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Sungroh Yoon

Sungroh Yoon appears in the imported research catalog. Authorship, coauthor and topic links are available while profile ownership is still unclaimed.

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Machine LearningComputer VisionArtificial IntelligenceGenomicsNeural and Evolutionary ComputingQuantitative MethodsComputation and Languageeess.ASMethodologySoundComputational Engineering, Finance, and ScienceCryptography and SecurityHardware ArchitectureInformation RetrievalOther Computer Science

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Published work

40 published item(s)

preprint2026arXiv

Diagnosing and Correcting Concept Omission in Multimodal Diffusion Transformers

Multimodal Diffusion Transformers (MM-DiTs) have achieved remarkable progress in text-to-image generation, yet they frequently suffer from concept omission, where specified objects or attributes fail to emerge in the generated image. By performing linear probing on text tokens, we demonstrate that text embeddings can distinguish a characteristic `omission signal' representing the absence of target concepts. Leveraging this insight, we propose Omission Signal Intervention (OSI), which amplifies the omission signal to actively catalyze the generation of missing concepts. Comprehensive experiments on FLUX.1-Dev and SD3.5-Medium demonstrate that OSI significantly alleviates concept omission even in extreme scenarios.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Omni-Persona: Systematic Benchmarking and Improving Omnimodal Personalization

While multimodal large language models have advanced across text, image, and audio, personalization research has remained primarily vision-language, with unified omnimodal benchmarking that jointly covers text, image, and audio still limited, and lacking the methodological rigor to account for absent-persona scenarios or systematic grounding studies. We introduce Omni-Persona, the first comprehensive benchmark for omnimodal personalization. We formalize the task as cross-modal routing over the \emph{Persona Modality Graph}, encompassing 4 task groups and 18 fine-grained tasks across ${\sim}750$ items. To rigorously diagnose grounding behavior, we propose \emph{Calibrated Accuracy ($\mathrm{Cal}$)}, which jointly rewards correct grounding and appropriate abstention, incorporating absent-persona queries within a unified evaluation framework. On our dedicated experiments, three diagnostic findings emerge: (i) open-source models show a consistent audio-vs-visual grounding gap that RLVR partially narrows via dense rule-based supervision; (ii) answerable recall and parameter scale are incomplete diagnostics, since strong recall can coexist with absent-persona hallucination and larger models do not always achieve higher $\mathrm{Cal}$, exposing calibration as a separate evaluation axis; and (iii) SFT is bounded by the difficulty of constructing annotated ground-truth supervision at scale, while RLVR generalizes more consistently through outcome-level verifiable feedback yet drifts toward conservative behavior and lower generation quality under our reward design. Omni-Persona thus serves as a diagnostic framework that surfaces the pitfalls of omnimodal personalization, guiding future post-training and reward design.

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

R2R2: Robust Representation for Intensive Experience Reuse via Redundancy Reduction in Self-Predictive Learning

For reinforcement learning in data-scarce domains like real-world robotics, intensive data reuse enhances efficiency but induces overfitting. While prior works focus on critic bias, representation-level instability in Self-Predictive Learning (SPL) under high Update-to-Data (UTD) regimes remains underexplored. To bridge this gap, we propose Robust Representation via Redundancy Reduction (R2R2), a regularization method within SPL. We theoretically identify that standard zero-centering conflicts with SPL's spectral properties and design a non-centered objective accordingly. We verify R2R2 on SPL-native algorithms like TD7. Furthermore, to demonstrate its orthogonality to prior advancements, we extend the state-of-the-art SimbaV2, which originally lacks SPL, by integrating a tailored SPL module, termed SimbaV2-SPL. Experiments across 11 continuous control tasks confirm that R2R2 effectively mitigates overfitting; specifically, at a UTD ratio of 20, it improves TD7 by ~22% and provides additional gains on top of SimbaV2-SPL, which itself establishes a new state-of-the-art. The code can be found at: https://github.com/songsang7/R2R2

0 citations0 reviewsNo code linkedOpen access
preprint2026arXiv

Verbal-R3: Verbal Reranker as the Missing Bridge between Retrieval and Reasoning

The conventional Retrieval-Augmented Generation (RAG) paradigm of injecting raw retrieved texts into the Large Language Model (LLM)'s context often results in suboptimal integration of retrieved information. This paper proposes to bridge retrieval results and the LLM's reasoning ability through Verbal Annotations, analytic narratives that explicitly articulate the logical connection between a search query and retrieved contexts. Our empirical investigation reveals the potential of Verbal Annotations to substantially enhance the LLM's ability to generate accurate, contextually-grounded responses. Motivated by this finding, we introduce Verbal-R3, a novel agentic RAG framework that consists of a Generator and a Verbal Reranker. The Generator performs iterative retrieval and reasoning, while the Verbal Reranker returns relevance scores and Verbal Annotations to guide the reasoning and answering process of the Generator. The inference process of Verbal-R3 is further refined through relevance-guided test-time scaling, which efficiently allocates test-time compute for effective trajectory expansion. Verbal-R3 achieves state-of-the-art performance on complex Question Answering benchmarks, validating the effectiveness of the proposed framework.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Anti-Adversarially Manipulated Attributions for Weakly Supervised Semantic Segmentation and Object Localization

Obtaining accurate pixel-level localization from class labels is a crucial process in weakly supervised semantic segmentation and object localization. Attribution maps from a trained classifier are widely used to provide pixel-level localization, but their focus tends to be restricted to a small discriminative region of the target object. An AdvCAM is an attribution map of an image that is manipulated to increase the classification score produced by a classifier before the final softmax or sigmoid layer. This manipulation is realized in an anti-adversarial manner, so that the original image is perturbed along pixel gradients in directions opposite to those used in an adversarial attack. This process enhances non-discriminative yet class-relevant features, which make an insufficient contribution to previous attribution maps, so that the resulting AdvCAM identifies more regions of the target object. In addition, we introduce a new regularization procedure that inhibits the incorrect attribution of regions unrelated to the target object and the excessive concentration of attributions on a small region of the target object. Our method achieves a new state-of-the-art performance in weakly and semi-supervised semantic segmentation, on both the PASCAL VOC 2012 and MS COCO 2014 datasets. In weakly supervised object localization, it achieves a new state-of-the-art performance on the CUB-200-2011 and ImageNet-1K datasets.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

AutoSNN: Towards Energy-Efficient Spiking Neural Networks

Spiking neural networks (SNNs) that mimic information transmission in the brain can energy-efficiently process spatio-temporal information through discrete and sparse spikes, thereby receiving considerable attention. To improve accuracy and energy efficiency of SNNs, most previous studies have focused solely on training methods, and the effect of architecture has rarely been studied. We investigate the design choices used in the previous studies in terms of the accuracy and number of spikes and figure out that they are not best-suited for SNNs. To further improve the accuracy and reduce the spikes generated by SNNs, we propose a spike-aware neural architecture search framework called AutoSNN. We define a search space consisting of architectures without undesirable design choices. To enable the spike-aware architecture search, we introduce a fitness that considers both the accuracy and number of spikes. AutoSNN successfully searches for SNN architectures that outperform hand-crafted SNNs in accuracy and energy efficiency. We thoroughly demonstrate the effectiveness of AutoSNN on various datasets including neuromorphic datasets.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Bridging the Gap between Classification and Localization for Weakly Supervised Object Localization

Weakly supervised object localization aims to find a target object region in a given image with only weak supervision, such as image-level labels. Most existing methods use a class activation map (CAM) to generate a localization map; however, a CAM identifies only the most discriminative parts of a target object rather than the entire object region. In this work, we find the gap between classification and localization in terms of the misalignment of the directions between an input feature and a class-specific weight. We demonstrate that the misalignment suppresses the activation of CAM in areas that are less discriminative but belong to the target object. To bridge the gap, we propose a method to align feature directions with a class-specific weight. The proposed method achieves a state-of-the-art localization performance on the CUB-200-2011 and ImageNet-1K benchmarks.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Dataset Condensation with Contrastive Signals

Recent studies have demonstrated that gradient matching-based dataset synthesis, or dataset condensation (DC), methods can achieve state-of-the-art performance when applied to data-efficient learning tasks. However, in this study, we prove that the existing DC methods can perform worse than the random selection method when task-irrelevant information forms a significant part of the training dataset. We attribute this to the lack of participation of the contrastive signals between the classes resulting from the class-wise gradient matching strategy. To address this problem, we propose Dataset Condensation with Contrastive signals (DCC) by modifying the loss function to enable the DC methods to effectively capture the differences between classes. In addition, we analyze the new loss function in terms of training dynamics by tracking the kernel velocity. Furthermore, we introduce a bi-level warm-up strategy to stabilize the optimization. Our experimental results indicate that while the existing methods are ineffective for fine-grained image classification tasks, the proposed method can successfully generate informative synthetic datasets for the same tasks. Moreover, we demonstrate that the proposed method outperforms the baselines even on benchmark datasets such as SVHN, CIFAR-10, and CIFAR-100. Finally, we demonstrate the high applicability of the proposed method by applying it to continual learning tasks.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Demystifying the Neural Tangent Kernel from a Practical Perspective: Can it be trusted for Neural Architecture Search without training?

In Neural Architecture Search (NAS), reducing the cost of architecture evaluation remains one of the most crucial challenges. Among a plethora of efforts to bypass training of each candidate architecture to convergence for evaluation, the Neural Tangent Kernel (NTK) is emerging as a promising theoretical framework that can be utilized to estimate the performance of a neural architecture at initialization. In this work, we revisit several at-initialization metrics that can be derived from the NTK and reveal their key shortcomings. Then, through the empirical analysis of the time evolution of NTK, we deduce that modern neural architectures exhibit highly non-linear characteristics, making the NTK-based metrics incapable of reliably estimating the performance of an architecture without some amount of training. To take such non-linear characteristics into account, we introduce Label-Gradient Alignment (LGA), a novel NTK-based metric whose inherent formulation allows it to capture the large amount of non-linear advantage present in modern neural architectures. With minimal amount of training, LGA obtains a meaningful level of rank correlation with the post-training test accuracy of an architecture. Lastly, we demonstrate that LGA, complemented with few epochs of training, successfully guides existing search algorithms to achieve competitive search performances with significantly less search cost. The code is available at: https://github.com/nutellamok/DemystifyingNTK.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Energy-efficient Knowledge Distillation for Spiking Neural Networks

Spiking neural networks (SNNs) have been gaining interest as energy-efficient alternatives of conventional artificial neural networks (ANNs) due to their event-driven computation. Considering the future deployment of SNN models to constrained neuromorphic devices, many studies have applied techniques originally used for ANN model compression, such as network quantization, pruning, and knowledge distillation, to SNNs. Among them, existing works on knowledge distillation reported accuracy improvements of student SNN model. However, analysis on energy efficiency, which is also an important feature of SNN, was absent. In this paper, we thoroughly analyze the performance of the distilled SNN model in terms of accuracy and energy efficiency. In the process, we observe a substantial increase in the number of spikes, leading to energy inefficiency, when using the conventional knowledge distillation methods. Based on this analysis, to achieve energy efficiency, we propose a novel knowledge distillation method with heterogeneous temperature parameters. We evaluate our method on two different datasets and show that the resulting SNN student satisfies both accuracy improvement and reduction of the number of spikes. On MNIST dataset, our proposed student SNN achieves up to 0.09% higher accuracy and produces 65% less spikes compared to the student SNN trained with conventional knowledge distillation method. We also compare the results with other SNN compression techniques and training methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Guided-TTS 2: A Diffusion Model for High-quality Adaptive Text-to-Speech with Untranscribed Data

We propose Guided-TTS 2, a diffusion-based generative model for high-quality adaptive TTS using untranscribed data. Guided-TTS 2 combines a speaker-conditional diffusion model with a speaker-dependent phoneme classifier for adaptive text-to-speech. We train the speaker-conditional diffusion model on large-scale untranscribed datasets for a classifier-free guidance method and further fine-tune the diffusion model on the reference speech of the target speaker for adaptation, which only takes 40 seconds. We demonstrate that Guided-TTS 2 shows comparable performance to high-quality single-speaker TTS baselines in terms of speech quality and speaker similarity with only a ten-second untranscribed data. We further show that Guided-TTS 2 outperforms adaptive TTS baselines on multi-speaker datasets even with a zero-shot adaptation setting. Guided-TTS 2 can adapt to a wide range of voices only using untranscribed speech, which enables adaptive TTS with the voice of non-human characters such as Gollum in \textit{"The Lord of the Rings"}.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Guided-TTS: A Diffusion Model for Text-to-Speech via Classifier Guidance

We propose Guided-TTS, a high-quality text-to-speech (TTS) model that does not require any transcript of target speaker using classifier guidance. Guided-TTS combines an unconditional diffusion probabilistic model with a separately trained phoneme classifier for classifier guidance. Our unconditional diffusion model learns to generate speech without any context from untranscribed speech data. For TTS synthesis, we guide the generative process of the diffusion model with a phoneme classifier trained on a large-scale speech recognition dataset. We present a norm-based scaling method that reduces the pronunciation errors of classifier guidance in Guided-TTS. We show that Guided-TTS achieves a performance comparable to that of the state-of-the-art TTS model, Grad-TTS, without any transcript for LJSpeech. We further demonstrate that Guided-TTS performs well on diverse datasets including a long-form untranscribed dataset.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Out of Sight, Out of Mind: A Source-View-Wise Feature Aggregation for Multi-View Image-Based Rendering

To estimate the volume density and color of a 3D point in the multi-view image-based rendering, a common approach is to inspect the consensus existence among the given source image features, which is one of the informative cues for the estimation procedure. To this end, most of the previous methods utilize equally-weighted aggregation features. However, this could make it hard to check the consensus existence when some outliers, which frequently occur by occlusions, are included in the source image feature set. In this paper, we propose a novel source-view-wise feature aggregation method, which facilitates us to find out the consensus in a robust way by leveraging local structures in the feature set. We first calculate the source-view-wise distance distribution for each source feature for the proposed aggregation. After that, the distance distribution is converted to several similarity distributions with the proposed learnable similarity mapping functions. Finally, for each element in the feature set, the aggregation features are extracted by calculating the weighted means and variances, where the weights are derived from the similarity distributions. In experiments, we validate the proposed method on various benchmark datasets, including synthetic and real image scenes. The experimental results demonstrate that incorporating the proposed features improves the performance by a large margin, resulting in the state-of-the-art performance.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Perception Prioritized Training of Diffusion Models

Diffusion models learn to restore noisy data, which is corrupted with different levels of noise, by optimizing the weighted sum of the corresponding loss terms, i.e., denoising score matching loss. In this paper, we show that restoring data corrupted with certain noise levels offers a proper pretext task for the model to learn rich visual concepts. We propose to prioritize such noise levels over other levels during training, by redesigning the weighting scheme of the objective function. We show that our simple redesign of the weighting scheme significantly improves the performance of diffusion models regardless of the datasets, architectures, and sampling strategies.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Rare Tokens Degenerate All Tokens: Improving Neural Text Generation via Adaptive Gradient Gating for Rare Token Embeddings

Recent studies have determined that the learned token embeddings of large-scale neural language models are degenerated to be anisotropic with a narrow-cone shape. This phenomenon, called the representation degeneration problem, facilitates an increase in the overall similarity between token embeddings that negatively affect the performance of the models. Although the existing methods that address the degeneration problem based on observations of the phenomenon triggered by the problem improves the performance of the text generation, the training dynamics of token embeddings behind the degeneration problem are still not explored. In this study, we analyze the training dynamics of the token embeddings focusing on rare token embedding. We demonstrate that the specific part of the gradient for rare token embeddings is the key cause of the degeneration problem for all tokens during training stage. Based on the analysis, we propose a novel method called, adaptive gradient gating (AGG). AGG addresses the degeneration problem by gating the specific part of the gradient for rare token embeddings. Experimental results from language modeling, word similarity, and machine translation tasks quantitatively and qualitatively verify the effectiveness of AGG.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Stein Latent Optimization for Generative Adversarial Networks

Generative adversarial networks (GANs) with clustered latent spaces can perform conditional generation in a completely unsupervised manner. In the real world, the salient attributes of unlabeled data can be imbalanced. However, most of existing unsupervised conditional GANs cannot cluster attributes of these data in their latent spaces properly because they assume uniform distributions of the attributes. To address this problem, we theoretically derive Stein latent optimization that provides reparameterizable gradient estimations of the latent distribution parameters assuming a Gaussian mixture prior in a continuous latent space. Structurally, we introduce an encoder network and novel unsupervised conditional contrastive loss to ensure that data generated from a single mixture component represent a single attribute. We confirm that the proposed method, named Stein Latent Optimization for GANs (SLOGAN), successfully learns balanced or imbalanced attributes and achieves state-of-the-art unsupervised conditional generation performance even in the absence of attribute information (e.g., the imbalance ratio). Moreover, we demonstrate that the attributes to be learned can be manipulated using a small amount of probe data.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Towards a Rigorous Evaluation of Time-series Anomaly Detection

In recent years, proposed studies on time-series anomaly detection (TAD) report high F1 scores on benchmark TAD datasets, giving the impression of clear improvements in TAD. However, most studies apply a peculiar evaluation protocol called point adjustment (PA) before scoring. In this paper, we theoretically and experimentally reveal that the PA protocol has a great possibility of overestimating the detection performance; that is, even a random anomaly score can easily turn into a state-of-the-art TAD method. Therefore, the comparison of TAD methods after applying the PA protocol can lead to misguided rankings. Furthermore, we question the potential of existing TAD methods by showing that an untrained model obtains comparable detection performance to the existing methods even when PA is forbidden. Based on our findings, we propose a new baseline and an evaluation protocol. We expect that our study will help a rigorous evaluation of TAD and lead to further improvement in future researches.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Weakly Supervised Semantic Segmentation using Out-of-Distribution Data

Weakly supervised semantic segmentation (WSSS) methods are often built on pixel-level localization maps obtained from a classifier. However, training on class labels only, classifiers suffer from the spurious correlation between foreground and background cues (e.g. train and rail), fundamentally bounding the performance of WSSS. There have been previous endeavors to address this issue with additional supervision. We propose a novel source of information to distinguish foreground from the background: Out-of-Distribution (OoD) data, or images devoid of foreground object classes. In particular, we utilize the hard OoDs that the classifier is likely to make false-positive predictions. These samples typically carry key visual features on the background (e.g. rail) that the classifiers often confuse as foreground (e.g. train), so these cues let classifiers correctly suppress spurious background cues. Acquiring such hard OoDs does not require an extensive amount of annotation efforts; it only incurs a few additional image-level labeling costs on top of the original efforts to collect class labels. We propose a method, W-OoD, for utilizing the hard OoDs. W-OoD achieves state-of-the-art performance on Pascal VOC 2012.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Adversarial Vertex Mixup: Toward Better Adversarially Robust Generalization

Adversarial examples cause neural networks to produce incorrect outputs with high confidence. Although adversarial training is one of the most effective forms of defense against adversarial examples, unfortunately, a large gap exists between test accuracy and training accuracy in adversarial training. In this paper, we identify Adversarial Feature Overfitting (AFO), which may cause poor adversarially robust generalization, and we show that adversarial training can overshoot the optimal point in terms of robust generalization, leading to AFO in our simple Gaussian model. Considering these theoretical results, we present soft labeling as a solution to the AFO problem. Furthermore, we propose Adversarial Vertex mixup (AVmixup), a soft-labeled data augmentation approach for improving adversarially robust generalization. We complement our theoretical analysis with experiments on CIFAR10, CIFAR100, SVHN, and Tiny ImageNet, and show that AVmixup significantly improves the robust generalization performance and that it reduces the trade-off between standard accuracy and adversarial robustness.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

iCaps: An Interpretable Classifier via Disentangled Capsule Networks

We propose an interpretable Capsule Network, iCaps, for image classification. A capsule is a group of neurons nested inside each layer, and the one in the last layer is called a class capsule, which is a vector whose norm indicates a predicted probability for the class. Using the class capsule, existing Capsule Networks already provide some level of interpretability. However, there are two limitations which degrade its interpretability: 1) the class capsule also includes classification-irrelevant information, and 2) entities represented by the class capsule overlap. In this work, we address these two limitations using a novel class-supervised disentanglement algorithm and an additional regularizer, respectively. Through quantitative and qualitative evaluations on three datasets, we demonstrate that the resulting classifier, iCaps, provides a prediction along with clear rationales behind it with no performance degradation.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Joint Contrastive Learning for Unsupervised Domain Adaptation

Enhancing feature transferability by matching marginal distributions has led to improvements in domain adaptation, although this is at the expense of feature discrimination. In particular, the ideal joint hypothesis error in the target error upper bound, which was previously considered to be minute, has been found to be significant, impairing its theoretical guarantee. In this paper, we propose an alternative upper bound on the target error that explicitly considers the joint error to render it more manageable. With the theoretical analysis, we suggest a joint optimization framework that combines the source and target domains. Further, we introduce Joint Contrastive Learning (JCL) to find class-level discriminative features, which is essential for minimizing the joint error. With a solid theoretical framework, JCL employs contrastive loss to maximize the mutual information between a feature and its label, which is equivalent to maximizing the Jensen-Shannon divergence between conditional distributions. Experiments on two real-world datasets demonstrate that JCL outperforms the state-of-the-art methods.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

Patch SVDD: Patch-level SVDD for Anomaly Detection and Segmentation

In this paper, we address the problem of image anomaly detection and segmentation. Anomaly detection involves making a binary decision as to whether an input image contains an anomaly, and anomaly segmentation aims to locate the anomaly on the pixel level. Support vector data description (SVDD) is a long-standing algorithm used for an anomaly detection, and we extend its deep learning variant to the patch-based method using self-supervised learning. This extension enables anomaly segmentation and improves detection performance. As a result, anomaly detection and segmentation performances measured in AUROC on MVTec AD dataset increased by 9.8% and 7.0%, respectively, compared to the previous state-of-the-art methods. Our results indicate the efficacy of the proposed method and its potential for industrial application. Detailed analysis of the proposed method offers insights regarding its behavior, and the code is available online.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

T2FSNN: Deep Spiking Neural Networks with Time-to-first-spike Coding

Spiking neural networks (SNNs) have gained considerable interest due to their energy-efficient characteristics, yet lack of a scalable training algorithm has restricted their applicability in practical machine learning problems. The deep neural network-to-SNN conversion approach has been widely studied to broaden the applicability of SNNs. Most previous studies, however, have not fully utilized spatio-temporal aspects of SNNs, which has led to inefficiency in terms of number of spikes and inference latency. In this paper, we present T2FSNN, which introduces the concept of time-to-first-spike coding into deep SNNs using the kernel-based dynamic threshold and dendrite to overcome the aforementioned drawback. In addition, we propose gradient-based optimization and early firing methods to further increase the efficiency of the T2FSNN. According to our results, the proposed methods can reduce inference latency and number of spikes to 22% and less than 1%, compared to those of burst coding, which is the state-of-the-art result on the CIFAR-100.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Deep Learning in Bioinformatics

In the era of big data, transformation of biomedical big data into valuable knowledge has been one of the most important challenges in bioinformatics. Deep learning has advanced rapidly since the early 2000s and now demonstrates state-of-the-art performance in various fields. Accordingly, application of deep learning in bioinformatics to gain insight from data has been emphasized in both academia and industry. Here, we review deep learning in bioinformatics, presenting examples of current research. To provide a useful and comprehensive perspective, we categorize research both by the bioinformatics domain (i.e., omics, biomedical imaging, biomedical signal processing) and deep learning architecture (i.e., deep neural networks, convolutional neural networks, recurrent neural networks, emergent architectures) and present brief descriptions of each study. Additionally, we discuss theoretical and practical issues of deep learning in bioinformatics and suggest future research directions. We believe that this review will provide valuable insights and serve as a starting point for researchers to apply deep learning approaches in their bioinformatics studies.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

deepMiRGene: Deep Neural Network based Precursor microRNA Prediction

Since microRNAs (miRNAs) play a crucial role in post-transcriptional gene regulation, miRNA identification is one of the most essential problems in computational biology. miRNAs are usually short in length ranging between 20 and 23 base pairs. It is thus often difficult to distinguish miRNA-encoding sequences from other non-coding RNAs and pseudo miRNAs that have a similar length, and most previous studies have recommended using precursor miRNAs instead of mature miRNAs for robust detection. A great number of conventional machine-learning-based classification methods have been proposed, but they often have the serious disadvantage of requiring manual feature engineering, and their performance is limited as well. In this paper, we propose a novel miRNA precursor prediction algorithm, deepMiRGene, based on recurrent neural networks, specifically long short-term memory networks. deepMiRGene automatically learns suitable features from the data themselves without manual feature engineering and constructs a model that can successfully reflect structural characteristics of precursor miRNAs. For the performance evaluation of our approach, we have employed several widely used evaluation metrics on three recent benchmark datasets and verified that deepMiRGene delivered comparable performance among the current state-of-the-art tools.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

DeepSpark: A Spark-Based Distributed Deep Learning Framework for Commodity Clusters

The increasing complexity of deep neural networks (DNNs) has made it challenging to exploit existing large-scale data processing pipelines for handling massive data and parameters involved in DNN training. Distributed computing platforms and GPGPU-based acceleration provide a mainstream solution to this computational challenge. In this paper, we propose DeepSpark, a distributed and parallel deep learning framework that exploits Apache Spark on commodity clusters. To support parallel operations, DeepSpark automatically distributes workloads and parameters to Caffe/Tensorflow-running nodes using Spark, and iteratively aggregates training results by a novel lock-free asynchronous variant of the popular elastic averaging stochastic gradient descent based update scheme, effectively complementing the synchronized processing capabilities of Spark. DeepSpark is an on-going project, and the current release is available at http://deepspark.snu.ac.kr.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

deepTarget: End-to-end Learning Framework for microRNA Target Prediction using Deep Recurrent Neural Networks

MicroRNAs (miRNAs) are short sequences of ribonucleic acids that control the expression of target messenger RNAs (mRNAs) by binding them. Robust prediction of miRNA-mRNA pairs is of utmost importance in deciphering gene regulations but has been challenging because of high false positive rates, despite a deluge of computational tools that normally require laborious manual feature extraction. This paper presents an end-to-end machine learning framework for miRNA target prediction. Leveraged by deep recurrent neural networks-based auto-encoding and sequence-sequence interaction learning, our approach not only delivers an unprecedented level of accuracy but also eliminates the need for manual feature extraction. The performance gap between the proposed method and existing alternatives is substantial (over 25% increase in F-measure), and deepTarget delivers a quantum leap in the long-standing challenge of robust miRNA target prediction.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Intrinsic Geometric Information Transfer Learning on Multiple Graph-Structured Datasets

Graphs provide a powerful means for representing complex interactions between entities. Recently, deep learning approaches are emerging for representing and modeling graph-structured data, although the conventional deep learning methods (such as convolutional neural networks and recurrent neural networks) have mainly focused on grid-structured inputs (image and audio). Leveraged by the capability of representation learning, deep learning based techniques are reporting promising results for graph applications by detecting structural characteristics of graphs in an automated fashion. In this paper, we attempt to advance deep learning for graph-structured data by incorporating another component, transfer learning. By transferring the intrinsic geometric information learned in the source domain, our approach can help us to construct a model for a new but related task in the target domain without collecting new data and without training a new model from scratch. We thoroughly test our approach with large-scale real corpora and confirm the effectiveness of the proposed transfer learning framework for deep learning on graphs. According to our experiments, transfer learning is most effective when the source and target domains bear a high level of structural similarity in their graph representations.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

LSTM-Based System-Call Language Modeling and Robust Ensemble Method for Designing Host-Based Intrusion Detection Systems

In computer security, designing a robust intrusion detection system is one of the most fundamental and important problems. In this paper, we propose a system-call language-modeling approach for designing anomaly-based host intrusion detection systems. To remedy the issue of high false-alarm rates commonly arising in conventional methods, we employ a novel ensemble method that blends multiple thresholding classifiers into a single one, making it possible to accumulate 'highly normal' sequences. The proposed system-call language model has various advantages leveraged by the fact that it can learn the semantic meaning and interactions of each system call that existing methods cannot effectively consider. Through diverse experiments on public benchmark datasets, we demonstrate the validity and effectiveness of the proposed method. Moreover, we show that our model possesses high portability, which is one of the key aspects of realizing successful intrusion detection systems.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Manifold Regularized Deep Neural Networks using Adversarial Examples

Learning meaningful representations using deep neural networks involves designing efficient training schemes and well-structured networks. Currently, the method of stochastic gradient descent that has a momentum with dropout is one of the most popular training protocols. Based on that, more advanced methods (i.e., Maxout and Batch Normalization) have been proposed in recent years, but most still suffer from performance degradation caused by small perturbations, also known as adversarial examples. To address this issue, we propose manifold regularized networks (MRnet) that utilize a novel training objective function that minimizes the difference between multi-layer embedding results of samples and those adversarial. Our experimental results demonstrated that MRnet is more resilient to adversarial examples and helps us to generalize representations on manifolds. Furthermore, combining MRnet and dropout allowed us to achieve competitive classification performances for three well-known benchmarks: MNIST, CIFAR-10, and SVHN.

0 citations0 reviewsNo code linkedOpen access
preprint2016arXiv

Neural Universal Discrete Denoiser

We present a new framework of applying deep neural networks (DNN) to devise a universal discrete denoiser. Unlike other approaches that utilize supervised learning for denoising, we do not require any additional training data. In such setting, while the ground-truth label, i.e., the clean data, is not available, we devise "pseudo-labels" and a novel objective function such that DNN can be trained in a same way as supervised learning to become a discrete denoiser. We experimentally show that our resulting algorithm, dubbed as Neural DUDE, significantly outperforms the previous state-of-the-art in several applications with a systematic rule of choosing the hyperparameter, which is an attractive feature in practice.

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preprint2016arXiv

Regularization and Kernelization of the Maximin Correlation Approach

Robust classification becomes challenging when each class consists of multiple subclasses. Examples include multi-font optical character recognition and automated protein function prediction. In correlation-based nearest-neighbor classification, the maximin correlation approach (MCA) provides the worst-case optimal solution by minimizing the maximum misclassification risk through an iterative procedure. Despite the optimality, the original MCA has drawbacks that have limited its wide applicability in practice. That is, the MCA tends to be sensitive to outliers, cannot effectively handle nonlinearities in datasets, and suffers from having high computational complexity. To address these limitations, we propose an improved solution, named regularized maximin correlation approach (R-MCA). We first reformulate MCA as a quadratically constrained linear programming (QCLP) problem, incorporate regularization by introducing slack variables in the primal problem of the QCLP, and derive the corresponding Lagrangian dual. The dual formulation enables us to apply the kernel trick to R-MCA so that it can better handle nonlinearities. Our experimental results demonstrate that the regularization and kernelization make the proposed R-MCA more robust and accurate for various classification tasks than the original MCA. Furthermore, when the data size or dimensionality grows, R-MCA runs substantially faster by solving either the primal or dual (whichever has a smaller variable dimension) of the QCLP.

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preprint2016arXiv

Training IBM Watson using Automatically Generated Question-Answer Pairs

IBM Watson is a cognitive computing system capable of question answering in natural languages. It is believed that IBM Watson can understand large corpora and answer relevant questions more effectively than any other question-answering system currently available. To unleash the full power of Watson, however, we need to train its instance with a large number of well-prepared question-answer pairs. Obviously, manually generating such pairs in a large quantity is prohibitively time consuming and significantly limits the efficiency of Watson's training. Recently, a large-scale dataset of over 30 million question-answer pairs was reported. Under the assumption that using such an automatically generated dataset could relieve the burden of manual question-answer generation, we tried to use this dataset to train an instance of Watson and checked the training efficiency and accuracy. According to our experiments, using this auto-generated dataset was effective for training Watson, complementing manually crafted question-answer pairs. To the best of the authors' knowledge, this work is the first attempt to use a large-scale dataset of automatically generated question-answer pairs for training IBM Watson. We anticipate that the insights and lessons obtained from our experiments will be useful for researchers who want to expedite Watson training leveraged by automatically generated question-answer pairs.

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preprint2015arXiv

A High-Performance Solid-State Disk with Double-Data-Rate NAND Flash Memory

We propose a novel solid-state disk (SSD) architecture that utilizes a double-data-rate synchronous NAND flash interface for improving read and write performance. Unlike the conventional design, the data transfer rate in the proposed design is doubled in harmony with synchronous signaling. The new architecture does not require any extra pins with respect to the conventional architecture, thereby guaranteeing backward compatibility. For performance evaluation, we simulated various SSD designs that adopt the proposed architecture and measured their performance in terms of read/write bandwidths and energy consumption. Both NAND flash cell types, namely single-level cells (SLCs) and multi-level cells (MLCs), were considered. In the experiments using SLC-type NAND flash chips, the read and write speeds of the proposed architecture were 1.65-2.76 times and 1.09-2.45 times faster than those of the conventional architecture, respectively. Similar improvements were observed for the MLC-based architectures tested. It was particularly effective to combine the proposed architecture with the way-interleaving technique that multiplexes the data channel between the controller and each flash chip. For a reasonably high degree of way interleaving, the read/write performance and the energy consumption of our approach were notably better than those of the conventional design.

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preprint2015arXiv

DNA-Level Splice Junction Prediction using Deep Recurrent Neural Networks

A eukaryotic gene consists of multiple exons (protein coding regions) and introns (non-coding regions), and a splice junction refers to the boundary between a pair of exon and intron. Precise identification of spice junctions on a gene is important for deciphering its primary structure, function, and interaction. Experimental techniques for determining exon/intron boundaries include RNA-seq, which is often accompanied by computational approaches. Canonical splicing signals are known, but computational junction prediction still remains challenging because of a large number of false positives and other complications. In this paper, we exploit deep recurrent neural networks (RNNs) to model DNA sequences and to detect splice junctions thereon. We test various RNN units and architectures including long short-term memory units, gated recurrent units, and recently proposed iRNN for in-depth design space exploration. According to our experimental results, the proposed approach significantly outperforms not only conventional machine learning-based methods but also a recent state-of-the-art deep belief network-based technique in terms of prediction accuracy.

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preprint2015arXiv

FRAME: Fast and Realistic Attacker Modeling and Evaluation for Temporal Logical Correlation in Static Noise

We propose a method called Fast and Realistic Attacker Modeling and Evaluation (FRAME) that can reduce pessimism in static noise analysis by exploiting temporal logical correlation of attackers and using novel techniques termed envelopes and $σ$ functions. Unlike conventional pruning-based approaches, FRAME efficiently considers all relevant attackers, thereby producing more realistic results. FRAME was tested with complex industrial design and successfully reduced the pessimism of conventional techniques by 30.4% on average, with little computational overhead.

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preprint2015arXiv

Will solid-state drives accelerate your bioinformatics? In-depth profiling, performance analysis, and beyond

A wide variety of large-scale data has been produced in bioinformatics. In response, the need for efficient handling of biomedical big data has been partly met by parallel computing. However, the time demand of many bioinformatics programs still remains high for large-scale practical uses due to factors that hinder acceleration by parallelization. Recently, new generations of storage devices have emerged, such as NAND flash-based solid-state drives (SSDs), and with the renewed interest in near-data processing, they are increasingly becoming acceleration methods that can accompany parallel processing. In certain cases, a simple drop-in replacement of hard disk drives (HDDs) by SSDs results in dramatic speedup. Despite the various advantages and continuous cost reduction of SSDs, there has been little review of SSD-based profiling and performance exploration of important but time-consuming bioinformatics programs. For an informative review, we perform in-depth profiling and analysis of 23 key bioinformatics programs using multiple types of devices. Based on the insight we obtain from this research, we further discuss issues related to design and optimize bioinformatics algorithms and pipelines to fully exploit SSDs. The programs we profile cover traditional and emerging areas of importance, such as alignment, assembly, mapping, expression analysis, variant calling, and metagenomics. We explain how acceleration by parallelization can be combined with SSDs for improved performance and also how using SSDs can expedite important bioinformatics pipelines, such as variant calling by the Genome Analysis Toolkit (GATK) and transcriptome analysis using RNA sequencing (RNA-seq). We hope that this review can provide useful directions and tips to accompany future bioinformatics algorithm design procedures that properly consider new generations of powerful storage devices.

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preprint2013arXiv

High-dimensional Fused Lasso Regression using Majorization-Minimization and Parallel Processing

In this paper, we propose a majorization-minimization (MM) algorithm for high-dimensional fused lasso regression (FLR) suitable for parallelization using graphics processing units (GPUs). The MM algorithm is stable and flexible as it can solve the FLR problems with various types of design matrices and penalty structures within a few tens of iterations. We also show that the convergence of the proposed algorithm is guaranteed. We conduct numerical studies to compare our algorithm with other existing algorithms, demonstrating that the proposed MM algorithm is competitive in many settings including the two-dimensional FLR with arbitrary design matrices. The merit of GPU parallelization is also exhibited.

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preprint2013arXiv

HiTRACE-Web: an online tool for robust analysis of high-throughput capillary electrophoresis

To facilitate the analysis of large-scale high-throughput capillary electrophoresis data, we previously proposed a suite of efficient analysis software named HiTRACE (High Throughput Robust Analysis of Capillary Electrophoresis). HiTRACE has been used extensively for quantitating data from RNA and DNA structure mapping experiments, including mutate-and-map contact inference, chromatin footprinting, the EteRNA RNA design project and other high-throughput applications. However, HiTRACE is based on a suite of command-line MATLAB scripts that requires nontrivial efforts to learn, use, and extend. Here we present HiTRACE-Web, an online version of HiTRACE that includes standard features previously available in the command-line version as well as additional features such as automated band annotation and flexible adjustment of annotations, all via a user-friendly environment. By making use of parallelization, the on-line workflow is also faster than software implementations available to most users on their local computers. Free access: http://hitrace.org

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preprint2011arXiv

HiTRACE: High-throughput robust analysis for capillary electrophoresis

Motivation: Capillary electrophoresis (CE) of nucleic acids is a workhorse technology underlying high-throughput genome analysis and large-scale chemical mapping for nucleic acid structural inference. Despite the wide availability of CE-based instruments, there remain challenges in leveraging their full power for quantitative analysis of RNA and DNA structure, thermodynamics, and kinetics. In particular, the slow rate and poor automation of available analysis tools have bottlenecked a new generation of studies involving hundreds of CE profiles per experiment. Results: We propose a computational method called high-throughput robust analysis for capillary electrophoresis (HiTRACE) to automate the key tasks in large-scale nucleic acid CE analysis, including the profile alignment that has heretofore been a rate-limiting step in the highest throughput experiments. We illustrate the application of HiTRACE on thirteen data sets representing 4 different RNAs, three chemical modification strategies, and up to 480 single mutant variants; the largest data sets each include 87,360 bands. By applying a series of robust dynamic programming algorithms, HiTRACE outperforms prior tools in terms of alignment and fitting quality, as assessed by measures including the correlation between quantified band intensities between replicate data sets. Furthermore, while the smallest of these data sets required 7 to 10 hours of manual intervention using prior approaches, HiTRACE quantitation of even the largest data sets herein was achieved in 3 to 12 minutes. The HiTRACE method therefore resolves a critical barrier to the efficient and accurate analysis of nucleic acid structure in experiments involving tens of thousands of electrophoretic bands.

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