Joohwan Ko

Minsu Kim, Joohwan Ko, Taeyoung Yun et al. · mila

GFlowNets are probabilistic models that sequentially generate compositional structures through a stochastic policy. Among GFlowNets, temperature-conditional GFlowNets can introduce temperature-based controllability for exploration and exploitation. We propose \textit{Logit-scaling GFlowNets} (Logit-GFN), a novel architectural design that greatly accelerates the training of temperature-conditional GFlowNets. It is based on the idea that previously proposed approaches introduced numerical challenges in the deep network training, since different temperatures may give rise to very different gradient profiles as well as magnitudes of the policy's logits. We find that the challenge is greatly reduced if a learned function of the temperature is used to scale the policy's logits directly. Also, using Logit-GFN, GFlowNets can be improved by having better generalization capabilities in offline learning and mode discovery capabilities in online learning, which is empirically verified in various biological and chemical tasks. Our code is available at \url{https://github.com/dbsxodud-11/logit-gfn}

Joohwan Ko, Justin Domke

Amortized inference promises fast test-time Bayesian inference, but existing methods are inherently tied to fixed models. Extending amortization to unseen models typically requires retraining or costly test-time finetuning. In this paper, we ask: is it possible to build a single inference network capable of generalizing across varying priors, likelihoods, and dimensionality? We introduce Amortized Factor Inference Networks (AFINs), a family of encode-merge-decode inference networks built on dimension-independent modules that map a model specification and its observations to the parameters of a variational posterior. Experimentally, a single trained AFIN achieves posterior accuracy comparable to NUTS and several variational inference methods, while requiring 2 to 4 orders of magnitude less test-time compute. Code is available at https://github.com/joohwanko/AFINs.

Joohwan Ko, Tomas Geffner

Denoising score matching (DSM) for training diffusion models may suffer from high variance at low noise levels. Target Score Matching (TSM) mitigates this when clean data scores are available, providing a low-variance objective. In many applications clean scores are inaccessible due to the presence of latent variables, leaving only joint signals exposed. We propose Latent Target Score Matching (LTSM), an extension of TSM to leverage joint scores for low-variance supervision of the marginal score. While LTSM is effective at low noise levels, a mixture with DSM ensures robustness across noise scales. Across simulation-based inference tasks, LTSM consistently improves variance, score accuracy, and sample quality.

Minseon Gwak, Seongrok Moon, Joohwan Ko et al.

Due to the lack of state dimension optimization methods, deep state space models (SSMs) have sacrificed model capacity, training search space, or stability to alleviate computational costs caused by high state dimensions. In this work, we provide a structured pruning method for SSMs, Layer-Adaptive STate pruning (LAST), which reduces the state dimension of each layer in minimizing model-level output energy loss by extending modal truncation for a single system. LAST scores are evaluated using the $\mathcal{H}_{\infty}$ norms of subsystems and layer-wise energy normalization. The scores serve as global pruning criteria, enabling cross-layer comparison of states and layer-adaptive pruning. Across various sequence benchmarks, LAST optimizes previous SSMs, revealing the redundancy and compressibility of their state spaces. Notably, we demonstrate that, on average, pruning 33% of states still maintains performance with 0.52% accuracy loss in multi-input multi-output SSMs without retraining. Code is available at https://github.com/msgwak/LAST.

Minho Lee, Yun Young Choi, Sun Woo Park et al.

Graph Neural Networks (GNNs) and Transformer-based models have been increasingly adopted to learn the complex vector representations of spatio-temporal graphs, capturing intricate spatio-temporal dependencies crucial for applications such as traffic datasets. Although many existing methods utilize multi-head attention mechanisms and message-passing neural networks (MPNNs) to capture both spatial and temporal relations, these approaches encode temporal and spatial relations independently, and reflect the graph's topological characteristics in a limited manner. In this work, we introduce the Cycle to Mixer (Cy2Mixer), a novel spatio-temporal GNN based on topological non-trivial invariants of spatio-temporal graphs with gated multi-layer perceptrons (gMLP). The Cy2Mixer is composed of three blocks based on MLPs: A temporal block for capturing temporal properties, a message-passing block for encapsulating spatial information, and a cycle message-passing block for enriching topological information through cyclic subgraphs. We bolster the effectiveness of Cy2Mixer with mathematical evidence emphasizing that our cycle message-passing block is capable of offering differentiated information to the deep learning model compared to the message-passing block. Furthermore, empirical evaluations substantiate the efficacy of the Cy2Mixer, demonstrating state-of-the-art performances across various spatio-temporal benchmark datasets. The source code is available at \url{https://github.com/leemingo/cy2mixer}.

Joohwan Ko, Andrew A. Li

Models of choice are a fundamental input to many now-canonical optimization problems in the field of Operations Management, including assortment, inventory, and price optimization. Naturally, accurate estimation of these models from data is a critical step in the application of these optimization problems in practice. Concurrently, recent advancements in deep learning have sparked interest in integrating these techniques into choice modeling. However, there is a noticeable research gap at the intersection of deep learning and choice modeling, particularly with both theoretical and empirical foundations. Thus motivated, we first propose a choice model that is the first to successfully (both theoretically and practically) leverage a modern neural network architectural concept (self-attention). Theoretically, we show that our attention-based choice model is a low-rank generalization of the Halo Multinomial Logit (Halo-MNL) model. We prove that whereas the Halo-MNL requires $Ω(m^2)$ data samples to estimate, where $m$ is the number of products, our model supports a natural nonconvex estimator (in particular, that which a standard neural network implementation would apply) which admits a near-optimal stationary point with $O(m)$ samples. Additionally, we establish the first realistic-scale benchmark for choice model estimation on real data, conducting the most extensive evaluation of existing models to date, thereby highlighting our model's superior performance.

Joohwan Ko, Aristofanis Rontogiannis, Yih-En Andrew Ban et al.

Protein design using structure prediction models such as AlphaFold2 has shown remarkable success, but existing approaches like relaxed sequence optimization (RSO) rely on single-path gradient descent and ignore sequence-space constraints, limiting diversity and designability. We introduce Relaxed Sequence Sampling (RSS), a Markov chain Monte Carlo (MCMC) framework that integrates structural and evolutionary information for protein design. RSS operates in continuous logit space, combining gradient-guided exploration with protein language model-informed jumps. Its energy function couples AlphaFold2-derived structural objectives with ESM2-derived sequence priors, balancing accuracy and biological plausibility. In an in silico protein binder design task, RSS produces 5$\times$ more designable structures and 2-3$\times$ greater structural diversity than RSO baselines, at equal computational cost. These results highlight RSS as a principled approach for efficiently exploring the protein design landscape.

Joohwan Ko, Justin Domke

Variational inference often struggles with the posterior geometry exhibited by complex hierarchical Bayesian models. Recent advances in flow-based variational families and Variationally Inferred Parameters (VIP) each address aspects of this challenge, but their formal relationship is unexplored. Here, we prove that the combination of VIP and a full-rank Gaussian can be represented exactly as a forward autoregressive flow augmented with a translation term and input from the model's prior. Guided by this theoretical insight, we introduce the Model-Informed Flow (MIF) architecture, which adds the necessary translation mechanism, prior information, and hierarchical ordering. Empirically, MIF delivers tighter posterior approximations and matches or exceeds state-of-the-art performance across a suite of hierarchical and non-hierarchical benchmarks.

Kyurae Kim, Joohwan Ko, Yi-An Ma et al.

Optimization objectives in the form of a sum of intractable expectations are rising in importance (e.g., diffusion models, variational autoencoders, and many more), a setting also known as "finite sum with infinite data." For these problems, a popular strategy is to employ SGD with doubly stochastic gradients (doubly SGD): the expectations are estimated using the gradient estimator of each component, while the sum is estimated by subsampling over these estimators. Despite its popularity, little is known about the convergence properties of doubly SGD, except under strong assumptions such as bounded variance. In this work, we establish the convergence of doubly SGD with independent minibatching and random reshuffling under general conditions, which encompasses dependent component gradient estimators. In particular, for dependent estimators, our analysis allows fined-grained analysis of the effect correlations. As a result, under a per-iteration computational budget of $b \times m$, where $b$ is the minibatch size and $m$ is the number of Monte Carlo samples, our analysis suggests where one should invest most of the budget in general. Furthermore, we prove that random reshuffling (RR) improves the complexity dependence on the subsampling noise.

Joohwan Ko, Kyurae Kim, Woo Chang Kim et al.

Variational families with full-rank covariance approximations are known not to work well in black-box variational inference (BBVI), both empirically and theoretically. In fact, recent computational complexity results for BBVI have established that full-rank variational families scale poorly with the dimensionality of the problem compared to e.g. mean-field families. This is particularly critical to hierarchical Bayesian models with local variables; their dimensionality increases with the size of the datasets. Consequently, one gets an iteration complexity with an explicit $\mathcal{O}(N^2)$ dependence on the dataset size $N$. In this paper, we explore a theoretical middle ground between mean-field variational families and full-rank families: structured variational families. We rigorously prove that certain scale matrix structures can achieve a better iteration complexity of $\mathcal{O}\left(N\right)$, implying better scaling with respect to $N$. We empirically verify our theoretical results on large-scale hierarchical models.