Author name cluster

Sungsoo Ahn

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41 papers

2 author rows

ICLR Conference 2025 Conference Paper

Adaptive teachers for amortized samplers

Minsu Kim 0004
Sanghyeok Choi
Taeyoung Yun
Emmanuel Bengio
Leo Feng
Jarrid Rector-Brooks
Sungsoo Ahn
Jinkyoo Park

Amortized inference is the task of training a parametric model, such as a neural network, to approximate a distribution with a given unnormalized density where exact sampling is intractable. When sampling is modeled as a sequential decision-making process, reinforcement learning (RL) methods, such as generative flow networks, can be used to train the sampling policy. Off-policy RL training facilitates the discovery of diverse, high-reward candidates, but existing methods still face challenges in efficient exploration. We propose to use an adaptive training distribution (the Teacher) to guide the training of the primary amortized sampler (the Student). The Teacher, an auxiliary behavior model, is trained to sample high-loss regions of the Student and can generalize across unexplored modes, thereby enhancing mode coverage by providing an efficient training curriculum. We validate the effectiveness of this approach in a synthetic environment designed to present an exploration challenge, two diffusion-based sampling tasks, and four biochemical discovery tasks demonstrating its ability to improve sample efficiency and mode coverage. Source code is available at https://github.com/alstn12088/adaptive-teacher.

TMLR Journal 2025 Journal Article

Decoupled Sequence and Structure Generation for Realistic Antibody Design

Nayoung Kim
Minsu Kim
Sungsoo Ahn
Jinkyoo Park

Recently, deep learning has made rapid progress in antibody design, which plays a key role in the advancement of therapeutics. A dominant paradigm is to train a model to jointly generate the antibody sequence and the structure as a candidate. However, the joint generation requires the model to generate both the discrete amino acid categories and the continuous 3D coordinates; this limits the space of possible architectures and may lead to suboptimal performance. In response, we propose an antibody sequence-structure decoupling (ASSD) framework, which separates sequence generation and structure prediction. Although our approach is simple, our idea allows the use of powerful neural architectures and demonstrates notable performance improvements. We also find that the widely used non-autoregressive generators promote sequences with overly repeating tokens. Such sequences are both out-of-distribution and prone to undesirable developability properties that can trigger harmful immune responses in patients. To resolve this, we introduce a composition-based objective that allows an efficient trade-off between high performance and low token repetition. ASSD shows improved performance in various antibody design experiments, while the composition-based objective successfully mitigates token repetition of non-autoregressive models.

NeurIPS Conference 2025 Conference Paper

Energy-based generator matching: A neural sampler for general state space

Dongyeop Woo
Minsu Kim
Minkyu Kim
Kiyoung Seong
Sungsoo Ahn

We propose Energy-based generator matching (EGM), a modality-agnostic approach to train generative models from energy functions in the absence of data. Extending the recently proposed generator matching, EGM enables training of arbitrary continuous-time Markov processes, e. g. , diffusion, flow, and jump, and can generate data from continuous, discrete, and a mixture of two modalities. To this end, we propose estimating the generator matching loss using self-normalized importance sampling with an additional bootstrapping trick to reduce variance in the importance weight. We validate EGM on both discrete and multimodal tasks up to 100 and 20 dimensions, respectively.

NeurIPS Conference 2025 Conference Paper

Flexible MOF Generation with Torsion-Aware Flow Matching

Nayoung Kim
Seongsu Kim
Sungsoo Ahn

Designing metal-organic frameworks (MOFs) with novel chemistries is a longstanding challenge due to their large combinatorial space and complex 3D arrangements of the building blocks. While recent deep generative models have enabled scalable MOF generation, they assume (1) a fixed set of building blocks and (2) known local 3D coordinates of building blocks. However, this limits their ability to (1) design novel MOFs and (2) generate the structure using novel building blocks. We propose a two-stage MOF generation framework that overcomes these limitations by modeling both chemical and geometric degrees of freedom. First, we train an SMILES-based autoregressive model to generate metal and organic building blocks, paired with a cheminformatics toolkit for 3D structure initialization. Second, we introduce a flow matching model that predicts translations, rotations, and torsional angles to assemble the blocks into valid 3D frameworks. Our experiments demonstrate improved reconstruction accuracy, the generation of valid, novel, and unique MOFs, and the ability to create novel building blocks. Our code is available at https: //github. com/nayoung10/MOFFlow-2.

ICLR Conference 2025 Conference Paper

Generative Flows on Synthetic Pathway for Drug Design

Seonghwan Seo
Minsu Kim 0004
Tony Shen
Martin Ester
Jinkyoo Park
Sungsoo Ahn
Woo Youn Kim

Generative models in drug discovery have recently gained attention as efficient alternatives to brute-force virtual screening. However, most existing models do not account for synthesizability, limiting their practical use in real-world scenarios. In this paper, we propose RxnFlow, which sequentially assembles molecules using predefined molecular building blocks and chemical reaction templates to constrain the synthetic chemical pathway. We then train on this sequential generating process with the objective of generative flow networks (GFlowNets) to generate both highly rewarded and diverse molecules. To mitigate the large action space of synthetic pathways in GFlowNets, we implement a novel action space subsampling method. This enables RxnFlow to learn generative flows over extensive action spaces comprising combinations of 1.2 million building blocks and 71 reaction templates without significant computational overhead. Additionally, RxnFlow can employ modified or expanded action spaces for generation without retraining, allowing for the introduction of additional objectives or the incorporation of newly discovered building blocks. We experimentally demonstrate that RxnFlow outperforms existing reaction-based and fragment-based models in pocket-specific optimization across various target pockets. Furthermore, RxnFlow achieves state-of-the-art performance on CrossDocked2020 for pocket-conditional generation, with an average Vina score of –8.85 kcal/mol and 34.8% synthesizability. Code is available at https://github.com/SeonghwanSeo/RxnFlow.

NeurIPS Conference 2025 Conference Paper

High-order Equivariant Flow Matching for Density Functional Theory Hamiltonian Prediction

Seongsu Kim
Nayoung Kim
Dongwoo Kim
Sungsoo Ahn

Density functional theory (DFT) is a fundamental method for simulating quantum chemical properties, but it remains expensive due to the iterative self-consistent field (SCF) process required to solve the Kohn–Sham equations. Recently, deep learning methods are gaining attention as a way to bypass this step by directly predicting the Hamiltonian. However, they rely on deterministic regression and do not consider the highly structured nature of Hamiltonians. In this work, we propose QHFlow, a high-order equivariant flow matching framework that generates Hamiltonian matrices conditioned on molecular geometry. Flow matching models continuous-time trajectories between simple priors and complex targets, learning the structured distributions over Hamiltonians instead of direct regression. To further incorporate symmetry, we use a neural architecture that predicts SE(3)-equivariant vector fields, improving accuracy and generalization across diverse geometries. To further enhance physical fidelity, we additionally introduce a fine-tuning scheme to align predicted orbital energies with the target. QHFlow achieves state-of-the-art performance, reducing Hamiltonian error by 71% on MD17 and 53% on QH9. Moreover, we further show that QHFlow accelerates the DFT process without trading off the solution quality when initializing SCF iterations with the predicted Hamiltonian, significantly reducing the number of iterations and runtime.

ICLR Conference 2025 Conference Paper

MOFFlow: Flow Matching for Structure Prediction of Metal-Organic Frameworks

Nayoung Kim
Seongsu Kim
Minsu Kim 0004
Jinkyoo Park
Sungsoo Ahn

Metal-organic frameworks (MOFs) are a class of crystalline materials with promising applications in many areas such as carbon capture and drug delivery. In this work, we introduce MOFFlow, the first deep generative model tailored for MOF structure prediction. Existing approaches, including ab initio calculations and even deep generative models, struggle with the complexity of MOF structures due to the large number of atoms in the unit cells. To address this limitation, we propose a novel Riemannian flow matching framework that reduces the dimensionality of the problem by treating the metal nodes and organic linkers as rigid bodies, capitalizing on the inherent modularity of MOFs. By operating in the $SE(3)$ space, MOFFlow effectively captures the roto-translational dynamics of these rigid components in a scalable way. Our experiment demonstrates that MOFFlow accurately predicts MOF structures containing several hundred atoms, significantly outperforming conventional methods and state-of-the-art machine learning baselines while being much faster. Code available at https://github.com/nayoung10/MOFFlow.

NeurIPS Conference 2025 Conference Paper

On scalable and efficient training of diffusion samplers

Minkyu Kim
Kiyoung Seong
Dongyeop Woo
Sungsoo Ahn
Minsu Kim

We address the challenge of training diffusion models to sample from unnormalized energy distributions in the absence of data, the so-called diffusion samplers. Although these approaches have shown promise, they struggle to scale in more demanding scenarios where energy evaluations are expensive and the sampling space is high-dimensional. To address this limitation, we propose a scalable and sample-efficient framework that properly harmonizes the powerful classical sampling method and the diffusion sampler. Specifically, we utilize Monte Carlo Markov chain (MCMC) samplers with a novelty-based auxiliary energy as a Searcher to collect off-policy samples, using an auxiliary energy function to compensate for exploring modes the diffusion sampler rarely visits. These off-policy samples are then combined with on-policy data to train the diffusion sampler, thereby expanding its coverage of the energy landscape. Furthermore, we identify primacy bias, i. e. , the preference of samplers for early experience during training, as the main cause of mode collapse during training, and introduce a periodic re-initialization trick to resolve this issue. Our method significantly improves sample efficiency on standard benchmarks for diffusion samplers and also excels at higher-dimensional problems and real-world molecular conformer generation.

ICLR Conference 2025 Conference Paper

REBIND: Enhancing Ground-state Molecular Conformation Prediction via Force-Based Graph Rewiring

Taewon Kim
Hyunjin Seo
Sungsoo Ahn
Eunho Yang

Predicting the ground-state 3D molecular conformations from 2D molecular graphs is critical in computational chemistry due to its profound impact on molecular properties. Deep learning (DL) approaches have recently emerged as promising alternatives to computationally-heavy classical methods such as density functional theory (DFT). However, we discover that existing DL methods inadequately model inter-atomic forces, particularly for non-bonded atomic pairs, due to their naive usage of bonds and pairwise distances. Consequently, significant prediction errors occur for atoms with low degree (ie., low coordination numbers) whose conformations are primarily influenced by non-bonded interactions. To address this, we propose ReBIND, a novel framework that rewires molecular graphs by adding edges based on the Lennard-Jones potential to capture non-bonded interactions for low-degree atoms. Experimental results demonstrate that ReBIND significantly outperforms state-of-the-art methods across various molecular sizes, achieving up to a 20% reduction in prediction error. The code is available in: https://github.com/holymollyhao/ReBIND

ICLR Conference 2025 Conference Paper

Transition Path Sampling with Improved Off-Policy Training of Diffusion Path Samplers

Kiyoung Seong
Seonghyun Park 0004
Seonghwan Kim 0004
Woo Youn Kim
Sungsoo Ahn

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines. We also provide links to [project page](https://kiyoung98.github.io/tps-dps/) and [code](https://github.com/kiyoung98/tps-dps).

ICLR Conference 2024 Conference Paper

A Simple and Scalable Representation for Graph Generation

Yunhui Jang
Seul Lee
Sungsoo Ahn

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.

ICML Conference 2024 Conference Paper

Breadth-First Exploration on Adaptive Grid for Reinforcement Learning

Youngsik Yoon
Gangbok Lee
Sungsoo Ahn
Jungseul Ok

Graph-based planners have gained significant attention for goal-conditioned reinforcement learning (RL), where they construct a graph consisting of confident transitions between subgoals as edges and run shortest path algorithms to exploit the confident edges. Meanwhile, identifying and avoiding unattainable transitions are also crucial yet overlooked by the previous graph-based planners, leading to wasting an excessive number of attempts at unattainable subgoals. To address this oversight, we propose a graph construction method that efficiently manages all the achieved and unattained subgoals on a grid graph adaptively discretizing the goal space. This enables a breadth-first exploration strategy, grounded in the local adaptive grid refinement, that prioritizes broad probing of subgoals on a coarse grid over meticulous one on a dense grid. We conducted a theoretical analysis and demonstrated the effectiveness of our approach through empirical evidence, showing that only BEAG succeeds in complex environments under the proposed fixed-goal setting.

IJCAI Conference 2024 Conference Paper

EPIC: Graph Augmentation with Edit Path Interpolation via Learnable Cost

Jaeseung Heo
Seungbeom Lee
Sungsoo Ahn
Dongwoo Kim

Data augmentation plays a critical role in improving model performance across various domains, but it becomes challenging with graph data due to their complex and irregular structure. To address this issue, we propose EPIC (Edit Path Interpolation via learnable Cost), a novel interpolation-based method for augmenting graph datasets. To interpolate between two graphs lying in an irregular domain, EPIC leverages the concept of graph edit distance, constructing an edit path that represents the transformation process between two graphs via edit operations. Moreover, our method introduces a context-sensitive cost model that accounts for the importance of specific edit operations formulated through a learning framework. This allows for a more nuanced transformation process, where the edit distance is not merely count-based but reflects meaningful graph attributes. With randomly sampled graphs from the edit path, we enrich the training set to enhance the generalization capability of classification models. Experimental evaluations across several benchmark datasets demonstrate that our approach outperforms existing augmentation techniques in many tasks.

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ICML Conference 2024 Conference Paper

Gaussian Plane-Wave Neural Operator for Electron Density Estimation

Seongsu Kim
Sungsoo Ahn

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.

ICLR Conference 2024 Conference Paper

Graph Generation with K2-trees

Yunhui Jang
Dongwoo Kim 0002
Sungsoo Ahn

Generating graphs from a target distribution is a significant challenge across many domains, including drug discovery and social network analysis. In this work, we introduce a novel graph generation method leveraging $K^2$ representation, originally designed for lossless graph compression. The $K^2$ representation enables compact generation while concurrently capturing an inherent hierarchical structure of a graph. In addition, we make contributions by (1) presenting a sequential $K^2$ representation that incorporates pruning, flattening, and tokenization processes and (2) introducing a Transformer-based architecture designed to generate the sequence by incorporating a specialized tree positional encoding scheme. Finally, we extensively evaluate our algorithm on four general and two molecular graph datasets to confirm its superiority for graph generation.

TMLR Journal 2024 Journal Article

Holistic Molecular Representation Learning via Multi-view Fragmentation

Seojin Kim
Jaehyun Nam
Junsu Kim
Hankook Lee
Sungsoo Ahn
Jinwoo Shin

Learning chemically meaningful representations from unlabeled molecules plays a vital role in AI-based drug design and discovery. In response to this, several self-supervised learning methods have been developed, focusing either on global (e.g., graph-level) or local (e.g., motif-level) information of molecular graphs. However, it is still unclear which approach is more effective for learning better molecular representations. In this paper, we propose a novel holistic self-supervised molecular representation learning framework that effectively learns both global and local molecular information. Our key idea is to utilize fragmentation, which decomposes a molecule into a set of chemically meaningful fragments (e.g., functional groups), to associate a global graph structure to a set of local substructures, thereby preserving chemical properties and learn both information via contrastive learning between them. Additionally, we also consider the 3D geometry of molecules as another view for contrastive learning. We demonstrate that our framework outperforms prior molecular representation learning methods across various molecular property prediction tasks.

ICML Conference 2024 Conference Paper

Hybrid Neural Representations for Spherical Data

Hyomin Kim
Yunhui Jang
Jaeho Lee 0001
Sungsoo Ahn

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 cosmic 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 multi-layer perceptron 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.

ICML Conference 2024 Conference Paper

Improving Robustness to Multiple Spurious Correlations by Multi-Objective Optimization

Nayeong Kim
Juwon Kang
Sungsoo Ahn
Jungseul Ok
Suha Kwak

We study the problem of training an unbiased and accurate model given a dataset with multiple biases. This problem is challenging since the multiple biases cause multiple undesirable shortcuts during training, and even worse, mitigating one may exacerbate the other. We propose a novel training method to tackle this challenge. Our method first groups training data so that different groups induce different shortcuts, and then optimizes a linear combination of group-wise losses while adjusting their weights dynamically to alleviate conflicts between the groups in performance; this approach, rooted in the multi-objective optimization theory, encourages to achieve the minimax Pareto solution. We also present a new benchmark with multiple biases, dubbed MultiCelebA, for evaluating debiased training methods under realistic and challenging scenarios. Our method achieved the best on three datasets with multiple biases, and also showed superior performance on conventional single-bias datasets.

ICLR Conference 2024 Conference Paper

Learning Energy Decompositions for Partial Inference in GFlowNets

Hyosoon Jang
Minsu Kim
Sungsoo Ahn

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.

ICLR Conference 2024 Conference Paper

Local Search GFlowNets

Minsu Kim 0004
Taeyoung Yun
Emmanuel Bengio
Dinghuai Zhang
Yoshua Bengio
Sungsoo Ahn
Jinkyoo Park

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 backtracking 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}.

TMLR Journal 2024 Journal Article

Non-backtracking Graph Neural Networks

Seonghyun Park
Narae Ryu
Gahee Kim
Dongyeop Woo
Se-Young Yun
Sungsoo Ahn

The celebrated message-passing updates for graph neural networks allow representing large-scale graphs with local and computationally tractable updates. However, the updates suffer from backtracking, i.e., a message flowing through the same edge twice and revisiting 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 relevant for downstream tasks. In this work, we propose to resolve such a redundancy issue via the non-backtracking graph neural network (NBA-GNN) that updates a message without incorporating the message from the previously visited node. We theoretically 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. Furthermore, we empirically verify the effectiveness of our NBA-GNN on the long-range graph benchmark and transductive node classification problems.

NeurIPS Conference 2024 Conference Paper

Pessimistic Backward Policy for GFlowNets

Hyosoon Jang
Yunhui Jang
Minsu Kim
Jinkyoo Park
Sungsoo Ahn

This paper studies Generative Flow Networks (GFlowNets), which learn to sample objects proportionally to a given reward function through the trajectory of state transitions. In this work, we observe that GFlowNets tend to under-exploit the high-reward objects due to training on insufficient number of trajectories, which may lead to a large gap between the estimated flow and the (known) reward value. In response to this challenge, we propose a pessimistic backward policy for GFlowNets (PBP-GFN), which maximizes the observed flow to align closely with the true reward for the object. We extensively evaluate PBP-GFN across eight benchmarks, including hyper-grid environment, bag generation, structured set generation, molecular generation, and four RNA sequence generation tasks. In particular, PBP-GFN enhances the discovery of high-reward objects, maintains the diversity of the objects, and consistently outperforms existing methods.

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ICML Conference 2024 Conference Paper

Symmetric Replay Training: Enhancing Sample Efficiency in Deep Reinforcement Learning for Combinatorial Optimization

Hyeonah Kim
Minsu Kim 0004
Sungsoo Ahn
Jinkyoo Park

Deep reinforcement learning (DRL) has significantly advanced the field of combinatorial optimization (CO). However, its practicality is hindered by the necessity for a large number of reward evaluations, especially in scenarios involving computationally intensive function assessments. To enhance the sample efficiency, we propose a simple but effective method, called symmetric replay training (SRT), which can be easily integrated into various DRL methods. Our method leverages high-reward samples to encourage exploration of the under-explored symmetric regions without additional online interactions - free. Through replay training, the policy is trained to maximize the likelihood of the symmetric trajectories of discovered high-rewarded samples. Experimental results demonstrate the consistent improvement of our method in sample efficiency across diverse DRL methods applied to real-world tasks, such as molecular optimization and hardware design.

ICML Conference 2024 Conference Paper

Tackling Prevalent Conditions in Unsupervised Combinatorial Optimization: Cardinality, Minimum, Covering, and More

Fanchen Bu
Hyeonsoo Jo
Soo Yong Lee
Sungsoo Ahn
Kijung Shin

Combinatorial optimization (CO) is naturally discrete, making machine-learning techniques based on differentiable optimization inapplicable. Karalias & Loukas (2020) adapted the probabilistic method by Erdős & Spencer (1974), to incorporate CO into differentiable optimization. Their work ignited the research on unsupervised learning for CO, composed of two main components: probabilistic objectives and derandomization. However, each component confronts unique challenges. First, deriving objectives under complex conditions and constraints is nontrivial. Second, the derandomization process is underexplored, and the existing derandomization methods are either random sampling or naive rounding. In this work, we aim to tackle complex conditions in unsupervised CO. First, we concretize the targets for probabilistic objective construction and derandomization with theoretical justification. Then, for various complex conditions commonly involved in different CO problems, we derive nontrivial objectives and derandomization to meet the targets. Finally, we apply the derivations to various CO problems. Via extensive experiments on synthetic and real-world graphs, we validate the correctness of our derivations and show our empirical superiority w. r. t. both optimization quality and speed.

ICML Conference 2023 Conference Paper

A Closer Look at the Intervention Procedure of Concept Bottleneck Models

Sungbin Shin
Yohan Jo
Sungsoo Ahn
Namhoon Lee

Concept bottleneck models (CBMs) are a class of interpretable neural network models that predict the target response of a given input based on its high-level concepts. Unlike the standard end-to-end models, CBMs enable domain experts to intervene on the predicted concepts and rectify any mistakes at test time, so that more accurate task predictions can be made at the end. While such intervenability provides a powerful avenue of control, many aspects of the intervention procedure remain rather unexplored. In this work, we develop various ways of selecting intervening concepts to improve the intervention effectiveness and conduct an array of in-depth analyses as to how they evolve under different circumstances. Specifically, we find that an informed intervention strategy can reduce the task error more than ten times compared to the current baseline under the same amount of intervention counts in realistic settings, and yet, this can vary quite significantly when taking into account different intervention granularity. We verify our findings through comprehensive evaluations, not only on the standard real datasets, but also on synthetic datasets that we generate based on a set of different causal graphs. We further discover some major pitfalls of the current practices which, without a proper addressing, raise concerns on reliability and fairness of the intervention procedure.

NeurIPS Conference 2023 Conference Paper

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

Minsu Kim
Federico Berto
Sungsoo Ahn
Jinkyoo Park

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: https: //github. com/kaist-silab/bootgen.

NeurIPS Conference 2023 Conference Paper

Diffusion Probabilistic Models for Structured Node Classification

Hyosoon Jang
Seonghyun Park
Sangwoo Mo
Sungsoo Ahn

This paper studies structured node classification on graphs, where the predictions should consider dependencies between the node labels. In particular, we focus on solving the problem for partially labeled graphs where it is essential to incorporate the information in the known label for predicting the unknown labels. To address this issue, we propose a novel framework leveraging the diffusion probabilistic model for structured node classification (DPM-SNC). At the heart of our framework is the extraordinary capability of DPM-SNC to (a) learn a joint distribution over the labels with an expressive reverse diffusion process and (b) make predictions conditioned on the known labels utilizing manifold-constrained sampling. Since the DPMs lack training algorithms for partially labeled data, we design a novel training algorithm to apply DPMs, maximizing a new variational lower bound. We also theoretically analyze how DPMs benefit node classification by enhancing the expressive power of GNNs based on proposing AGG-WL, which is strictly more powerful than the classic 1-WL test. We extensively verify the superiority of our DPM-SNC in diverse scenarios, which include not only the transductive setting on partially labeled graphs but also the inductive setting and unlabeled graphs.

ICLR Conference 2023 Conference Paper

Imitating Graph-Based Planning with Goal-Conditioned Policies

Junsu Kim
Younggyo Seo
Sungsoo Ahn
Kyunghwan Son
Jinwoo Shin

Recently, graph-based planning algorithms have gained much attention to solve goal-conditioned reinforcement learning (RL) tasks: they provide a sequence of subgoals to reach the target-goal, and the agents learn to execute subgoal-conditioned policies. However, the sample-efficiency of such RL schemes still remains a challenge, particularly for long-horizon tasks. To address this issue, we present a simple yet effective self-imitation scheme which distills a subgoal-conditioned policy into the target-goal-conditioned policy. Our intuition here is that to reach a target-goal, an agent should pass through a subgoal, so target-goal- and subgoal- conditioned policies should be similar to each other. We also propose a novel scheme of stochastically skipping executed subgoals in a planned path, which further improves performance. Unlike prior methods that only utilize graph-based planning in an execution phase, our method transfers knowledge from a planner along with a graph into policy learning. We empirically show that our method can significantly boost the sample-efficiency of the existing goal-conditioned RL methods under various long-horizon control tasks.

NeurIPS Conference 2023 Conference Paper

Multi-resolution Spectral Coherence for Graph Generation with Score-based Diffusion

Hyuna Cho
Minjae Jeong
Sooyeon Jeon
Sungsoo Ahn
Won Hwa Kim

Successful graph generation depends on the accurate estimation of the joint distribution of graph components such as nodes and edges from training data. While recent deep neural networks have demonstrated sampling of realistic graphs together with diffusion models, however, they still suffer from oversmoothing problems which are inherited from conventional graph convolution and thus high-frequency characteristics of nodes and edges become intractable. To overcome such issues and generate graphs with high fidelity, this paper introduces a novel approach that captures the dependency between nodes and edges at multiple resolutions in the spectral space. By modeling the joint distribution of node and edge signals in a shared graph wavelet space, together with a score-based diffusion model, we propose a Wavelet Graph Diffusion Model (Wave-GD) which lets us sample synthetic graphs with real-like frequency characteristics of nodes and edges. Experimental results on four representative benchmark datasets validate the superiority of the Wave-GD over existing approaches, highlighting its potential for a wide range of applications that involve graph data.

ICML Conference 2022 Conference Paper

Disentangling Sources of Risk for Distributional Multi-Agent Reinforcement Learning

Kyunghwan Son
Junsu Kim
Sungsoo Ahn
Roben Delos Reyes
Yung Yi
Jinwoo Shin

In cooperative multi-agent reinforcement learning, the outcomes of agent-wise policies are highly stochastic due to the two sources of risk: (a) random actions taken by teammates and (b) random transition and rewards. Although the two sources have very distinct characteristics, existing frameworks are insufficient to control the risk-sensitivity of agent-wise policies in a disentangled manner. To this end, we propose Disentangled RIsk-sensitive Multi-Agent reinforcement learning (DRIMA) to separately access the risk sources. For example, our framework allows an agent to be optimistic with respect to teammates (who can prosocially adapt) but more risk-neutral with respect to the environment (which does not adapt). Our experiments demonstrate that DRIMA significantly outperforms prior state-of-the-art methods across various scenarios in the StarCraft Multi-agent Challenge environment. Notably, DRIMA shows robust performance where prior methods learn only a highly suboptimal policy, regardless of reward shaping, exploration scheduling, and noisy (random or adversarial) agents.

NeurIPS Conference 2022 Conference Paper

Learning Debiased Classifier with Biased Committee

Nayeong Kim
Sehyun Hwang
Sungsoo Ahn
Jaesik Park
Suha Kwak

Neural networks are prone to be biased towards spurious correlations between classes and latent attributes exhibited in a major portion of training data, which ruins their generalization capability. We propose a new method for training debiased classifiers with no spurious attribute label. The key idea is to employ a committee of classifiers as an auxiliary module that identifies bias-conflicting data, i. e. , data without spurious correlation, and assigns large weights to them when training the main classifier. The committee is learned as a bootstrapped ensemble so that a majority of its classifiers are biased as well as being diverse, and intentionally fail to predict classes of bias-conflicting data accordingly. The consensus within the committee on prediction difficulty thus provides a reliable cue for identifying and weighting bias-conflicting data. Moreover, the committee is also trained with knowledge transferred from the main classifier so that it gradually becomes debiased along with the main classifier and emphasizes more difficult data as training progresses. On five real-world datasets, our method outperforms prior arts using no spurious attribute label like ours and even surpasses those relying on bias labels occasionally. Our code is available at https: //github. com/nayeong-v-kim/LWBC.

ICLR Conference 2022 Conference Paper

Spanning Tree-based Graph Generation for Molecules

Sungsoo Ahn
Binghong Chen
Tianzhe Wang
Le Song

In this paper, we explore the problem of generating molecules using deep neural networks, which has recently gained much interest in chemistry. To this end, we propose a spanning tree-based graph generation (STGG) framework based on formulating molecular graph generation as a construction of a spanning tree and the residual edges. Such a formulation exploits the sparsity of molecular graphs and allows using compact tree-constructive operations to define the molecular graph connectivity. Based on the intermediate graph structure of the construction process, our framework can constrain its generation to molecular graphs that satisfy the chemical valence rules. We also newly design a Transformer architecture with tree-based relative positional encodings for realizing the tree construction procedure. Experiments on QM9, ZINC250k, and MOSES benchmarks verify the effectiveness of the proposed framework in metrics such as validity, Frechet ChemNet distance, and fragment similarity. We also demonstrate the usefulness of STGG in maximizing penalized LogP value of molecules.

ICLR Conference 2022 Conference Paper

What Makes Better Augmentation Strategies? Augment Difficult but Not too Different

Jaehyung Kim 0001
Dongyeop Kang
Sungsoo Ahn
Jinwoo Shin

The practice of data augmentation has been extensively used to boost the performance of deep neural networks for various NLP tasks. It is more effective when only a limited number of labeled samples is available, e.g., low-data or class-imbalanced regimes. Most current augmentation techniques rely on parameter tuning or inherent randomness; hence, their effectiveness largely varies on the tasks. To efficiently find the best augmentation strategy for each task, learning data augmentation policy is a promising solution, but the question of what makes a good augmentation in NLP tasks and how to design the reward function for learning a good policy remains under-explored. To answer this, we hypothesize that good data augmentation should construct more diverse and challenging samples for providing informative training signals, while avoiding the risk of losing the semantics of original samples. Therefore, we design a novel reward function for updating the augmentation policy to construct difficult but not too different samples (DND). Particularly, we jointly optimize a data augmentation policy while training the model, to construct the augmented samples with low confidence but a high semantic similarity with original ones. In addition, we introduce a sample re-weighting scheme to focus on difficult augmented samples after the original ones are learned confidently for more effective learning from the augmented ones. Our learning-based augmentation outperforms the recent state-of-the-art augmentation schemes on various text classification tasks and GLUE benchmark by successfully discovering the effective augmentations for each task. Remarkably, our method is more effective on the challenging low-data and class-imbalanced regimes, and the learned augmentation policy is well-transferable to the different tasks and models.

ICLR Conference 2021 Conference Paper

Layer-adaptive Sparsity for the Magnitude-based Pruning

Jaeho Lee 0001
Sejun Park
Sangwoo Mo
Sungsoo Ahn
Jinwoo Shin

Recent discoveries on neural network pruning reveal that, with a carefully chosen layerwise sparsity, a simple magnitude-based pruning achieves state-of-the-art tradeoff between sparsity and performance. However, without a clear consensus on ``how to choose,'' the layerwise sparsities are mostly selected algorithm-by-algorithm, often resorting to handcrafted heuristics or an extensive hyperparameter search. To fill this gap, we propose a novel importance score for global pruning, coined layer-adaptive magnitude-based pruning (LAMP) score; the score is a rescaled version of weight magnitude that incorporates the model-level $\ell_2$ distortion incurred by pruning, and does not require any hyperparameter tuning or heavy computation. Under various image classification setups, LAMP consistently outperforms popular existing schemes for layerwise sparsity selection. Furthermore, we observe that LAMP continues to outperform baselines even in weight-rewinding setups, while the connectivity-oriented layerwise sparsity (the strongest baseline overall) performs worse than a simple global magnitude-based pruning in this case. Code: https://github.com/jaeho-lee/layer-adaptive-sparsity

IJCAI Conference 2021 Conference Paper

RetCL: A Selection-based Approach for Retrosynthesis via Contrastive Learning

Hankook Lee
Sungsoo Ahn
Seung-Woo Seo
You Young Song
Eunho Yang
Sung Ju Hwang
Jinwoo Shin

Retrosynthesis, of which the goal is to find a set of reactants for synthesizing a target product, is an emerging research area of deep learning. While the existing approaches have shown promising results, they currently lack the ability to consider availability (e. g. , stability or purchasability) of the reactants or generalize to unseen reaction templates (i. e. , chemical reaction rules). In this paper, we propose a new approach that mitigates the issues by reformulating retrosynthesis into a selection problem of reactants from a candidate set of commercially available molecules. To this end, we design an efficient reactant selection framework, named RetCL (retrosynthesis via contrastive learning), for enumerating all of the candidate molecules based on selection scores computed by graph neural networks. For learning the score functions, we also propose a novel contrastive training scheme with hard negative mining. Extensive experiments demonstrate the benefits of the proposed selection-based approach. For example, when all 671k reactants in the USPTO database are given as candidates, our RetCL achieves top-1 exact match accuracy of 71. 3% for the USPTO-50k benchmark, while a recent transformer-based approach achieves 59. 6%. We also demonstrate that RetCL generalizes well to unseen templates in various settings in contrast to template-based approaches.

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NeurIPS Conference 2021 Conference Paper

RoMA: Robust Model Adaptation for Offline Model-based Optimization

Sihyun Yu
Sungsoo Ahn
Le Song
Jinwoo Shin

We consider the problem of searching an input maximizing a black-box objective function given a static dataset of input-output queries. A popular approach to solving this problem is maintaining a proxy model, e. g. , a deep neural network (DNN), that approximates the true objective function. Here, the main challenge is how to avoid adversarially optimized inputs during the search, i. e. , the inputs where the DNN highly overestimates the true objective function. To handle the issue, we propose a new framework, coined robust model adaptation (RoMA), based on gradient-based optimization of inputs over the DNN. Specifically, it consists of two steps: (a) a pre-training strategy to robustly train the proxy model and (b) a novel adaptation procedure of the proxy model to have robust estimates for a specific set of candidate solutions. At a high level, our scheme utilizes the local smoothness prior to overcome the brittleness of the DNN. Experiments under various tasks show the effectiveness of RoMA compared with previous methods, obtaining state-of-the-art results, e. g. , RoMA outperforms all at 4 out of 6 tasks and achieves runner-up results at the remaining tasks.

ICML Conference 2021 Conference Paper

Self-Improved Retrosynthetic Planning

Junsu Kim
Sungsoo Ahn
Hankook Lee
Jinwoo Shin

Retrosynthetic planning is a fundamental problem in chemistry for finding a pathway of reactions to synthesize a target molecule. Recently, search algorithms have shown promising results for solving this problem by using deep neural networks (DNNs) to expand their candidate solutions, i. e. , adding new reactions to reaction pathways. However, the existing works on this line are suboptimal; the retrosynthetic planning problem requires the reaction pathways to be (a) represented by real-world reactions and (b) executable using “building block” molecules, yet the DNNs expand reaction pathways without fully incorporating such requirements. Motivated by this, we propose an end-to-end framework for directly training the DNNs towards generating reaction pathways with the desirable properties. Our main idea is based on a self-improving procedure that trains the model to imitate successful trajectories found by itself. We also propose a novel reaction augmentation scheme based on a forward reaction model. Our experiments demonstrate that our scheme significantly improves the success rate of solving the retrosynthetic problem from 86. 84% to 96. 32% while maintaining the performance of DNN for predicting valid reactions.

NeurIPS Conference 2020 Conference Paper

Guiding Deep Molecular Optimization with Genetic Exploration

Sungsoo Ahn
Junsu Kim
Hankook Lee
Jinwoo Shin

De novo molecular design attempts to search over the chemical space for molecules with the desired property. Recently, deep learning has gained considerable attention as a promising approach to solve the problem. In this paper, we propose genetic expert-guided learning (GEGL), a simple yet novel framework for training a deep neural network (DNN) to generate highly-rewarding molecules. Our main idea is to design a "genetic expert improvement" procedure, which generates high-quality targets for imitation learning of the DNN. Extensive experiments show that GEGL significantly improves over state-of-the-art methods. For example, GEGL manages to solve the penalized octanol-water partition coefficient optimization with a score of 31. 40, while the best-known score in the literature is 27. 22. Besides, for the GuacaMol benchmark with 20 tasks, our method achieves the highest score for 19 tasks, in comparison with state-of-the-art methods, and newly obtains the perfect score for three tasks. Our training code is available at https: //github. com/sungsoo-ahn/genetic-expert-guided-learning.

NeurIPS Conference 2020 Conference Paper

Learning from Failure: De-biasing Classifier from Biased Classifier

Junhyun Nam
Hyuntak Cha
Sungsoo Ahn
Jaeho Lee
Jinwoo Shin

Neural networks often learn to make predictions that overly rely on spurious corre- lation existing in the dataset, which causes the model to be biased. While previous work tackles this issue by using explicit labeling on the spuriously correlated attributes or presuming a particular bias type, we instead utilize a cheaper, yet generic form of human knowledge, which can be widely applicable to various types of bias. We first observe that neural networks learn to rely on the spurious correlation only when it is “easier” to learn than the desired knowledge, and such reliance is most prominent during the early phase of training. Based on the obser- vations, we propose a failure-based debiasing scheme by training a pair of neural networks simultaneously. Our main idea is twofold; (a) we intentionally train the first network to be biased by repeatedly amplifying its “prejudice”, and (b) we debias the training of the second network by focusing on samples that go against the prejudice of the biased network in (a). Extensive experiments demonstrate that our method significantly improves the training of network against various types of biases in both synthetic and real-world datasets. Surprisingly, our framework even occasionally outperforms the debiasing methods requiring explicit supervision of the spuriously correlated attributes.

ICML Conference 2020 Conference Paper

Learning What to Defer for Maximum Independent Sets

Sungsoo Ahn
Younggyo Seo
Jinwoo Shin

Designing efficient algorithms for combinatorial optimization appears ubiquitously in various scientific fields. Recently, deep reinforcement learning (DRL) frameworks have gained considerable attention as a new approach: they can automate the design of a solver while relying less on sophisticated domain knowledge of the target problem. However, the existing DRL solvers determine the solution using a number of stages proportional to the number of elements in the solution, which severely limits their applicability to large-scale graphs. In this paper, we seek to resolve this issue by proposing a novel DRL scheme, coined learning what to defer (LwD), where the agent adaptively shrinks or stretch the number of stages by learning to distribute the element-wise decisions of the solution at each stage. We apply the proposed framework to the maximum independent set (MIS) problem, and demonstrate its significant improvement over the current state-of-the-art DRL scheme. We also show that LwD can outperform the conventional MIS solvers on large-scale graphs having millions of vertices, under a limited time budget.

ICML Conference 2018 Conference Paper

Bucket Renormalization for Approximate Inference

Sungsoo Ahn
Michael Chertkov
Adrian Weller
Jinwoo Shin

Probabilistic graphical models are a key tool in machine learning applications. Computing the partition function, i. e. , normalizing constant, is a fundamental task of statistical inference but is generally computationally intractable, leading to extensive study of approximation methods. Iterative variational methods are a popular and successful family of approaches. However, even state of the art variational methods can return poor results or fail to converge on difficult instances. In this paper, we instead consider computing the partition function via sequential summation over variables. We develop robust approximate algorithms by combining ideas from mini-bucket elimination with tensor network and renormalization group methods from statistical physics. The resulting “convergence-free” methods show good empirical performance on both synthetic and real-world benchmark models, even for difficult instances.