ICLR 2024 Papers

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods.

Cooperative multi-agent reinforcement learning (MARL) is extensively used for solving complex cooperative tasks, and value decomposition methods are a prevalent approach for this domain. However, these methods have not been successful in addressing both homogeneous and heterogeneous tasks simultaneously which is a crucial aspect for the practical application of cooperative agents. On one hand, value decomposition methods demonstrate superior performance in homogeneous tasks. Nevertheless, they tend to produce agents with similar policies, which is unsuitable for heterogeneous tasks. On the other hand, solutions based on personalized observation or assigned roles are well-suited for heterogeneous tasks. However, they often lead to a trade-off situation where the agent's performance in homogeneous scenarios is negatively affected due to the aggregation of distinct policies. An alternative approach is to adopt sequential execution policies, which offer a flexible form for learning both types of tasks. However, learning sequential execution policies poses challenges in terms of credit assignment, and the limited information about subsequently executed agents can lead to sub-optimal solutions, which is known as the relative over-generalization problem. To tackle these issues, this paper proposes Greedy Sequential Execution (GSE) as a solution to learn the optimal policy that covers both scenarios. In the proposed GSE framework, we introduce an individual utility function into the framework of value decomposition to consider the complex interactions between agents. This function is capable of representing both the homogeneous and heterogeneous optimal policies. Furthermore, we utilize greedy marginal contribution calculated by the utility function as the credit value of the sequential execution policy to address the credit assignment and relative over-generalization problem. We evaluated GSE in both homogeneous and heterogeneous scenarios. The results demonstrate that GSE achieves significant improvement in performance across multiple domains, especially in scenarios involving both homogeneous and heterogeneous tasks.

Federated learning (FL) enhances data privacy with collaborative in-situ training on decentralized clients. Nevertheless, FL encounters challenges due to non-independent and identically distributed (non-i.i.d) data, leading to potential performance degradation and hindered convergence. While prior studies predominantly addressed the issue of skewed label distribution, our research addresses a crucial yet frequently overlooked problem known as multi-domain FL. In this scenario, clients' data originate from diverse domains with distinct feature distributions, instead of label distributions. To address the multi-domain problem in FL, we propose a novel method called Federated Learning Without Normalizations (FedWon). FedWon draws inspiration from the observation that batch normalization (BN) faces challenges in effectively modeling the statistics of multiple domains, while existing normalization techniques possess their own limitations. In order to address these issues, FedWon eliminates the normalization layers in FL and reparameterizes convolution layers with scaled weight standardization. Through extensive experimentation on five datasets and five models, our comprehensive experimental results demonstrate that FedWon surpasses both FedAvg and the current state-of-the-art method (FedBN) across all experimental setups, achieving notable accuracy improvements of more than 10% in certain domains. Furthermore, FedWon is versatile for both cross-silo and cross-device FL, exhibiting robust domain generalization capability, showcasing strong performance even with a batch size as small as 1, thereby catering to resource-constrained devices. Additionally, FedWon can also effectively tackle the challenge of skewed label distribution.

In this work, we define a diffusion-based generative model capable of both music generation and source separation by learning the score of the joint probability density of sources sharing a context. Alongside the classic total inference tasks (i.e., generating a mixture, separating the sources), we also introduce and experiment on the partial generation task of source imputation, where we generate a subset of the sources given the others (e.g., play a piano track that goes well with the drums). Additionally, we introduce a novel inference method for the separation task based on Dirac likelihood functions. We train our model on Slakh2100, a standard dataset for musical source separation, provide qualitative results in the generation settings, and showcase competitive quantitative results in the source separation setting. Our method is the first example of a single model that can handle both generation and separation tasks, thus representing a step toward general audio models.

Diffusion models have emerged as a powerful tool rivaling GANs in generating high-quality samples with improved fidelity, flexibility, and robustness. A key component of these models is to learn the score function through score matching. Despite empirical success on various tasks, it remains unclear whether gradient-based algorithms can learn the score function with a provable accuracy. As a first step toward answering this question, this paper establishes a mathematical framework for analyzing score estimation using neural networks trained by gradient descent. Our analysis covers both the optimization and the generalization aspects of the learning procedure. In particular, we propose a parametric form to formulate the denoising score-matching problem as a regression with noisy labels. Compared to the standard supervised learning setup, the score-matching problem introduces distinct challenges, including unbounded input, vector-valued output, and an additional time variable, preventing existing techniques from being applied directly. In this paper, we show that with proper designs, the evolution of neural networks during training can be accurately modeled by a series of kernel regression tasks. Furthermore, by applying an early-stopping rule for gradient descent and leveraging recent developments in neural tangent kernels, we establish the first generalization error (sample complexity) bounds for learning the score function with neural networks, despite the presence of noise in the observations. Our analysis is grounded in a novel parametric form of the neural network and an innovative connection between score matching and regression analysis, facilitating the application of advanced statistical and optimization techniques.

We introduce Graph-Induced Sum-Product Networks (GSPNs), a new probabilistic framework for graph representation learning that can tractably answer probabilistic queries. Inspired by the computational trees induced by vertices in the context of message-passing neural networks, we build hierarchies of sum-product networks (SPNs) where the parameters of a parent SPN are learnable transformations of the a-posterior mixing probabilities of its children's sum units. Due to weight sharing and the tree-shaped computation graphs of GSPNs, we obtain the efficiency and efficacy of deep graph networks with the additional advantages of a probabilistic model. We show the model's competitiveness on scarce supervision scenarios, under missing data, and for graph classification in comparison to popular neural models. We complement the experiments with qualitative analyses on hyper-parameters and the model's ability to answer probabilistic queries.

Retrosynthetic planning is a sequential decision-making process of identifying synthetic routes from the available building block materials to reach a desired target molecule. Though existing planning approaches show promisingly high solving rates and low costs, the trivial route cost evaluation via pre-trained forward reaction prediction models certainly falls short of real-world chemical practice. An alternative option is to annotate the actual cost of a route, such as yield, through chemical experiments or input from chemists, while this often leads to substantial query costs. In order to strike the balance between query costs and route quality evaluation, we propose an Active Retrosynthetic Planning (ARP) framework that remains compatible with the established retrosynthetic planners. On one hand, the proposed ARP trains an actor that decides whether to query the cost of a reaction; on the other hand, it resorts to a critic to estimate the value of a molecule with its preceding reaction cost as input. Those molecules with low reaction costs are preferred to expand first. We apply our framework to different existing approaches on both the benchmark and an expert dataset and demonstrate that it outperforms the existing state-of-the-art approach by 6.2\% in route quality while reducing the query cost by 12.8\%. In addition, ARP consistently plans high-quality routes with either abundant or sparse annotations.

GNN-to-MLP distillation aims to utilize knowledge distillation (KD) to learn computationally-efficient multi-layer perceptron (student MLP) on graph data by mimicking the output representations of teacher GNN. Existing methods mainly make the MLP to mimic the GNN predictions over a few class labels. However, the class space may not be expressive enough for covering numerous diverse local graph structures, thus limiting the performance of knowledge transfer from GNN to MLP. To address this issue, we propose to learn a new powerful graph representation space by directly labeling nodes' diverse local structures for GNN-to-MLP distillation. Specifically, we propose a variant of VQ-VAE to learn a structure-aware tokenizer on graph data that can encode each node's local substructure as a discrete code. The discrete codes constitute a codebook as a new graph representation space that is able to identify different local graph structures of nodes with the corresponding code indices. Then, based on the learned codebook, we propose a new distillation target, namely soft code assignments, to directly transfer the structural knowledge of each node from GNN to MLP. The resulting framework VQGraph achieves new state-of-the-art performance on GNN-to-MLP distillation in both transductive and inductive settings across seven graph datasets. We show that VQGraph with better performance infers faster than GNNs by 828×, and also achieves accuracy improvement over GNNs and stand-alone MLPs by 3.90% and 28.05% on average, respectively. Our code is available at https://github.com/YangLing0818/VQGraph

Dataset distillation aims to optimize a small set so that a model trained on the set achieves performance similar to that of a model trained on the full dataset. While many supervised methods have achieved remarkable success in distilling a large dataset into a small set of representative samples, however, they are not designed to produce a distilled dataset that can be effectively used to facilitate self-supervised pre-training. To this end, we propose a novel problem of distilling an unlabeled dataset into a set of small synthetic samples for efficient self-supervised learning (SSL). We first prove that a gradient of synthetic samples with respect to a SSL objective in naive bilevel optimization is \textit{biased} due to the randomness originating from data augmentations or masking for inner optimization. To address this issue, we propose to minimize the mean squared error (MSE) between a model's representations of the synthetic examples and their corresponding learnable target feature representations for the inner objective, which does not introduce any randomness. Our primary motivation is that the model obtained by the proposed inner optimization can mimic the \textit{self-supervised target model}. To achieve this, we also introduce the MSE between representations of the inner model and the self-supervised target model on the original full dataset for outer optimization. We empirically validate the effectiveness of our method on transfer learning. Our code is available at https://github.com/db-Lee/selfsup_dd

Recently, a series of papers proposed deep learning-based approaches to sample from target distributions using controlled diffusion processes, being trained only on the unnormalized target densities without access to samples. Building on previous work, we identify these approaches as special cases of a generalized Schrödinger bridge problem, seeking a stochastic evolution between a given prior distribution and the specified target. We further generalize this framework by introducing a variational formulation based on divergences between path space measures of time-reversed diffusion processes. This abstract perspective leads to practical losses that can be optimized by gradient-based algorithms and includes previous objectives as special cases. At the same time, it allows us to consider divergences other than the reverse Kullback-Leibler divergence that is known to suffer from mode collapse. In particular, we propose the so-called \textit{log-variance loss}, which exhibits favorable numerical properties and leads to significantly improved performance across all considered approaches.

We present DFormer, a novel RGB-D pretraining framework to learn transferable representations for RGB-D segmentation tasks. DFormer has two new key innovations: 1) Unlike previous works that encode RGB-D information with RGB pretrained backbone, we pretrain the backbone using image-depth pairs from ImageNet-1K, and thus the DFormer is endowed with the capacity to encode RGB-D representations; 2) DFormer comprises a sequence of RGB-D blocks, which are tailored for encoding both RGB and depth information through a novel building block design. DFormer avoids the mismatched encoding of the 3D geometry relationships in depth maps by RGB pretrained backbones, which widely lies in existing methods but has not been resolved. We finetune the pretrained DFormer on two popular RGB-D tasks, i.e., RGB-D semantic segmentation and RGB-D salient object detection, with a lightweight decoder head. Experimental results show that our DFormer achieves new state-of-the-art performance on these two tasks with less than half of the computational cost of the current best methods on two RGB-D semantic segmentation datasets and five RGB-D salient object detection datasets. Code will be made publicly available.

As robustness verification methods are becoming more precise, training certifiably robust neural networks is becoming ever more relevant. To this end, certified training methods compute and then optimize an upper bound on the worst-case loss over a robustness specification. Curiously, training methods based on the imprecise interval bound propagation (IBP) consistently outperform those leveraging more precise bounds. Still, we lack a theoretical understanding of the mechanisms making IBP so successful. In this work, we investigate these mechanisms by leveraging a novel metric measuring the tightness of IBP bounds. We first show theoretically that, for deep linear models (DLNs), tightness decreases with width and depth at initialization, but improves with IBP training. We, then, derive sufficient and necessary conditions on weight matrices for IBP bounds to become exact and demonstrate that these impose strong regularization, providing an explanation for the observed robustness-accuracy trade-off. Finally, we show how these results on DLNs transfer to ReLU networks, before conducting an extensive empirical study, (i) confirming this transferability and yielding state-of-the-art certified accuracy, (ii) finding that while all IBP-based training methods lead to high tightness, this increase is dominated by the size of the propagated input regions rather than the robustness specification, and finally (iii) observing that non-IBP-based methods do not increase tightness. Together, these results help explain the success of recent certified training methods and may guide the development of new ones.

While Large Language Models (LLMs) are the dominant models for generative tasks in language, they do not perform as well as diffusion models on image and video generation. To effectively use LLMs for visual generation, one crucial component is the visual tokenizer that maps pixel-space inputs to discrete tokens appropriate for LLM learning. In this paper, we introduce \modelname{}, a video tokenizer designed to generate concise and expressive tokens for both videos and images using a common token vocabulary. Equipped with this new tokenizer, we show that LLMs outperform diffusion models on standard image and video generation benchmarks including ImageNet and Kinetics. In addition, we demonstrate that our tokenizer surpasses the previously top-performing video tokenizer on two more tasks: (1) video compression comparable to the next-generation video codec (VCC) according to human evaluations, and (2) learning effective representations for action recognition tasks.

Rigorousness and clarity are both essential for interpretations of DNNs to engender human trust. Path methods are commonly employed to generate rigorous attributions that satisfy three axioms. However, the meaning of attributions remains ambiguous due to distinct path choices. To address the ambiguity, we introduce Concentration Principle, which centrally allocates high attributions to indispensable features, thereby endowing aesthetic and sparsity. We then present SAMP, a model-agnostic interpreter, which efficiently searches the near-optimal path from a pre-defined set of manipulation paths. Moreover, we propose the infinitesimal constraint (IC) and momentum strategy (MS) to improve the rigorousness and optimality. Visualizations show that SAMP can precisely reveal DNNs by pinpointing salient image pixels. We also perform quantitative experiments and observe that our method significantly outperforms the counterparts.

We extend JAX with the capability to automatically differentiate higher-order functions (functionals and operators). By representing functions as infinite dimensional generalization of arrays, we seamlessly use JAX's existing primitive system to implement higher-order functions. We present a set of primitive operators that serve as foundational building blocks for constructing several key types of functionals. For every introduced primitive operator, we derive and implement both linearization and transposition rules, aligning with JAX's internal protocols for forward and reverse mode automatic differentiation. This enhancement allows for functional differentiation in the same syntax traditionally use for functions. The resulting functional gradients are themselves functions ready to be invoked in python. We showcase this tool's efficacy and simplicity through applications where functional derivatives are indispensable.

Optimizing and certifying the positivity of polynomials are fundamental primitives across mathematics and engineering applications, from dynamical systems to operations research. However, solving these problems in practice requires large semidefinite programs, with poor scaling in dimension and degree. In this work, we demonstrate for the first time that neural networks can effectively solve such problems in a data-driven fashion, achieving tenfold speedups while retaining high accuracy. Moreover, we observe that these polynomial learning problems are equivariant to the non-compact group $SL(2,\mathbb{R})$, which consists of area-preserving linear transformations. We therefore adapt our learning pipelines to accommodate this structure, including data augmentation, a new $SL(2,\mathbb{R})$-equivariant architecture, and an architecture equivariant with respect to its maximal compact subgroup, $SO(2, \mathbb{R})$. Surprisingly, the most successful approaches in practice do not enforce equivariance to the entire group, which we prove arises from an unusual lack of architecture universality for $SL(2,\mathbb{R})$ in particular. A consequence of this result, which is of independent interest, is that there exists an equivariant function for which there is no sequence of equivariant polynomials multiplied by arbitrary invariants that approximates the original function. This is a rare example of a symmetric problem where data augmentation outperforms a fully equivariant architecture, and provides interesting lessons in both theory and practice for other problems with non-compact symmetries.

Mesh deformation plays a pivotal role in many 3D vision tasks including dynamic simulations, rendering, and reconstruction. However, defining an efficient discrepancy between predicted and target meshes remains an open problem. A prevalent approach in current deep learning is the set-based approach which measures the discrepancy between two surfaces by comparing two randomly sampled point-clouds from the two meshes with Chamfer pseudo-distance. Nevertheless, the set-based approach still has limitations such as lacking a theoretical guarantee for choosing the number of points in sampled point-clouds, and the pseudo-metricity and the quadratic complexity of the Chamfer divergence. To address these issues, we propose a novel metric for learning mesh deformation. The metric is defined by sliced Wasserstein distance on meshes represented as probability measures that generalize the set-based approach. By leveraging probability measure space, we gain flexibility in encoding meshes using diverse forms of probability measures, such as continuous, empirical, and discrete measures via \textit{varifold} representation. After having encoded probability measures, we can compare meshes by using the sliced Wasserstein distance which is an effective optimal transport distance with linear computational complexity and can provide a fast statistical rate for approximating the surface of meshes. To the end, we employ a neural ordinary differential equation (ODE) to deform the input surface into the target shape by modeling the trajectories of the points on the surface. Our experiments on cortical surface reconstruction demonstrate that our approach surpasses other competing methods in multiple datasets and metrics.

Zero Redundancy Optimizer (ZeRO) has been used to train a wide range of large language models on massive GPU clusters due to its ease of use, efficiency, and good scalability. However, when training on low-bandwidth clusters, and/or when small batch size per GPU is used, ZeRO’s effective throughput is limited due to communication overheads. To alleviate this limitation, this paper introduces ZeRO++ composing of three communication volume reduction techniques (lowprecision all-gather, data remapping, and low-precision gradient averaging) to significantly reduce the communication volume up to 4x that enables up to 2.16x better throughput at 384 GPU scale. Our results also show ZeRO++ can speedup the RLHF by 3.3x compared to vanilla ZeRO. To verify the convergence of ZeRO++, we test up to 13B model for pretraining with 8/6-bits all gather and up to 30B model for finetuning with 4/2-bits all gather, and demonstrate on-par accuracy as original ZeRO (aka standard training). As a byproduct, the model trained with ZeRO++ is naturally weight-quantized, which can be directly used for inference without post-training quantization or quantization-aware training.

Structure learning is a crucial task in science, especially in fields such as medicine and biology, where the wrong identification of (in)dependencies among random variables can have significant implications. The primary objective of structure learning is to learn a Directed Acyclic Graph (DAG) that represents the underlying probability distribution of the data. Many prominent DAG learners rely on least square losses or log-likelihood losses for optimization. It is well-known from regression models that least square losses are heavily influenced by the scale of the variables. Recently it has been demonstrated that the scale of data also affects performance of structure learning algorithms, though with a strong focus on linear 2-node systems and simulated data. Moving beyond these results, we provide conditions under which square-based losses are minimal for wrong DAGs in $d$-dimensional cases. Furthermore, we also show that scale can impair performance of structure learners if relations among variables are non-linear for both square based and log-likelihood based losses. We confirm our theoretical findings through extensive experiments on synthetic and real-world data.