Recently, large language models (LLMs) have shown significant progress, approaching human perception levels. In this work, we demonstrate that despite these advances, LLMs still struggle to reason using molecular structural information. This gap is critical because many molecular properties, including functional groups, depend heavily on such structural details. To address this limitation, we propose an approach that sketches molecular structures for reasoning. Specifically, we introduce Molecular Structural Reasoning (MSR) framework to enhance the understanding of LLMs by explicitly incorporating the key structural features. We present two frameworks for scenarios where the target molecule is known or unknown. We verify that our MSR improves molecular understanding through extensive experiments.

Large language models (LLMs) are increasingly recognized as powerful tools for scientific discovery, particularly in molecular science.A fundamental requirement for these models is the ability to accurately understand molecular structures, commonly encoded in the SMILES representation.However, current LLMs struggle to interpret SMILES, even failing to carry out basic tasks such as counting molecular rings.To address this limitation, we introduce CLEANMOL, a novel framework that formulates SMILES parsing into a suite of clean and deterministic tasks explicitly designed to promote graph-level molecular comprehension.These tasks span from subgraph matching to global graph matching, providing structured supervision aligned with molecular structural properties.We construct a molecular pretraining dataset with adaptive difficulty scoring and pre-train open-source LLMs on these tasks.Our results show that CLEANMOL not only enhances structural comprehension but also achieves the best or competes with the baseline on the Mol-Instructions benchmark.

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.

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.

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

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.

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).

Combinatorial optimization (CO) is fundamental to several realworld applications, from logistics and scheduling to hardware design and resource allocation.Deep reinforcement learning (RL) has recently shown significant benefits in solving CO problems, reducing reliance on domain expertise and improving computational efficiency.However, the absence of a unified benchmarking framework leads to inconsistent evaluations, limits reproducibility, and increases engineering overhead, raising barriers to adoption for new researchers.To address these challenges, we introduce RL4CO, a unified and extensive benchmark with in-depth library coverage of 27 CO problem environments and 23 state-of-the-art baselines.Built on efficient software libraries and best practices in implementation, RL4CO features modularized implementation and flexible configurations of diverse environments, policy architectures, RL algorithms, and utilities with extensive documentation.RL4CO helps researchers build on existing successes while exploring and developing their own designs, facilitating the entire research process by decoupling science from heavy engineering.We finally provide extensive benchmark studies to inspire new insights and future work.RL4CO has already attracted numerous researchers in the community and is open-sourced at https://github.com/ai4co/rl4co 1 .

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.

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.

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.

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.

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.

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.

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.

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}.

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.

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.

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.

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.

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.

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.

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.

Generative modeling has seen significant advancements in recent years, especially in the realm of text-to-image synthesis. Despite this progress, the medical field has yet to fully leverage the capabilities of large-scale foundational models for synthetic data generation. This paper introduces a framework for text-conditional magnetic resonance (MR) imaging generation, addressing the complexities associated with multi-modality considerations. The framework comprises a pre-trained large language model, a diffusion-based prompt-conditional image generation architecture, and an additional denoising network for input structural binary masks. Experimental results demonstrate that the proposed framework is capable of generating realistic, high-resolution, and high-fidelity multi-modal MR images that align with medical language text prompts. Further, the study interprets the cross-attention maps of the generated results based on text-conditional statements. The contributions of this research lay a robust foundation for future studies in text-conditional medical image generation and hold significant promise for accelerating advancements in medical imaging research.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

Transferring knowledge from a teacher neural network pretrained on the same or a similar task to a student neural network can significantly improve the performance of the student neural network. Existing knowledge transfer approaches match the activations or the corresponding hand-crafted features of the teacher and the student networks. We propose an information-theoretic framework for knowledge transfer which formulates knowledge transfer as maximizing the mutual information between the teacher and the student networks. We compare our method with existing knowledge transfer methods on both knowledge distillation and transfer learning tasks and show that our method consistently outperforms existing methods. We further demonstrate the strength of our method on knowledge transfer across heterogeneous network architectures by transferring knowledge from a convolutional neural network (CNN) to a multi-layer perceptron (MLP) on CIFAR-10. The resulting MLP significantly outperforms the-state-of-the-art methods and it achieves similar performance to the CNN with a single convolutional layer.

Computing the partition function Z of a discrete graphical model is a fundamental inference challenge. Since this is computationally intractable, variational approximations are often used in practice. Recently, so-called gauge transformations were used to improve variational lower bounds on Z. In this paper, we propose a new gauge-variational approach, termed WMBE-G, which combines gauge transformations with the weighted mini-bucket elimination (WMBE) method. WMBE-G can provide both upper and lower bounds on Z, and is easier to optimize than the prior gauge-variational algorithm. We show that WMBE-G strictly improves the earlier WMBE approximation for symmetric models including Ising models with no magnetic field. Our experimental results demonstrate the effectiveness of WMBE-G even for generic, nonsymmetric models.

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.

We study the maximum weight matching (MWM) problem for general graphs through the max-product belief propagation (BP) and related Linear Programming (LP). The BP approach provides distributed heuristics for finding the maximum a posteriori (MAP) assignment in a joint probability distribution represented by a graphical model (GM), and respective LPs can be considered as continuous relaxations of the discrete MAP problem. It was recently shown that a BP algorithm converges to the correct MAP/MWM assignment under a simple GM formulation of MWM, as long as the corresponding LP relaxation is tight. First, under the motivation for forcing the tightness condition, we consider a new GM formulation of MWM, say C-GM, using non-intersecting odd-sized cycles in the graph; the new corresponding LP relaxation, say C-LP, becomes tight for more MWM instances. However, the tightness of C-LP now does not guarantee such convergence and correctness of the new BP on C-GM. To address the issue, we introduce a novel graph transformation applied to C-GM, which results in another GM formulation of MWM, and prove that the respective BP on it converges to the correct MAP/MWM assignment, as long as C-LP is tight. Finally, we also show that C-LP always has half-integral solutions, which leads to an efficient BP-based MWM heuristic consisting of making sequential, “cutting plane”, modifications to the underlying GM. Our experiments show that this BP-based cutting plane heuristic performs, as well as that based on traditional LP solvers.

Computing partition function is the most important statistical inference task arising in applications of Graphical Models (GM). Since it is computationally intractable, approximate methods have been used in practice, where mean-field (MF) and belief propagation (BP) are arguably the most popular and successful approaches of a variational type. In this paper, we propose two new variational schemes, coined Gauged-MF (G-MF) and Gauged-BP (G-BP), improving MF and BP, respectively. Both provide lower bounds for the partition function by utilizing the so-called gauge transformation which modifies factors of GM while keeping the partition function invariant. Moreover, we prove that both G-MF and G-BP are exact for GMs with a single loop of a special structure, even though the bare MF and BP perform badly in this case. Our extensive experiments indeed confirm that the proposed algorithms outperform and generalize MF and BP.

Markov Chain Monte Carlo (MCMC) and Belief Propagation (BP) are the most popular algorithms for computational inference in Graphical Models (GM). In principle, MCMC is an exact probabilistic method which, however, often suffers from exponentially slow mixing. In contrast, BP is a deterministic method, which is typically fast, empirically very successful, however in general lacking control of accuracy over loopy graphs. In this paper, we introduce MCMC algorithms correcting the approximation error of BP, i.e., we provide a way to compensate for BP errors via a consecutive BP-aware MCMC. Our framework is based on the Loop Calculus (LC) approach which allows to express the BP error as a sum of weighted generalized loops. Although the full series is computationally intractable, it is known that a truncated series, summing up all 2-regular loops, is computable in polynomial-time for planar pair-wise binary GMs and it also provides a highly accurate approximation empirically. Motivated by this, we, first, propose a polynomial-time approximation MCMC scheme for the truncated series of general (non-planar) pair-wise binary models. Our main idea here is to use the Worm algorithm, known to provide fast mixing in other (related) problems, and then design an appropriate rejection scheme to sample 2-regular loops. Furthermore, we also design an efficient rejection-free MCMC scheme for approximating the full series. The main novelty underlying our design is in utilizing the concept of cycle basis, which provides an efficient decomposition of the generalized loops. In essence, the proposed MCMC schemes run on transformed GM built upon the non-trivial BP solution, and our experiments show that this synthesis of BP and MCMC outperforms both direct MCMC and bare BP schemes.

Max-product Belief Propagation (BP) is a popular message-passing algorithm for computing a Maximum-A-Posteriori (MAP) assignment over a distribution represented by a Graphical Model (GM). It has been shown that BP can solve a number of combinatorial optimization problems including minimum weight matching, shortest path, network flow and vertex cover under the following common assumption: the respective Linear Programming (LP) relaxation is tight, i.e., no integrality gap is present. However, when LP shows an integrality gap, no model has been known which can be solved systematically via sequential applications of BP. In this paper, we develop the first such algorithm, coined Blossom-BP, for solving the minimum weight matching problem over arbitrary graphs. Each step of the sequential algorithm requires applying BP over a modified graph constructed by contractions and expansions of blossoms, i.e., odd sets of vertices. Our scheme guarantees termination in O(n^2) of BP runs, where n is the number of vertices in the original graph. In essence, the Blossom-BP offers a distributed version of the celebrated Edmonds' Blossom algorithm by jumping at once over many sub-steps with a single BP. Moreover, our result provides an interpretation of the Edmonds' algorithm as a sequence of LPs.

This paper proposes a new blind adaptive algorithm for computing the weight vector of an antenna array system that provides the beam pattern having its maximum gain along the direction of the mobile target signal source in the presence of strong interference. The proposed algorithm provides a suboptimal weight vector maximizing the SINR (signal to interference plus noise ratio) with a linear computational load. Based on the analysis obtained from various simulations, it is observed that the proposed algorithm is suitable for practical IMT2000 mobile communication environments.