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Sun Kim

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Machine Learning math.NT Computation and Language Information Retrieval Computation Human-Computer Interaction

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preprint2026arXiv

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.

preprint2022arXiv

Sparse Structure Learning via Graph Neural Networks for Inductive Document Classification

Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word ambiguity, (2) word synonymity, and (3) dynamic contextual dependency. To address these challenges, we propose a novel GNN-based sparse structure learning model for inductive document classification. Specifically, a document-level graph is initially generated by a disjoint union of sentence-level word co-occurrence graphs. Our model collects a set of trainable edges connecting disjoint words between sentences and employs structure learning to sparsely select edges with dynamic contextual dependencies. Graphs with sparse structures can jointly exploit local and global contextual information in documents through GNNs. For inductive learning, the refined document graph is further fed into a general readout function for graph-level classification and optimization in an end-to-end manner. Extensive experiments on several real-world datasets demonstrate that the proposed model outperforms most state-of-the-art results, and reveal the necessity to learn sparse structures for each document.

preprint2022arXiv

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.

preprint2021arXiv

Balanced Derivatives, Identities, and Bounds for Trigonometric and Bessel Series

Motivated by two identities published with Ramanujan's lost notebook and connected, respectively, with the Gauss circle problem and the Dirichlet divisor problem, in an earlier paper, three of the present authors derived representations for certain sums of products of trigonometric functions as double series of Bessel functions. These series are generalized in the present paper by introducing the novel notion of balanced derivatives, leading to further theorems. As we will see below, the regions of convergence in the unbalanced case are entirely different than those in the balanced case. From this viewpoint, it is remarkable that Ramanujan had the intuition to formulate entries that are, in our new terminology, "balanced". If $x$ denotes the number of products of the trigonometric functions appearing in our sums, in addition to proving the identities mentioned above, theorems and conjectures for upper and lower bounds for the sums as $x\to\infty$ are established.

preprint2020arXiv

TeamTat: a collaborative text annotation tool

Manually annotated data is key to developing text-mining and information-extraction algorithms. However, human annotation requires considerable time, effort and expertise. Given the rapid growth of biomedical literature, it is paramount to build tools that facilitate speed and maintain expert quality. While existing text annotation tools may provide user-friendly interfaces to domain experts, limited support is available for image display, project management, and multi-user team annotation. In response, we developed TeamTat (teamtat.org), a web-based annotation tool (local setup available), equipped to manage team annotation projects engagingly and efficiently. TeamTat is a novel tool for managing multi-user, multi-label document annotation, reflecting the entire production life cycle. Project managers can specify annotation schema for entities and relations and select annotator(s) and distribute documents anonymously to prevent bias. Document input format can be plain text, PDF or BioC, (uploaded locally or automatically retrieved from PubMed or PMC), and output format is BioC with inline annotations. TeamTat displays figures from the full text for the annotators convenience. Multiple users can work on the same document independently in their workspaces, and the team manager can track task completion. TeamTat provides corpus-quality assessment via inter-annotator agreement statistics, and a user-friendly interface convenient for annotation review and inter-annotator disagreement resolution to improve corpus quality.

preprint2020arXiv

The distribution of spacings between the fractional parts of $\boldsymbol{n^dα}$

We study the distribution of spacings between the fractional parts of $n^dα$. For $α$ of high enough Diophantine type we prove a necessary and sufficient condition for $n^dα\mod 1, 1\leq n\leq N,$ to be Poissonian as $N\to \infty$ along a suitable subsequence.

preprint2019arXiv

BioConceptVec: creating and evaluating literature-based biomedical concept embeddings on a large scale

Capturing the semantics of related biological concepts, such as genes and mutations, is of significant importance to many research tasks in computational biology such as protein-protein interaction detection, gene-drug association prediction, and biomedical literature-based discovery. Here, we propose to leverage state-of-the-art text mining tools and machine learning models to learn the semantics via vector representations (aka. embeddings) of over 400,000 biological concepts mentioned in the entire PubMed abstracts. Our learned embeddings, namely BioConceptVec, can capture related concepts based on their surrounding contextual information in the literature, which is beyond exact term match or co-occurrence-based methods. BioConceptVec has been thoroughly evaluated in multiple bioinformatics tasks consisting of over 25 million instances from nine different biological datasets. The evaluation results demonstrate that BioConceptVec has better performance than existing methods in all tasks. Finally, BioConceptVec is made freely available to the research community and general public via https://github.com/ncbi-nlp/BioConceptVec.

preprint2016arXiv

On a theorem of A. I. Popov on sums of squares

Let $r_k(n)$ denote the number of representations of the positive integer $n$ as the sum of $k$ squares. In 1934, the Russian mathematician A.~I.~Popov stated, but did not rigorously prove, a beautiful series transformation involving $r_k(n)$ and certain Bessel functions. We provide a proof of this identity for the first time, as well as for another identity, which can be regarded as both an analogue of Popov's identity and an identity involving $r_2(n)$ from Ramanujan's lost notebook.