Hybrid Neural Representations for Spherical Data

In this paper, we study hybrid neural representations for spherical data, a domain of increasing relevance in scientific research. In particular, our work focuses on weather and climate data as well as comic microwave background (CMB) data. Although previous studies have delved into coordinate-based neural representations for spherical signals, they often fail to capture the intricate details of highly nonlinear signals. To address this limitation, we introduce a novel approach named Hybrid Neural Representations for Spherical data (HNeR-S). Our main idea is to use spherical feature-grids to obtain positional features which are combined with a multilayer perception to predict the target signal. We consider feature-grids with equirectangular and hierarchical equal area isolatitude pixelization structures that align with weather data and CMB data, respectively. We extensively verify the effectiveness of our HNeR-S for regression, super-resolution, temporal interpolation, and compression tasks.

Gaussian Plane-Wave Neural Operator for Electron Density Estimation

This work studies machine learning for electron density prediction, which is fundamental for understanding chemical systems and density functional theory (DFT) simulations. To this end, we introduce the Gaussian plane-wave neural operator (GPWNO), which operates in the infinite-dimensional functional space using the plane-wave and Gaussian-type orbital bases, widely recognized in the context of DFT. In particular, both high- and low-frequency components of the density can be effectively represented due to the complementary nature of the two bases. Extensive experiments on QM9, MD, and material project datasets demonstrate GPWNO's superior performance over ten baselines.

Triplet Edge Attention for Algorithmic Reasoning

This work investigates neural algorithmic reasoning to develop neural networks capable of learning from classical algorithms. The main challenge is to develop graph neural networks that are expressive enough to predict the given algorithm outputs while generalizing well to out-of-distribution data. In this work, we introduce a new graph neural network layer called Triplet Edge Attention (TEA), an edge-aware graph attention layer. Our algorithm works by precisely computing edge latent, aggregating multiple triplet messages using edge-based attention. We empirically validate our TEA layer in the CLRS benchmark and demonstrate a $5%$ improvement on average. In particular, we achieve a $30%$ improvement for the string algorithms compared to the state-of-the-art model.

A Simple and Scalable Representation for Graph Generation

Recently, there has been a surge of interest in employing neural networks for graph generation, a fundamental statistical learning problem with critical applications like molecule design and community analysis. However, most approaches encounter significant limitations when generating large-scale graphs. This is due to their requirement to output the full adjacency matrices whose size grows quadratically with the number of nodes. In response to this challenge, we introduce a new, simple, and scalable graph representation named gap encoded edge list (GEEL) that has a small representation size that aligns with the number of edges. In addition, GEEL significantly reduces the vocabulary size by incorporating the gap encoding and bandwidth restriction schemes. GEEL can be autoregressively generated with the incorporation of node positional encoding, and we further extend GEEL to deal with attributed graphs by designing a new grammar. Our findings reveal that the adoption of this compact representation not only enhances scalability but also bolsters performance by simplifying the graph generation process. We conduct a comprehensive evaluation across ten non-attributed and two molecular graph generation tasks, demonstrating the effectiveness of GEEL.

Non-backtracking Graph Neural Networks

The celebrated message-passing updates for graph neural networks allow the representation of large-scale graphs with local and computationally tractable updates. However, the local updates suffer from backtracking, i.e., a message flows through the same edge twice and revisits the previously visited node. Since the number of message flows increases exponentially with the number of updates, the redundancy in local updates prevents the graph neural network from accurately recognizing a particular message flow for downstream tasks. In this work, we propose to resolve such a redundancy via the non-backtracking graph neural network (NBA-GNN) that updates a message without incorporating the message from the previously visited node. We further investigate how NBA-GNN alleviates the over-squashing of GNNs, and establish a connection between NBA-GNN and the impressive performance of non-backtracking updates for stochastic block model recovery. We empirically verify the effectiveness of our NBA-GNN on long-range graph benchmark and transductive node classification problems.

Learning Energy Decompositions for Partial Inference of GFlowNets

This paper studies generative flow networks (GFlowNets) to sample objects from the Boltzmann energy distribution via a sequence of actions. In particular, we focus on improving GFlowNet with partial inference: training flow functions with the evaluation of the intermediate states or transitions. To this end, the recently developed forward-looking GFlowNet reparameterizes the flow functions based on evaluating the energy of intermediate states. However, such an evaluation of intermediate energies may (i) be too expensive or impossible to evaluate and (ii) even provide misleading training signals under large energy fluctuations along the sequence of actions. To resolve this issue, we propose learning energy decompositions for GFlowNets (LED-GFN). Our main idea is to (i) decompose the energy of an object into learnable potential functions defined on state transitions and (ii) reparameterize the flow functions using the potential functions. In particular, to produce informative local credits, we propose to regularize the potential to change smoothly over the sequence of actions. It is also noteworthy that training GFlowNet with our learned potential can preserve the optimal policy. We empirically verify the superiority of LED-GFN in five problems including the generation of unstructured and maximum independent sets, molecular graphs, and RNA sequences.

Local Search GFlowNets

Generative Flow Networks (GFlowNets) are amortized sampling methods that learn a distribution over discrete objects proportional to their rewards. GFlowNets exhibit a remarkable ability to generate diverse samples, yet occasionally struggle to consistently produce samples with high rewards due to over-exploration on wide sample space. This paper proposes to train GFlowNets with local search which focuses on exploiting high rewarded sample space to resolve this issue. Our main idea is to explore the local neighborhood via destruction and reconstruction guided by backward and forward policies, respectively. This allows biasing the samples toward high-reward solutions, which is not possible for a typical GFlowNet solution generation scheme which uses the forward policy to generate the solution from scratch. Extensive experiments demonstrate a remarkable performance improvement in several biochemical tasks. Source code is available: \url{https://github.com/dbsxodud-11/ls_gfn}.

Bootstrapped Training of Score-Conditioned Generator for Offline Design of Biological Sequences

We study the problem of optimizing biological sequences, e.g., proteins, DNA, and RNA, to maximize a black-box score function that is only evaluated in an offline dataset. We propose a novel solution, bootstrapped training of score-conditioned generator (BootGen) algorithm. Our algorithm repeats a two-stage process. In the first stage, our algorithm trains the biological sequence generator with rank-based weights to enhance the accuracy of sequence generation based on high scores. The subsequent stage involves bootstrapping, which augments the training dataset with self-generated data labeled by a proxy score function. Our key idea is to align the score-based generation with a proxy score function, which distills the knowledge of the proxy score function to the generator. After training, we aggregate samples from multiple bootstrapped generators and proxies to produce a diverse design. Extensive experiments show that our method outperforms competitive baselines on biological sequential design tasks. We provide reproducible source code: \href{https://github.com/kaist-silab/bootgen}{https://github.com/kaist-silab/bootgen}.

EPIC: Graph Augmentation with Edit Path Interpolation via Learnable Cost

Graph-based models have become increasingly important in various domains, but the limited size and diversity of existing graph datasets often limit their performance. To address this issue, we propose EPIC (Edit Path Interpolation via learnable Cost), a novel interpolation-based method for augmenting graph datasets. Our approach leverages graph edit distance to generate new graphs that are similar to the original ones but exhibit some variation in their structures. To achieve this, we learn the graph edit distance through a comparison of labeled graphs and utilize this knowledge to create graph edit paths between pairs of original graphs. With randomly sampled graphs from a graph edit path, we enrich the training set to enhance the generalization capability of classification models. We demonstrate the effectiveness of our approach on several benchmark datasets and show that it outperforms existing augmentation methods in graph classification tasks.

Symmetric Exploration in Combinatorial Optimization is Free!

Recently, deep reinforcement learning (DRL) has shown promise in solving combinatorial optimization (CO) problems. However, they often require a large number of evaluations on the objective function, which can be time-consuming in real-world scenarios. To address this issue, we propose a "free" technique to enhance the performance of any deep reinforcement learning (DRL) solver by exploiting symmetry without requiring additional objective function evaluations. Our key idea is to augment the training of DRL-based combinatorial optimization solvers by reward-preserving transformations. The proposed algorithm is likely to be impactful since it is simple, easy to integrate with existing solvers, and applicable to a wide range of combinatorial optimization tasks. Extensive empirical evaluations on NP-hard routing optimization, scheduling optimization, and de novo molecular optimization confirm that our method effortlessly improves the sample efficiency of state-of-the-art DRL algorithms. Our source code is available at https://github.com/kaist-silab/sym-rd.