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Seungho Choe

Publications and source records attributed to Seungho Choe.

18 recordsLinked to original sources

Mitosis Detection in the Wild: Multi-Tumor and Context-Aware Generalization in the MIDOG 2025 Challenge

Automated mitosis detection is a well-established task in computational pathology. While previous benchmarks focused on scanner-induced domain shift, clinical "real-world" application requires models to be robust across the vast variance to be expected in the histological landscape. The MItosis DOmain Generalization (MIDOG) 2025 challenge was designed to evaluate algorithmic performance across unprecedented biological and contextual diversity. We curated a test dataset of 365 cases, encompassing 12 distinct human, canine and feline tumor types, digitized across multiple scanning platforms. Moving beyond hand-selected hotspots, the challenge required detection also in random tissue areas (representative of the whole slide detection situation) and challenging areas (areas rich in hard negatives). In the second track, we introduced the classification of atypical mitotic figures (AMFs). There were 18 teams submitting to the detection track, with F1 scores ranging up to 0.740. In the AMF detection track, we had 21 submissions with balanced accuracy values up to 0.908. Our analysis reveals that while most models perform reliably in traditional hotspots, significant performance degradation occurs in challenging ROIs, where false positive rates tripled. Furthermore, performance varied significantly across the 12 tumor types, highlighting "blind spots" in current state-of-the-art architectures when encountering rare or highly pleomorphic malignancies. Moreover, we evaluated the effectiveness of ensembling and found a mean increases of 1.5 and 1.3 percentage points in F1 score and balanced accuracy, respectively. In contrast, TTA showed no relevant improvement. MIDOG 2025 demonstrates that "in the wild" mitosis detection remains a significant hurdle. The transition from hotspot-only evaluation to a multi-contextual framework provides a more realistic proxy for clinical reliability.

cs.CV

Teacher-Student Model for Detecting and Classifying Mitosis in the MIDOG 2025 Challenge

Counting mitotic figures is time-intensive for pathologists and leads to inter-observer variability. Artificial intelligence (AI) promises a solution by automatically detecting mitotic figures while maintaining decision consistency. However, AI tools are susceptible to domain shift, where a significant drop in performance can occur due to differences in the training and testing sets, including morphological diversity between organs, species, and variations in staining protocols. Furthermore, the number of mitoses is much less than the count of normal nuclei, which introduces severely imbalanced data for the detection task. In this work, we formulate mitosis detection as a pixel-level segmentation and propose a teacher-student model that simultaneously addresses mitosis detection (Track 1) and atypical mitosis classification (Track 2). Our method is based on a UNet segmentation backbone that integrates domain generalization modules, namely contrastive representation learning and domain-adversarial training. A teacher-student strategy is employed to generate pixel-level pseudo-masks not only for annotated mitoses and hard negatives but also for normal nuclei, thereby enhancing feature discrimination and improving robustness against domain shift. For the classification task, we introduce a multi-scale CNN classifier that leverages feature maps from the segmentation model within a multi-task learning paradigm. On the preliminary test set, the algorithm achieved an F1 score of 0.7660 in Track 1 and balanced accuracy of 0.8414 in Track 2, demonstrating the effectiveness of integrating segmentation-based detection and classification into a unified framework for robust mitosis analysis.

cs.CV

MLP-SRGAN: A Single-Dimension Super Resolution GAN using MLP-Mixer

We propose a novel architecture called MLP-SRGAN, which is a single-dimension Super Resolution Generative Adversarial Network (SRGAN) that utilizes Multi-Layer Perceptron Mixers (MLP-Mixers) along with convolutional layers to upsample in the slice direction. MLP-SRGAN is trained and validated using high resolution (HR) FLAIR MRI from the MSSEG2 challenge dataset. The method was applied to three multicentre FLAIR datasets (CAIN, ADNI, CCNA) of images with low spatial resolution in the slice dimension to examine performance on held-out (unseen) clinical data. Upsampled results are compared to several state-of-the-art SR networks. For images with high resolution (HR) ground truths, peak-signal-to-noise-ratio (PSNR) and structural similarity index (SSIM) are used to measure upsampling performance. Several new structural, no-reference image quality metrics were proposed to quantify sharpness (edge strength), noise (entropy), and blurriness (low frequency information) in the absence of ground truths. Results show MLP-SRGAN results in sharper edges, less blurring, preserves more texture and fine-anatomical detail, with fewer parameters, faster training/evaluation time, and smaller model size than existing methods. Code for MLP-SRGAN training and inference, data generators, models and no-reference image quality metrics will be available at https://github.com/IAMLAB-Ryerson/MLP-SRGAN.

cs.CV

Translocation of a single Arg9 peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method

It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few hundred ns) in all-atom molecular dynamics(MD) simulations because the time required for the translocation of usual CPPs is on the order of minutes or so. In this work, we report a spontaneous translocation of a single Arg$_9$(R9) across a DOPC/DOPG(4:1) model membrane within an order of a few tens ns scale by using the weighted ensemble(WE) method. We identify how water molecules and the orientation of Arg$_9$ play a role in translocation. We also show how lipid molecules are transported along with Arg$_9$. In addition, we present free energy profiles of the translocation across the membrane using umbrella sampling and show that a single Arg$_9$ translocation is energetically unfavorable. We expect that the WE method can help study interactions of CPPs with various model membranes within MD simulation approaches.

q-bio.BM

Free energy analyses of cell-penetrating peptides using the weighted ensemble method

Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg9 (nona-arginine) and Tat interact with a DOPC/DOPG (4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.

q-bio.BM

Molecular dynamics studies of interactions between Arg9(nona-arginine) and a DOPC/DOPG(4:1) membrane

It has been known that the uptake mechanisms of cell-penetrating peptides(CPPs) depend on the experimental conditions such as concentration of peptides, lipid composition, temperature, etc. In this study we investigate the temperature dependence of the penetration of Arg9s into a DOPC/DOPG(4:1) membrane using molecular dynamics(MD) simulations at two different temperatures, T = 310 K and T = 288 K. Although it is difficult to identify the temperature dependence because of having only one single simulation at each temperature and no evidence of translocation of Arg9s across the membrane at both temperatures, our simulations suggest that followings are strongly correlated with the penetration of Arg9s: a number of water molecules coordinated by Arg9s, electrostatic energy between Arg9s and the lipids molecules. We also present how Arg9s change a bending rigidity of the membrane and how a collective behavior between Arg9s enhances the penetration and the membrane bending. Our analyses can be applicable to any cell-penetrating peptides(CPPs) to investigate their interactions with various membranes using MD simulations.

q-bio.BM

CMB Spectral $μ$-Distortion of Multiple Inflation Scenario

In multiple inflation scenario having two inflations with an intermediate matter-dominated phase, the power spectrum is estimated to be enhanced on scales smaller than the horizon size at the beginning of the second inflation, $k > k_{\rm b}$. We require $k_{\rm b} > 10 {\rm Mpc}^{-1}$ to make sure that the enhanced power spectrum is consistent with large scale observation of cosmic microwave background (CMB). We consider the CMB spectral distortions generated by the dissipation of acoustic waves to constrain the power spectrum. The $μ$-distortion value can be $10$ times larger than the expectation of the standard $Λ$CDM model ($μ_{Λ\mathrm{CDM}} \simeq 2 \times 10^{-8}$) for $ k_{\rm b} \lesssim 10^3 {\rm Mpc}^{-1}$, while the $y$-distortion is hardly affected by the enhancement of the power spectrum.

astro-ph.CO

Lyapunov instability of rigid diatomic molecules in three dimensions - a simpler method

We present a new method to calculate Lyapunov exponents of rigid diatomic molecules in three dimensions (12N dimensional phase space). The spectra of Lyapunov exponents are obtained for 32 rigid diatomic molecules interacting through the Weeks-Chandler-Anderson(WCA) potential for various bond length and densities, and compared with those in Y.-H. Shin et al. [Phys. Rev. E 64, 041106 (2001)]. Our algorithm is easy to implement and total CPU time is relatively inexpensive.

cond-mat.stat-mech

Kaon-baryon coupling constants in the QCD sum rule approach

We improve our previous QCD sum rule calculation on G(KNΛ) and G(KNΣ) coupling constants by including the contributions from higher dimensional condensates, <\bar{q} g_s σ\cdot G q> and <\bar{q}q> <(α_s /π) G^2>, in the OPE. It is found that the contribution of these condensates is non-negligible compared to that of the quark condensates. Using a best-fit analysis we find |G(KNΛ)| = 2.49 $\pm$ 1.25 and |G(KNΣ)| = 0.395 $\pm$ 0.377.

nucl-th

f_K/f_pi ratio from QCD sum rules

Using the correlation function of the axial vector mesons, we present a QCD sum rule calculation for the decay constants f_pi and f_K. Our calculations are only weakly dependent on the SU(3) breaking-parameter for the QCD vacuum and give the ratio f_K/f_pi = 1.11 $\pm$ 0.02.

nucl-th

Multiquark picture for Sigma(1620)

In this work we report on a new QCD sum rule analysis to predict masses of the excited baryon states (e.g. Sigma(1620) and Lambda(1405)) by using multiquark interpolating fields ($(q\bar{q})(qqq)$). For the Sigma(1620) we consider the $\bar{K}N$, $πΣ$, and $πΛ$ (I=1) multiquark interpolating fields. The calculated mass from those multiquark states is about 1.592 GeV. For the Lambda(1405) we first show the result using the $π^+Σ^- + π^0Σ^0 + π^-Σ^+$ (I=0) multiquark interpolating field, and compare the calculated mass to that of our previous result using the $π^0Σ^0$ multiquark state. We then show that the mass 1.405 GeV is well reproduced when using the $\bar{K}N$ (I=0) multiquark state. The uncertainties in our sum rules are also discussed.

nucl-th

Lambda(1405) as a multiquark state

In the QCD sum rule approach we predict the $Λ$ (1405) mass by choosing the $π^0Σ^0$ multiquark interpolating field. It is found that the mass is about 1.419 GeV from $Π_1 (q^2)$ sum rule which is more reliable than $Π_q (q^2)$ sum rule, where $Π_q (q^2)$ and $Π_1 (q^2)$ are two invariant functions of the correlator $Π(q^2)$. We also present the sum rules for the $K^+ p$ and the $π^+Σ^+$ multiquark states, and compare to those for the $π^0Σ^0$ multiquark state. The mass of the $Λ$ (1600) can be also reproduced in our approach.

nucl-th

g_{πΛΣ} and g_{K ΣΞ} from QCD sum rules

The coupling constants g_{πΛΣ} and g_{K ΣΞ} are calculated in the QCD sum rule approach using the three-point function method and taking into account the SU(3) symmetry breaking effects. The pattern of SU(3) breaking appears to be different from that based on SU(3) relations.

nucl-th

Sign convention of residues in QCD sum rules

We show that signs of pole residues $λ_N, λ_Λ, λ_Σ, λ_Ξ$ for ${1\over2}^+$ octet baryons are identical in the QCD sum rule approach. To do this we compare signs of meson-baryon coupling constants $ g_{KN Λ}, g_{KN Σ}$, $g_{πΛΣ}$ and $g_{KΛΞ}$ each other.

nucl-th

Multiquark states and QCD sum rules

There have been arguments about hadronic molecules, which are weakly-bound states of two or more hadrons. We investigate the possibility of some candidates (f0 (980), a0 (980), f0 (1500), f0 (1710), etc.) using QCD sum rule approach and compare our results with multiquark states in the MIT bag model. We find that f0 (1500), f0 (1710) can be good candidates for vector-vector molecule-type multiquark states.

hep-ph

$g_{K N Λ}$ and $g_{K N Σ}$ from QCD sum rules

$g_{K N Λ}$ and $g_{K N Σ}$ are calculated using a QCD sum rule motivated method used by Reinders, Rubinstein and Yazaki to extract Hadron couplings to goldstone bosons. The SU(3) symmetry breaking effects are taken into account by including the contributions from the strange quark mass and assuming different values for the strange and the up down quark condensates. We find $g_{K N Λ}/\sqrt{4 π} = - 1.96 $ and $g_{K N Σ}/\sqrt{4 π} = 0.33 $

nucl-th

QCD sum rules and chiral logarithms

Standard QCD sum-rule analyses of the nucleon mass give results that are inconsistent with chiral perturbation theory due to an overly simple continuum ansatz on the phenomenological side of the sum rule. We show that a careful treatment of the continuum, including $π$-$N$ states and other states with virtual pions, resolves the inconsistency associated with chiral logs.

hep-ph