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Jongmin Kim

Publications and source records attributed to Jongmin Kim.

43 records · Page 3Linked to original sources

Automated Learning Rate Scheduler for Large-batch Training

Large-batch training has been essential in leveraging large-scale datasets and models in deep learning. While it is computationally beneficial to use large batch sizes, it often requires a specially designed learning rate (LR) schedule to achieve a comparable level of performance as in smaller batch training. Especially, when the number of training epochs is constrained, the use of a large LR and a warmup strategy is critical in the final performance of large-batch training due to the reduced number of updating steps. In this work, we propose an automated LR scheduling algorithm which is effective for neural network training with a large batch size under the given epoch budget. In specific, the whole schedule consists of two phases: adaptive warmup and predefined decay, where the LR is increased until the training loss no longer decreases and decreased to zero until the end of training. Here, whether the training loss has reached the minimum value is robustly checked with Gaussian process smoothing in an online manner with a low computational burden. Coupled with adaptive stochastic optimizers such as AdamP and LAMB, the proposed scheduler successfully adjusts the LRs without cumbersome hyperparameter tuning and achieves comparable or better performances than tuned baselines on various image classification benchmarks and architectures with a wide range of batch sizes.

cs.LG↗

Work-function modification of PEG(thiol) adsorbed on the Au(111) surface: A first-principles study

The possibility of modifying the work function of electrodes is important for optimizing the energy barriers for charge-injection (extraction) at the interface to an organic material. In this study, we perform density-functional-theory calculations to investigate the impact of dithiol-terminated polyethylene glycol (PEG(thiol)) based self-assembled monolayers (SAMs) with different numbers of PEG repeat units on the work function of the Au(111) surface. We find that a monolayer of PEG(thiol) decreases the work function of the Au(111) surface, where the magnitude of this reduction strongly depends on the length of the PEG backbone. The main contribution arises from the dipole due to the adsorption-induced charge rearrangement at the interface. Our work reveals a pronounced odd-even effect, which can be traced back to the dipole moment of the PEG(thiol) layer.

cond-mat.mtrl-sci↗

Robust mixing in self-consistent linearized augmented planewave calculations

We devise a mixing algorithm for full-potential (FP) all-electron calculations in the linearized augmented planewave (LAPW) method. Pulay's direct inversion in the iterative subspace is complemented with the Kerker preconditioner and further improvements to achieve smooth convergence, avoiding charge sloshing and noise in the exchange-correlation potential. As the Kerker preconditioner was originally designed for the planewave basis, we have adapted it to the FP-LAPW method and implemented in the exciting code. Applications to the $2\times 2$ Au(111) surface with a vacancy and to the Pd(111) surface demonstrate that this approach and our implementation work reliably with both density and potential mixing.

cond-mat.mtrl-sci↗

On the stability of nucleic acid feedback controllers

Recent work has shown how chemical reaction network theory may be used to design dynamical systems that can be implemented biologically in nucleic acid-based chemistry. While this has allowed the construction of advanced open-loop circuitry based on cascaded DNA strand displacement (DSD) reactions, little progress has so far been made in developing the requisite theoretical machinery to inform the systematic design of feedback controllers in this context. Here, we develop a number of foundational theoretical results on the equilibria, stability, and dynamics of nucleic acid controllers. In particular, we show that the implementation of feedback controllers using DSD reactions introduces additional nonlinear dynamics, even in the case of purely linear designs, e.g. PI controllers. By decomposing the effects of these non-observable nonlinear dynamics, we show that, in general, the stability of the linear system design does not necessarily imply the stability of the underlying chemical network, which can be lost under experimental variability when feedback interconnections are introduced. We provide an in-depth theoretical analysis of an example illustrating this phenomenon, whereby the linear design does not capture the instability of the full nonlinear system implemented as a DSD reaction network, and we further confirm these results using VisualDSD, a bespoke software tool for simulating nucleic acid-based circuits. Our analysis highlight the many interesting and unique characteristics of this important new class of feedback control systems.

eess.SY↗

Edge-labeling Graph Neural Network for Few-shot Learning

In this paper, we propose a novel edge-labeling graph neural network (EGNN), which adapts a deep neural network on the edge-labeling graph, for few-shot learning. The previous graph neural network (GNN) approaches in few-shot learning have been based on the node-labeling framework, which implicitly models the intra-cluster similarity and the inter-cluster dissimilarity. In contrast, the proposed EGNN learns to predict the edge-labels rather than the node-labels on the graph that enables the evolution of an explicit clustering by iteratively updating the edge-labels with direct exploitation of both intra-cluster similarity and the inter-cluster dissimilarity. It is also well suited for performing on various numbers of classes without retraining, and can be easily extended to perform a transductive inference. The parameters of the EGNN are learned by episodic training with an edge-labeling loss to obtain a well-generalizable model for unseen low-data problem. On both of the supervised and semi-supervised few-shot image classification tasks with two benchmark datasets, the proposed EGNN significantly improves the performances over the existing GNNs.

cs.LG↗

Belief propagation for joint sparse recovery

Compressed sensing (CS) demonstrates that sparse signals can be recovered from underdetermined linear measurements. We focus on the joint sparse recovery problem where multiple signals share the same common sparse support sets, and they are measured through the same sensing matrix. Leveraging a recent information theoretic characterization of single signal CS, we formulate the optimal minimum mean square error (MMSE) estimation problem, and derive a belief propagation algorithm, its relaxed version, for the joint sparse recovery problem and an approximate message passing algorithm. In addition, using density evolution, we provide a sufficient condition for exact recovery.

cs.IT↗

Bistability of an In Vitro Synthetic Autoregulatory Switch

The construction of synthetic biochemical circuits is an essential step for developing quantitative understanding of information processing in natural organisms. Here, we report construction and analysis of an in vitro circuit with positive autoregulation that consists of just four synthetic DNA strands and three enzymes, bacteriophage T7 RNA polymerase, Escherichia coli ribonuclease (RNase) H, and RNase R. The modularity of the DNA switch template allowed a rational design of a synthetic DNA switch regulated by its RNA output acting as a transcription activator. We verified that the thermodynamic and kinetic constraints dictated by the sequence design criteria were enough to experimentally achieve the intended dynamics: a transcription activator configured to regulate its own production. Although only RNase H is necessary to achieve bistability of switch states, RNase R is necessary to maintain stable RNA signal levels and to control incomplete degradation products. A simple mathematical model was used to fit ensemble parameters for the training set of experimental results and was then directly applied to predict time-courses of switch dynamics and sensitivity to parameter variations with reasonable agreement. The positive autoregulation switches can be used to provide constant input signals and store outputs of biochemical networks and are potentially useful for chemical control applications.

q-bio.MN↗