HOCs of their inputs efficiently. Here, we show that correlations between latent variables along the directions encoded in different input cumulants speed up learning from higher-order correlations. We show this effect analytically by deriving nearly sharp thresholds for the number of samples required by a single neuron to recover these directions using online SGD from a random start in high dimensions. Our analytical results are confirmed in simulations of two-layer neural networks and unveil a new mechanism for hierarchical learning in neural networks

Learning effective negotiation strategies poses two key challenges: the exploration-exploitation dilemma and dealing with large action spaces. However, there is an absence of learning-based approaches that effectively address these challenges in negotiation. This paper introduces a comprehensive formulation to tackle various negotiation problems. Our approach leverages contextual combinatorial multi-armed bandits, with the bandits resolving the exploration-exploitation dilemma, and the combinatorial nature handles large action spaces. Building upon this formulation, we introduce NegUCB, a novel method that also handles common issues such as partial observations and complex reward functions in negotiation. NegUCB is contextual and tailored for full-bandit feedback without constraints on the reward functions. Under mild assumptions, it ensures a sub-linear regret upper bound. Experiments conducted on three negotiation tasks demonstrate the superiority of our approach.

Hindsight experience replay and goal relabeling are successful in reinforcement learning (RL) since they enable agents to learn from failures. Despite their successes, we lack a theoretical understanding, such as (i) why hindsight experience replay improves sample efficiency and (ii) how to design a relabeling method that achieves sample efficiency. To this end, we construct an example to show the information-theoretical improvement in sample efficiency achieved by goal relabeling. Our example reveals that goal relabeling can enhance sample efficiency and exploit the rich information in observations through better hypothesis elimination. Based on these insights, we develop an RL algorithm called GOALIVE. To analyze the sample complexity of GOALIVE, we introduce a complexity measure, the goal-conditioned Bellman-Eluder (GOAL-BE) dimension, which characterizes the sample complexity of goal-conditioned RL problems. Compared to the Bellman-Eluder dimension, the goal-conditioned version offers an exponential improvement in the best case. To the best of our knowledge, our work provides the first characterization of the theoretical improvement in sample efficiency achieved by goal relabeling.

Generative models have the potential to accelerate key steps in the discovery of novel molecular therapeutics and materials. Diffusion models have recently emerged as a powerful approach, excelling at unconditional sample generation and, with data-driven guidance, conditional generation within their training domain. Reliably sampling from high-value regions beyond the training data, however, remains an open challenge---with current methods predominantly focusing on modifying the diffusion process itself. In this paper, we develop context-guided diffusion (CGD), a simple plug-and-play method that leverages unlabeled data and smoothness constraints to improve the out-of-distribution generalization of guided diffusion models. We demonstrate that this approach leads to substantial performance gains across various settings, including continuous, discrete, and graph-structured diffusion processes with applications across drug discovery, materials science, and protein design.

Can a mere next-token predictor faithfully model human thinking? Our work is aimed at crystallizing this intuitive concern, which is currently fragmented in the literature. First, we emphasize isolating the two phases of next-token prediction that are often conflated: autoregression during inference vs. teacher-forcing during training. We argue that the previously-identified problem of "exponential error accumulation" is a symptom of autoregressive inference. But more concerningly, we identify that teacher-forcing can let the model fit the training data by cheating, causing total in-distribution failure. We design a minimal planning task where empirically both the Transformer and the Mamba architecture fail in this manner - remarkably, despite the task being easy to learn. Overall, our work consolidates these and other essential arguments surrounding next-token prediction. We hope this effort can ground future discussions and inspire explorations beyond the next-token prediction paradigm.

Therapeutic peptides have proven to have great pharmaceutical value and potential in recent decades. However, methods of AI-assisted peptide drug discovery are not fully explored. To fill the gap, we propose a target-aware peptide design method called PPFlow, based on conditional flow matching on torus manifolds, to model the internal geometries of torsion angles for the peptide structure design. Besides, we establish a protein-peptide binding dataset named PPBench2024 to fill the void of massive data for the task of structure-based peptide drug design and to allow the training of deep learning methods. Extensive experiments show that PPFlow reaches state-of-the-art performance in tasks of peptide drug generation and optimization in comparison with baseline models, and can be generalized to other tasks including docking and side-chain packing.

Increasing works for antibody design are emerging to generate sequences and structures in Complementarity Determining Regions (CDRs), but problems still exist. We focus on two of them: (i) authenticity of the generated structure and (ii) rationality of the affinity maturation, and propose GeoAB as a solution. In specific, GeoAB-Designergenerates CDR structures with realistic internal geometries, composed of a generative geometry initializer (Geo-Initializer) and a position refiner (Geo-Refiner); GeoAB-Optimizer achieves affinity maturation by accurately predicting both the mutation effects and structures of mutant antibodies with the same network architecture as Geo-Refiner. Experiments show that GeoAB achieves state-of-the-art performance in CDR co-design and mutation effect predictions, and fulfills the discussed tasks effectively.

In the realm of Graph Neural Networks (GNNs), two exciting research directions have recently emerged: Subgraph GNNs and Graph Transformers. In this paper, we propose an architecture that integrates both approaches, dubbed *Subgraphormer*, which combines the enhanced expressive power, message-passing mechanisms, and aggregation schemes from Subgraph GNNs with attention and positional encodings, arguably the most important components in Graph Transformers. Our method is based on an intriguing new connection we reveal between Subgraph GNNs and product graphs, suggesting that Subgraph GNNs can be formulated as Message Passing Neural Networks (MPNNs) operating on a product of the graph with itself. We use this formulation to design our architecture: first, we devise an attention mechanism based on the connectivity of the product graph. Following this, we propose a novel and efficient positional encoding scheme for Subgraph GNNs, which we derive as a positional encoding for the product graph. Our experimental results demonstrate significant performance improvements over both Subgraph GNNs and Graph Transformers on a wide range of datasets.

Visually-conditioned language models (VLMs) have seen growing adoption in applications such as visual dialogue, scene understanding, and robotic task planning; adoption that has fueled a wealth of new models such as LLaVa, InstructBLIP, and PaLI-3. Despite the volume of new releases, key design decisions around image preprocessing, architecture, and optimization are under-explored, making it challenging to understand what factors account for model performance – a challenge further complicated by the lack of objective, consistent evaluations. To address these gaps, we first compile a suite of standardized evaluations spanning visual question answering, object localization, and challenge sets that probe properties such as hallucination; evaluations that provide fine-grained insight VLM capabilities. Second, we rigorously investigate VLMs along key design axes, including pretrained visual representations and training from base vs. instruct-tuned language models, amongst others. We couple our analysis with three resource contributions: (1) a unified framework for evaluating VLMs, (2) optimized, flexible training code, and (3) checkpoints for all models, including a family of VLMs at the 7-13B scale that strictly outperform InstructBLIP and LLaVa v1.5, the state-of-the-art in open VLMs.

Neural Radiance Fields (NeRFs) have emerged as powerful tools for capturing detailed 3D scenes through continuous volumetric representations. Recent NeRFs utilize feature grids to improve rendering quality and speed; however, these representations introduce significant storage overhead. This paper presents a novel method for efficiently compressing a grid-based NeRF model, addressing the storage overhead concern. Our approach is based on the non-linear transform coding paradigm, employing neural compression for compressing the model's feature grids. Due to the lack of training data involving many i.i.d scenes, we design an encoder-free, end-to-end optimized approach for individual scenes, using lightweight decoders. To leverage the spatial inhomogeneity of the latent feature grids, we introduce an importance-weighted rate-distortion objective and a sparse entropy model employing a masking mechanism. Our experimental results validate that our proposed method surpasses existing works in terms of grid-based NeRF compression efficacy and reconstruction quality.

Peptides, short chains of amino acid residues, play a vital role in numerous biological processes by interacting with other target molecules, offering substantial potential in drug discovery. In this work, we present *PepFlow*, the first multi-modal deep generative model grounded in the flow-matching framework for the design of full-atom peptides that target specific protein receptors. Drawing inspiration from the crucial roles of residue backbone orientations and side-chain dynamics in protein-peptide interactions, we characterize the peptide structure using rigid backbone frames within the $\mathrm{SE}(3)$ manifold and side-chain angles on high-dimensional tori. Furthermore, we represent discrete residue types in the peptide sequence as categorical distributions on the probability simplex. By learning the joint distributions of each modality using derived flows and vector fields on corresponding manifolds, our method excels in the fine-grained design of full-atom peptides. Harnessing the multi-modal paradigm, our approach adeptly tackles various tasks such as fix-backbone sequence design and side-chain packing through partial sampling. Through meticulously crafted experiments, we demonstrate that *PepFlow* exhibits superior performance in comprehensive benchmarks, highlighting its significant potential in computational peptide design and analysis.