arXiv subjects

Seojin Bang

Publications and source records attributed to Seojin Bang.

7 recordsLinked to original sources

arXiv2023

Active Learning Framework for Cost-Effective TCR-Epitope Binding Affinity Prediction

T cell receptors (TCRs) are critical components of adaptive immune systems, responsible for responding to threats by recognizing epitope sequences presented on host cell surface. Computational prediction of binding affinity between TCRs and epitope sequences using machine/deep learning has attracted intense attention recently. However, its success is hindered by the lack of large collections of annotated TCR-epitope pairs. Annotating their binding affinity requires expensive and time-consuming wet-lab evaluation. To reduce annotation cost, we present ActiveTCR, a framework that incorporates active learning and TCR-epitope binding affinity prediction models. Starting with a small set of labeled training pairs, ActiveTCR iteratively searches for unlabeled TCR-epitope pairs that are ''worth'' for annotation. It aims to maximize performance gains while minimizing the cost of annotation. We compared four query strategies with a random sampling baseline and demonstrated that ActiveTCR reduces annotation costs by approximately 40%. Furthermore, we showed that providing ground truth labels of TCR-epitope pairs to query strategies can help identify and reduce more than 40% redundancy among already annotated pairs without compromising model performance, enabling users to train equally powerful prediction models with less training data. Our work is the first systematic investigation of data optimization for TCR-epitope binding affinity prediction.

q-bio.QM↗

arXiv2021

Classifying Argumentative Relations Using Logical Mechanisms and Argumentation Schemes

While argument mining has achieved significant success in classifying argumentative relations between statements (support, attack, and neutral), we have a limited computational understanding of logical mechanisms that constitute those relations. Most recent studies rely on black-box models, which are not as linguistically insightful as desired. On the other hand, earlier studies use rather simple lexical features, missing logical relations between statements. To overcome these limitations, our work classifies argumentative relations based on four logical and theory-informed mechanisms between two statements, namely (i) factual consistency, (ii) sentiment coherence, (iii) causal relation, and (iv) normative relation. We demonstrate that our operationalization of these logical mechanisms classifies argumentative relations without directly training on data labeled with the relations, significantly better than several unsupervised baselines. We further demonstrate that these mechanisms also improve supervised classifiers through representation learning.

cs.CL↗

arXiv2020

Detecting Attackable Sentences in Arguments

Finding attackable sentences in an argument is the first step toward successful refutation in argumentation. We present a first large-scale analysis of sentence attackability in online arguments. We analyze driving reasons for attacks in argumentation and identify relevant characteristics of sentences. We demonstrate that a sentence's attackability is associated with many of these characteristics regarding the sentence's content, proposition types, and tone, and that an external knowledge source can provide useful information about attackability. Building on these findings, we demonstrate that machine learning models can automatically detect attackable sentences in arguments, significantly better than several baselines and comparably well to laypeople.

cs.CL↗

arXiv2020

Dropout Prediction over Weeks in MOOCs via Interpretable Multi-Layer Representation Learning

Massive Open Online Courses (MOOCs) have become popular platforms for online learning. While MOOCs enable students to study at their own pace, this flexibility makes it easy for students to drop out of class. In this paper, our goal is to predict if a learner is going to drop out within the next week, given clickstream data for the current week. To this end, we present a multi-layer representation learning solution based on branch and bound (BB) algorithm, which learns from low-level clickstreams in an unsupervised manner, produces interpretable results, and avoids manual feature engineering. In experiments on Coursera data, we show that our model learns a representation that allows a simple model to perform similarly well to more complex, task-specific models, and how the BB algorithm enables interpretable results. In our analysis of the observed limitations, we discuss promising future directions.

cs.LG↗

arXiv2019

A Mixture Model to Detect Edges in Sparse Co-expression Graphs

In the early days of gene expression data, researchers have focused on gene-level analysis, and particularly on finding differentially expressed genes. This usually involved making a simplifying assumption that genes are independent, which made likelihood derivations feasible and allowed for relatively simple implementations. In recent years, the scope has expanded to include pathway and `gene set' analysis in an attempt to understand the relationships between genes. We develop a method to recover a gene network's structure from co-expression data, measured in terms of normalized Pearson's correlation coefficients between gene pairs. We treat these co-expression measurements as weights in the complete graph in which nodes correspond to genes. To decide which edges exist in the gene network, we fit a three-component mixture model such that the observed weights of `null edges' follow a normal distribution with mean 0, and the non-null edges follow a mixture of two lognormal distributions, one for positively- and one for negatively-correlated pairs. We show that this so-called L2N mixture model outperforms other methods in terms of power to detect edges, and it allows us to control the false discovery rate. Importantly, the method makes no assumptions about the true network structure.

stat.AP↗

arXiv2019

Explaining a black-box using Deep Variational Information Bottleneck Approach

Interpretable machine learning has gained much attention recently. Briefness and comprehensiveness are necessary in order to provide a large amount of information concisely when explaining a black-box decision system. However, existing interpretable machine learning methods fail to consider briefness and comprehensiveness simultaneously, leading to redundant explanations. We propose the variational information bottleneck for interpretation, VIBI, a system-agnostic interpretable method that provides a brief but comprehensive explanation. VIBI adopts an information theoretic principle, information bottleneck principle, as a criterion for finding such explanations. For each instance, VIBI selects key features that are maximally compressed about an input (briefness), and informative about a decision made by a black-box system on that input (comprehensive). We evaluate VIBI on three datasets and compare with state-of-the-art interpretable machine learning methods in terms of both interpretability and fidelity evaluated by human and quantitative metrics

cs.LG↗

arXiv2019

Robust Multiple Kernel k-means Clustering using Min-Max Optimization

Multiple kernel learning is a type of multiview learning that combines different data modalities by capturing view-specific patterns using kernels. Although supervised multiple kernel learning has been extensively studied, until recently, only a few unsupervised approaches have been proposed. In the meanwhile, adversarial learning has recently received much attention. Many works have been proposed to defend against adversarial examples. However, little is known about the effect of adversarial perturbation in the context of multiview learning, and even less in the unsupervised case. In this study, we show that adversarial features added to a view can make the existing approaches with the min-max formulation in multiple kernel clustering yield unfavorable clusters. To address this problem and inspired by recent works in adversarial learning, we propose a multiple kernel clustering method with the min-max framework that aims to be robust to such adversarial perturbation. We evaluate the robustness of our method on simulation data under different types of adversarial perturbations and show that it outperforms several compared existing methods. In the real data analysis, We demonstrate the utility of our method on a real-world problem.

cs.LG↗