arXiv subjects

Seungik Cho

Publications and source records attributed to Seungik Cho.

6 recordsLinked to original sources

arXiv2026

BioKERN: Biological Kernel Regularization for Histology-to-Transcriptomics Neighborhood Retrieval

Spatially resolved biology requires representations that preserve biological neighborhood structure rather than only exact cross-modal correspondences. Existing histology--transcriptomics objectives can emphasize instance-level matching even when non-paired spots share molecular or spatial context. We introduce BioKERN, a multimodal spatial representation-learning framework that incorporates biological structure as an explicit, learnable inductive bias. BioKERN constructs a training-time biological kernel by combining transcriptomic similarity and spatial proximity, then uses it to provide graded neighborhood supervision and regularize embedding geometry. Evaluation uses a fixed, model-independent biological neighborhood definition shared by all methods. Across Mouse Brain Visium and Human Liver GSE240429, BioKERN consistently improves biological-neighborhood retrieval over BLEEP in both single- and multi-scale settings. Controlled shared-architecture experiments show that most of the improvement arises from biological-kernel regularization rather than increased model capacity. These results support explicit biological geometry as an interpretable inductive bias for multimodal learning in spatial biology.

cs.LG↗

arXiv2026

MedMIX: Modality-Internal Expert Fusion for Multimodal Medical Diagnosis

Multimodal clinical prediction faces three challenges: multiple foundation models (FMs) with complementary strengths per modality, pervasive missing modalities at training and test time, and sample-specific variation in modality contributions. We introduce MedMIX, a multimodal framework that combines intra-modality expert fusion, learned inter-modality fusion, and training-only large--small model collaboration for robust medical prediction under incomplete modalities. Within each modality, MedMIX aggregates complementary embeddings from multiple small expert models; across modalities, it performs learned fusion over available modalities; and during training, it leverages large teacher models to improve deployed representations without additional inference cost. Across three heterogeneous benchmarks (OpenI, MIMIC-IV-MM, and MMIST-ccRCC), MedMIX achieves consistently strong performance while remaining robust under controlled missing-modality perturbations, and further demonstrates sustained robustness under cross-cohort shift on MIMIC-III. These results highlight MedMIX as a practical framework that unifies within-modality expert collaboration, sample-specific cross-modality fusion, and efficient large--small model collaboration while remaining robust to incomplete modalities.

cs.LG↗

arXiv2026

MicroFuse: Protein-to-Genome Expert Fusion for Microbial Operon Reasoning

Predicting microbial operon co-membership requires integrating two complementary biological signals: protein-scale molecular identity and genome-context organization. While recent biological foundation models provide powerful representations of each view independently, naive concatenation of these modalities ignores a key biological property -- protein identity and genomic context may agree when adjacent genes form a coherent functional module, or conflict when sequence similarity is misleading but genomic layout indicates independent regulation. We present MicroFuse, a protein-to-genome expert fusion framework that integrates structure-aware protein representations from ProstT5 with genome-context representations from Bacformer through a four-expert Mixture-of-Experts module (protein, genome-context, agreement, and conflict experts) with a learned soft router. Training combines binary cross-entropy with symmetric cross-modal InfoNCE alignment and disagreement-weighted supervised contrastive shaping. We further construct OG-Operon100K, a 100,000-pair scaffold-level benchmark from the OMG metagenomic corpus with biologically grounded positive and negative criteria. On OG-Operon100K, MicroFuse achieves the strongest AUROC, AUPRC, mAP, and mAR among ProstT5-only, Bacformer-only, and Concat MLP baselines. Ablations identify cross-modal contrastive alignment as the dominant component, and a hard sequence-conflict subset reveals MicroFuse's largest gains precisely in biologically ambiguous cases where protein identity alone is misleading.

cs.LG↗

arXiv2026

TriFit: Trimodal Fusion with Protein Dynamics for Mutation Fitness Prediction

Predicting the functional impact of single amino acid substitutions (SAVs) is central to understanding genetic disease and engineering therapeutic proteins. While protein language models and structure-based methods have achieved strong performance on this task, they systematically neglect protein dynamics; residue flexibility, correlated motions, and allosteric coupling are well-established determinants of mutational tolerance in structural biology, yet have not been incorporated into supervised variant effect predictors. We present TriFit, a multimodal framework that integrates sequence, structure, and protein dynamics through a four-expert Mixture-of-Experts (MoE) fusion module with trimodal cross-modal contrastive learning. Sequence embeddings are extracted via masked marginal scoring with ESM-2 (650M); structural embeddings from AlphaFold2-predicted C-alpha geometries; and dynamics embeddings from Gaussian Network Model (GNM) B-factors, mode shapes, and residue-residue cross-correlations. The MoE router adaptively weights modality combinations conditioned on the input, enabling protein-specific fusion without fixed modality assumptions. On the ProteinGym substitution benchmark (217 DMS assays, 696k SAVs), TriFit achieves AUROC 0.897 +/- 0.0002, outperforming all supervised baselines including Kermut (0.864) and ProteinNPT (0.844), and the best zero-shot model ESM3 (0.769). Ablation studies confirm that dynamics provides the largest marginal contribution over pairwise modality combinations, and TriFit achieves well-calibrated probabilistic outputs (ECE = 0.044) without post-hoc correction.

cs.LG↗

arXiv2026

TopoGate: Quality-Aware Topology-Stabilized Gated Fusion for Longitudinal Low-Dose CT New-Lesion Prediction

Longitudinal low-dose CT follow-ups vary in noise, reconstruction kernels, and registration quality. These differences destabilize subtraction images and can trigger false new lesion alarms. We present TopoGate, a lightweight model that combines the follow-up appearance view with the subtraction view and controls their influence through a learned, quality-aware gate. The gate is driven by three case-specific signals: CT appearance quality, registration consistency, and stability of anatomical topology measured with topological metrics. On the NLST--New-Lesion--LongCT cohort comprising 152 pairs from 122 patients, TopoGate improves discrimination and calibration over single-view baselines, achieving an area under the ROC curve of 0.65 with a standard deviation of 0.05 and a Brier score of 0.14. Removing corrupted or low-quality pairs, identified by the quality scores, further increases the area under the ROC curve from 0.62 to 0.68 and reduces the Brier score from 0.14 to 0.12. The gate responds predictably to degradation, placing more weight on appearance when noise grows, which mirrors radiologist practice. The approach is simple, interpretable, and practical for reliable longitudinal LDCT triage.

eess.IV↗

arXiv2015

High Speed CAN Transmission Scheme Supporting Data Rate of over 100 Mbps

As the number of electronic components in the car increases, the requirement for the higher data transmission scheme among them is on the sharp rise. Controller area network (CAN) has been widely adopted to support the in-car communications needs but the data rate is far below what other schemes such as Ethernet and optical fibers can offer. A new scheme for enhancing the speed of CAN network has been proposed, where carrier modulated signal is introduced on top of the existing CAN signal whereby the data rate can be enhanced over 100Mbps. The proposed scheme is compatible with the existing CAN network and accordingly enables seamless upgrade of the existing network to support high speed demand using CAN protocol.

cs.IT↗