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Sun Kim

Publications and source records attributed to Sun Kim.

At least 19 recordsLinked to original sources
arXiv2026

VAmoS Bench: Voice Agent Simulation Bench

Production voice agents span cascaded, speech-to-speech, and hybrid architectures. Voice-agent benchmarks typically measure component quality and conversational properties such as word error rate, latency, naturalness, and turn-taking. Fewer measure whether the agent handled a phone call correctly on its own. Contact centers refer to this as ``containment'': the share of phone calls the automated system resolves without handing off to a human. On some phone calls the right outcome is refusal or a redirect. To address this gap, we introduce VAmoS Bench, the Voice Agent Simulation Bench. It measures complete voice-agent systems end to end in a stateful customer-support task. The agent is Riley, a credit-card support representative for a fictional bank who can freeze, cancel, replace, or activate a card. Each of 100 scenarios supplies a simulated caller with a private goal and a seeded PostgreSQL backend. The platform uses each scenario to populate and activate an isolated simulation in which the caller reaches Riley over audio; roughly one-third apply adversarial pressure. The agent can use five tools that execute real SQL against the backend. Each scenario also defines binary assertions. A grader evaluates them against the complete trace of what the caller and agent said and what the agent did, including tool invocations, arguments, and returned rows. This catches an agent that claims to have changed a card without updating the database, as well as one that makes the right database change while disclosing protected information. This first benchmark version focuses on financial services. Its evaluation protocol supports an evolving leaderboard: additional voice agents can be evaluated on the same version, while later versions can expand the tasks and scenarios.

cs.AI↗
arXiv2026

Predicting Therapeutic Outcome via Aligning Patient-Specific Knowledge Graph and Gene-Level Perturbation Representations

Accurate prediction of patient-specific therapeutic response from pre-treatment transcriptomes is hindered by the scarcity of matched clinical response labels and post-treatment molecular profiles. Preclinical transfer-learning models can simulate drug-induced expression changes but are often hard to interpret and unstable, whereas knowledge-graph methods provide mechanistic context yet remain static and fail to capture drug-induced transcriptomic perturbation dynamics. We propose PREDIKTOR, a patient-centered multi-view framework that aligns a personalized network view with a transferable transcriptomic perturbation view to predict clinical drug response. For each patient, we construct an individualized gene regulatory network from tumor expression using DysRegNet and augment it with drug-target links from DrugBank; a graph neural encoder yields a drug-centric, mechanistically grounded embedding. In parallel, a frozen condition-specific gene-gene attention model pretrained on LINCS L1000 generates a simulated post-perturbation transcriptomic profile for the same patient-drug pair. We align the two views in a shared latent space via a CLIP-style contrastive objective with drug-context hard negatives, then concatenate the representations for end-to-end response classification. On TCGA, PREDIKTOR consistently outperforms state-of-the-art baselines under patient-, drug-, and tissue-split evaluations, and transfers zero-shot to the I-SPY2 trial, improving AUROC by 5.6% over competing methods. The aligned embeddings yield stable gene and pathway attributions that recover known mechanisms, supporting actionable and interpretable precision oncology.

cs.LG↗
arXiv2026

ISAAC: Auditing Causal Reasoning in Deep Models for Drug-Target Interaction

Deep learning models for drug--target interaction (DTI) prediction often achieve strong benchmark performance without necessarily relying on mechanistically meaningful molecular features, a limitation that standard accuracy-based evaluation cannot detect. We introduce ISAAC (Intervention-based Structural Auditing Approach for Causal Reasoning), a post-hoc framework that evaluates prior-relative structural sensitivity by probing frozen models through matched mechanistic and spurious input-level interventions, independently of predictive accuracy. Applied to three sequence-based DTI architectures on the Davis benchmark, ISAAC reveals approximately 25\% relative differences in reasoning scores across models with comparable AUROC (within around 3\%), stable across training and intervention seeds and two distinct perturbation operators. These discrepancies, undetectable under conventional accuracy metrics, motivate the use of post-hoc structural auditing as a complement to standard performance evaluation in scientific machine learning for molecular modeling.

cs.LG↗
arXiv2026

CombiMOTS: Combinatorial Multi-Objective Tree Search for Dual-Target Molecule Generation

Dual-target molecule generation, which focuses on discovering compounds capable of interacting with two target proteins, has garnered significant attention due to its potential for improving therapeutic efficiency, safety and resistance mitigation. Existing approaches face two critical challenges. First, by simplifying the complex dual-target optimization problem to scalarized combinations of individual objectives, they fail to capture important trade-offs between target engagement and molecular properties. Second, they typically do not integrate synthetic planning into the generative process. This highlights a need for more appropriate objective function design and synthesis-aware methodologies tailored to the dual-target molecule generation task. In this work, we propose CombiMOTS, a Pareto Monte Carlo Tree Search (PMCTS) framework that generates dual-target molecules. CombiMOTS is designed to explore a synthesizable fragment space while employing vectorized optimization constraints to encapsulate target affinity and physicochemical properties. Extensive experiments on real-world databases demonstrate that CombiMOTS produces novel dual-target molecules with high docking scores, enhanced diversity, and balanced pharmacological characteristics, showcasing its potential as a powerful tool for dual-target drug discovery. The code and data is accessible through https://github.com/Tibogoss/CombiMOTS.

cs.LG↗
arXiv2025

SubDyve: Subgraph-Driven Dynamic Propagation for Virtual Screening Enhancement Controlling False Positive

Virtual screening (VS) aims to identify bioactive compounds from vast chemical libraries, but remains difficult in low-label regimes where only a few actives are known. Existing methods largely rely on general-purpose molecular fingerprints and overlook class-discriminative substructures critical to bioactivity. Moreover, they consider molecules independently, limiting effectiveness in low-label regimes. We introduce SubDyve, a network-based VS framework that constructs a subgraph-aware similarity network and propagates activity signals from a small known actives. When few active compounds are available, SubDyve performs iterative seed refinement, incrementally promoting new candidates based on local false discovery rate. This strategy expands the seed set with promising candidates while controlling false positives from topological bias and overexpansion. We evaluate SubDyve on ten DUD-E targets under zero-shot conditions and on the CDK7 target with a 10-million-compound ZINC dataset. SubDyve consistently outperforms existing fingerprint or embedding-based approaches, achieving margins of up to +34.0 on the BEDROC and +24.6 on the EF1% metric.

cs.LG↗
arXiv2025

Ninth degree analogue of Ramanujan's septic theta function identity

On page 206 in his lost notebook, Ramanujan recorded a seventh degree identity for his theta function $\varphi(q)$. We give an analogous ninth degree identity. We also provide an application of an entry from his second notebook on a cubic equation and an interpretation with theta functions for some of his trigonometric identities. Lastly, we calculate five examples for $\varphi(e^{-\pi\sqrt{n}})$.

math.NT↗
arXiv2025

AI-driven Automation of End-to-end Assessment of Suturing Expertise

We present an AI based approach to automate the End-to-end Assessment of Suturing Expertise (EASE), a suturing skills assessment tool that comprehensively defines criteria around relevant sub-skills.1 While EASE provides granular skills assessment related to suturing to provide trainees with an objective evaluation of their aptitude along with actionable insights, the scoring process is currently performed by human evaluators, which is time and resource consuming. The AI based approach solves this by enabling real-time score prediction with minimal resources during model inference. This enables the possibility of real-time feedback to the surgeons/trainees, potentially accelerating the learning process for the suturing task and mitigating critical errors during the surgery, improving patient outcomes. In this study, we focus on the following 7 EASE domains that come under 3 suturing phases: 1) Needle Handling: Number of Repositions, Needle Hold Depth, Needle Hold Ratio, and Needle Hold Angle; 2) Needle Driving: Driving Smoothness, and Wrist Rotation; 3) Needle Withdrawal: Wrist Rotation.

cs.CV↗
arXiv2025

GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention

Molecular language modeling tasks such as molecule captioning have been recognized for their potential to further understand molecular properties that can aid drug discovery or material synthesis based on chemical reactions. Unlike the common use of molecule graphs in predicting molecular properties, most methods in molecular language modeling rely heavily on SMILES sequences. This preference is because the task involves generating a sequence of multiple tokens using transformer-based models. Therefore, a main challenge is determining how to integrate graph data, which contains structural and spatial information about molecules, with text data. In addition, simply using both 1D SMILES text and 2D graph as inputs without addressing how they align and represent the molecule structure in different modalities makes it challenging to fully utilize structural knowledge about molecules. To this end, we propose GraphT5, a multi-modal framework that integrates 1D SMILES text and 2D graph representations of molecules for molecular language modeling. Specifically, we introduce a novel cross-token attention module in GraphT5 to bridge the gap arising from the fundamental differences between the two modalities of molecule representations. Cross-token attention exploits implicit information between SMILES and graphs of molecules, resulting from their interactions at a fine-grained token level that benefits molecular language modeling. Extensive experiments including molecule captioning, IUPAC name prediction tasks, and case studies show that our GraphT5 outperforms the latest baseline approaches, which validates the effectiveness of our GraphT5 in sufficiently utilizing 1D SMILES text and 2D graph representations.

cs.LG↗
arXiv2025

MV-CLAM: Multi-View Molecular Interpretation with Cross-Modal Projection via Language Model

Human expertise in chemistry and biomedicine relies on contextual molecular understanding, a capability that large language models (LLMs) can extend through fine-grained alignment between molecular structures and text. Recent multimodal learning advances focus on cross-modal alignment, but existing molecule-text models ignore complementary information in different molecular views and rely on single-view representations, limiting molecular understanding. Moreover, na\"ive multi-view alignment strategies face two challenges: (1) separate aligned spaces with inconsistent mappings between molecule and text embeddings, and that (2) existing loss objectives fail to preserve complementary information for fine-grained alignment. This can limit the LLM's ability to fully understand the molecular properties. To address these issues, we propose MV-CLAM, a novel framework that aligns multi-view molecular representations into a unified textual space using a multi-query transformer (MQ-Former). Our approach ensures cross-view consistency while a token-level contrastive loss preserves diverse molecular features across textual queries. MV-CLAM enhances molecular reasoning, improving retrieval and captioning accuracy. The source code of MV-CLAM is available in https://github.com/sumin124/mv-clam.git.

cs.CL↗
arXiv2024

SLM as Guardian: Pioneering AI Safety with Small Language Models

Most prior safety research of large language models (LLMs) has focused on enhancing the alignment of LLMs to better suit the safety requirements of humans. However, internalizing such safeguard features into larger models brought challenges of higher training cost and unintended degradation of helpfulness. To overcome such challenges, a modular approach employing a smaller LLM to detect harmful user queries is regarded as a convenient solution in designing LLM-based system with safety requirements. In this paper, we leverage a smaller LLM for both harmful query detection and safeguard response generation. We introduce our safety requirements and the taxonomy of harmfulness categories, and then propose a multi-task learning mechanism fusing the two tasks into a single model. We demonstrate the effectiveness of our approach, providing on par or surpassing harmful query detection and safeguard response performance compared to the publicly available LLMs.

cs.CL↗
arXiv2024

Taxonomy and Analysis of Sensitive User Queries in Generative AI Search

Although there has been a growing interest among industries in integrating generative LLMs into their services, limited experience and scarcity of resources act as a barrier in launching and servicing large-scale LLM-based services. In this paper, we share our experiences in developing and operating generative AI models within a national-scale search engine, with a specific focus on the sensitiveness of user queries. We propose a taxonomy for sensitive search queries, outline our approaches, and present a comprehensive analysis report on sensitive queries from actual users. We believe that our experiences in launching generative AI search systems can contribute to reducing the barrier in building generative LLM-based services.

cs.IR↗
arXiv2024

Evaluations and relations for finite trigonometric sums

Several methods are used to evaluate finite trigonometric sums. In each case, either the sum had not previously been evaluated, or it had been evaluated, but only by analytic means, e.g., by complex analysis or modular transformation formulas. We establish both reciprocity and three sum relations for trigonometric sums. Motivated by certain sums that we have evaluated, we add coprime conditions to the summands and thereby define analogues of Ramanujan sums, which we in turn evaluate. One of these analogues leads to a criterion for the Riemann Hypothesis, analogous to the Franel-Landau criterion.

math.NT↗
arXiv2024

Improving out-of-distribution generalization in graphs via hierarchical semantic environments

Out-of-distribution (OOD) generalization in the graph domain is challenging due to complex distribution shifts and a lack of environmental contexts. Recent methods attempt to enhance graph OOD generalization by generating flat environments. However, such flat environments come with inherent limitations to capture more complex data distributions. Considering the DrugOOD dataset, which contains diverse training environments (e.g., scaffold, size, etc.), flat contexts cannot sufficiently address its high heterogeneity. Thus, a new challenge is posed to generate more semantically enriched environments to enhance graph invariant learning for handling distribution shifts. In this paper, we propose a novel approach to generate hierarchical semantic environments for each graph. Firstly, given an input graph, we explicitly extract variant subgraphs from the input graph to generate proxy predictions on local environments. Then, stochastic attention mechanisms are employed to re-extract the subgraphs for regenerating global environments in a hierarchical manner. In addition, we introduce a new learning objective that guides our model to learn the diversity of environments within the same hierarchy while maintaining consistency across different hierarchies. This approach enables our model to consider the relationships between environments and facilitates robust graph invariant learning. Extensive experiments on real-world graph data have demonstrated the effectiveness of our framework. Particularly, in the challenging dataset DrugOOD, our method achieves up to 1.29% and 2.83% improvement over the best baselines on IC50 and EC50 prediction tasks, respectively.

cs.LG↗
arXiv2023

Clinical Note Owns its Hierarchy: Multi-Level Hypergraph Neural Networks for Patient-Level Representation Learning

Leveraging knowledge from electronic health records (EHRs) to predict a patient's condition is essential to the effective delivery of appropriate care. Clinical notes of patient EHRs contain valuable information from healthcare professionals, but have been underused due to their difficult contents and complex hierarchies. Recently, hypergraph-based methods have been proposed for document classifications. Directly adopting existing hypergraph methods on clinical notes cannot sufficiently utilize the hierarchy information of the patient, which can degrade clinical semantic information by (1) frequent neutral words and (2) hierarchies with imbalanced distribution. Thus, we propose a taxonomy-aware multi-level hypergraph neural network (TM-HGNN), where multi-level hypergraphs assemble useful neutral words with rare keywords via note and taxonomy level hyperedges to retain the clinical semantic information. The constructed patient hypergraphs are fed into hierarchical message passing layers for learning more balanced multi-level knowledge at the note and taxonomy levels. We validate the effectiveness of TM-HGNN by conducting extensive experiments with MIMIC-III dataset on benchmark in-hospital-mortality prediction.

cs.CL↗
arXiv2022

Exact evaluations and reciprocity theorems for finite trigonometric sums

We evaluate in closed form several classes of finite trigonometric sums. Two general methods are used. The first is new and involves sums of roots of unity. The second uses contour integration and extends a previous method used by two of the authors. Reciprocity theorems for certain trigonometric sums are also established.

math.NT↗
arXiv2022

SPGP: Structure Prototype Guided Graph Pooling

While graph neural networks (GNNs) have been successful for node classification tasks and link prediction tasks in graph, learning graph-level representations still remains a challenge. For the graph-level representation, it is important to learn both representation of neighboring nodes, i.e., aggregation, and graph structural information. A number of graph pooling methods have been developed for this goal. However, most of the existing pooling methods utilize k-hop neighborhood without considering explicit structural information in a graph. In this paper, we propose Structure Prototype Guided Pooling (SPGP) that utilizes prior graph structures to overcome the limitation. SPGP formulates graph structures as learnable prototype vectors and computes the affinity between nodes and prototype vectors. This leads to a novel node scoring scheme that prioritizes informative nodes while encapsulating the useful structures of the graph. Our experimental results show that SPGP outperforms state-of-the-art graph pooling methods on graph classification benchmark datasets in both accuracy and scalability.

cs.LG↗
arXiv2022

Triangular Contrastive Learning on Molecular Graphs

Recent contrastive learning methods have shown to be effective in various tasks, learning generalizable representations invariant to data augmentation thereby leading to state of the art performances. Regarding the multifaceted nature of large unlabeled data used in self-supervised learning while majority of real-word downstream tasks use single format of data, a multimodal framework that can train single modality to learn diverse perspectives from other modalities is an important challenge. In this paper, we propose TriCL (Triangular Contrastive Learning), a universal framework for trimodal contrastive learning. TriCL takes advantage of Triangular Area Loss, a novel intermodal contrastive loss that learns the angular geometry of the embedding space through simultaneously contrasting the area of positive and negative triplets. Systematic observation on embedding space in terms of alignment and uniformity showed that Triangular Area Loss can address the line-collapsing problem by discriminating modalities by angle. Our experimental results also demonstrate the outperformance of TriCL on downstream task of molecular property prediction which implies that the advantages of the embedding space indeed benefits the performance on downstream tasks.

cs.LG↗