MOTIVATION: Leveraging deep learning for the representation learning of Gene Ontology (GO) and Gene Ontology Annotation (GOA) holds significant promise for enhancing downstream biological tasks such as protein-protein interaction prediction. Prior approaches have predominantly used text- and graph-based methods, embedding GO and GOA in a single geometric space (e.g. Euclidean or hyperbolic). However, since the GO graph exhibits a complex and nonmonotonic hierarchy, single-space embeddings are insufficient to fully capture its structural nuances. RESULTS: In this study, we address this limitation by exploiting geometric interaction to better reflect the intricate hierarchical structure of GO. Our proposed method, Geometry-Aware Knowledge Graph Embeddings for GO and Genes (GeOKG), leverages interactions among various geometric representations during training, thereby modeling the complex hierarchy of GO more effectively. Experiments at the GO level demonstrate the benefits of incorporating these geometric interactions, while gene-level tests reveal that GeOKG outperforms existing methods in protein-protein interaction prediction. These findings highlight the potential of using geometric interaction for embedding heterogeneous biomedical networks. AVAILABILITY AND IMPLEMENTATION: https://github.com/ukjung21/GeOKG.

Graph neural networks (GNNs) have recently gained significant attention for their ability to model and analyze complex relationships, leading to numerous applications in a variety of fields. In line with this, explainable models such as GNNExplainer have been developed to provide insights into how GNN models make decisions. However, much of the research has focused on identifying important edges and subgraphs, with relatively less emphasis on feature importance. To address this gap, we propose a novel unsupervised feature scoring method aimed at extracting features that are well-aligned with graph structures. Our approach leverages the distinction between features that explain the overall structural characteristics of the graph and those that do not. Through comparative experiments with other algorithms, we demonstrated that our proposed method is effective in selecting important features in unsupervised settings. Additionally, empirical analysis of gene expression data confirmed that our method could aid in biomarker discovery, highlighting its potential for practical applications in biological studies.

We present a novel end-to-end personality-based synthetic dialogue data generation pipeline, specifically designed to elicit responses from large language models via prompting. We design the prompts to generate more human-like dialogues considering real-world scenarios when users engage with chatbots. We introduce PSYDIAL, the first Korean dialogue dataset focused on personality-based dialogues, curated using our proposed pipeline. Notably, we focus on the Extraversion dimension of the Big Five personality model in our research. Experimental results indicate that while pre-trained models and those fine-tuned with a chit-chat dataset struggle to generate responses reflecting personality, models trained with PSYDIAL show significant improvements. The versatility of our pipeline extends beyond dialogue tasks, offering potential for other non-dialogue related applications. This research opens doors for more nuanced, personality-driven conversational AI in Korean and potentially other languages.

Omnidirectional vision systems provide a 360-degree panoramic view, enabling full environmental awareness in various fields, such as Advanced Driver Assistance Systems (ADAS) and Virtual Reality (VR). Existing omnidirectional stitching methods rely on a single specialized 360-degree camera. However, due to hardware limitations such as high mounting heights and blind spots, adapting these methods to vehicles of varying sizes and geometries is challenging. These challenges include limited generalizability due to the reliance on predefined stitching regions for fixed camera arrays, performance degradation from distance parallax leading to large depth differences, and the absence of suitable datasets with ground truth for multi-camera omnidirectional systems. To overcome these challenges, we propose a novel omnidirectional stitching framework and a publicly available dataset tailored for varying distance scenarios with multiple cameras. The framework, referred to as OmniStitch, consists of a Stitching Region Maximization (SRM) module for automatic adaptation to different vehicles with multiple cameras and a Depth-Aware Stitching (DAS) module to handle depth differences caused by distance parallax between cameras. In addition, we create and release an omnidirectional stitching dataset, called GV360, which provides ground truth images that maintain the perspective of the 360-degree FOV, designed explicitly for vehicle-agnostic systems. Extensive evaluations of this dataset demonstrate that our framework outperforms state-of-the-art stitching models, especially in handling varying distance parallax. The proposed dataset and code are publicly available in https://github.com/tngh5004/Omnistitch.

The out-of-distribution (OOD) detection task assumes samples that follow the distribution of training data as in-distribution (ID), while samples from other data distributions are considered OOD. In recent years, the OOD detection tasks have made significant progress since many studies observed that the distribution mismatch between training and real datasets can severely deteriorate the reliability of AI systems. Nevertheless, the lack of precise interpretation for the in-distribution (ID) limits the application of the OOD detection methods to real-world systems. To tackle this, we decompose the definition of the ID into texture and semantics, motivated by the demands of real-world scenarios. We also design new benchmarks to measure the robustness that OOD detection methods should have. Our proposed benchmark verifies not only the precision but also the robustness of the detection models. It is crucial to measure both factors in OOD detection as they indicate different traits of the model. For instance, precision is relevant to scenarios that detect minor cracks in the conveyor belt of a smart factory, whereas robustness pertains to maintaining performance under diverse weather conditions, as required by autonomous driving. To achieve a good balance between the OOD detection performance and robustness, our method takes a divide-and-conquer approach. Specifically, the proposed model first handles each component of the texture and semantics separately and then fuses these later. This philosophy is empirically proven by a series of benchmarks including both the proposed and the conventional counterpart. By decomposing the prior “unclear” definition of the ID into texture and semantic components, our novel approach better suits the demands of a reliable machine learning system, which requires robustness and consistent performance across varied scenarios. Unlike prior works, our approach does not rely on any extra datasets or labels. This prevents our proposed framework from being dependent on a particular dataset distribution.

• Language-based Subject Generation faces challenge in accurate portrayal of subject. • Nowadays Reference Guided Generation lacks ability to preserve subject identity. • Exemplar-based instructions with visual tokens preserve visual details of subject. • Model based guidance samples better quality images with different pose. • Our model achieved highest CLIP, DINO score and user study compared to others. This paper presents a novel approach to subject-driven image generation that addresses the limitations of traditional text-to-image diffusion models. Our method generates images using reference images without relying on language-based prompts. We introduce a visual detail preserving module that captures intricate details and textures, addressing overfitting issues associated with limited training samples. The model's performance is further enhanced through a modified classifier-free guidance technique and feature concatenation, enabling the natural positioning and harmonization of subjects within diverse scenes. Quantitative assessments using CLIP, DINO and Quality scores (QS), along with a user study, demonstrate the superior quality of our generated images. Our work highlights the potential of pre-trained models and visual patch embeddings in subject-driven editing, balancing diversity and fidelity in image generation tasks. Our implementation is available at https://github.com/8eomio/Subject-Inpainting . To create your abstract, type over the instructions in the template box below. Fonts or abstract dimensions should not be changed or altered.

BACKGROUND: Intraoperative hypotension can lead to postoperative organ dysfunction. Previous studies primarily used invasive arterial pressure as the key biosignal for the detection of hypotension. However, these studies had limitations in incorporating different biosignal modalities and utilizing the periodic nature of biosignals. To address these limitations, we utilized frequency-domain information, which provides key insights that time-domain analysis cannot provide, as revealed by recent advances in deep learning. With the frequency-domain information, we propose a deep-learning approach that integrates multiple biosignal modalities. METHODS: We used the discrete Fourier transform technique, to extract frequency information from biosignal data, which we then combined with the original time-domain data as input for our deep learning model. To improve the interpretability of our results, we incorporated recent interpretable modules for deep-learning models into our analysis. RESULTS: We constructed 75 994 segments from the data of 3226 patients to predict hypotension during surgery. Our proposed frequency-domain deep-learning model outperformed conventional approaches that rely solely on time-domain information. Notably, our model achieved a greater increase in AUROC performance than the time-domain deep learning models when trained on non-invasive biosignal data only (AUROC 0.898 [95% CI: 0.885-0.91] vs. 0.853 [95% CI: 0.839-0.867]). Further analysis revealed that the 1.5-3.0 Hz frequency band played an important role in predicting hypotension events. CONCLUSION: Utilizing the frequency domain not only demonstrated high performance on invasive data but also showed significant performance improvement when applied to non-invasive data alone. Our proposed framework offers clinicians a novel perspective for predicting intraoperative hypotension.

Depression is a severe mental illness that impairs a person's capacity to function normally in personal and professional life. The assessment of depression usually requires a comprehensive examination by an expert professional. Recently, machine learning-based automatic depression assessment has received considerable attention for a reliable and efficient depression diagnosis. Various techniques for automated depression detection were developed; however, certain concerns still need to be investigated. In this work, we propose a novel deep multi-modal framework that effectively utilizes facial and verbal cues for an automated depression assessment. Specifically, we first partition the audio and video data into fixed-length segments. Then, these segments are fed into the Spatio-Temporal Networks as input, which captures both spatial and temporal features as well as assigns higher weights to the features that contribute most. In addition, Volume Local Directional Structural Pattern (VLDSP) based dynamic feature descriptor is introduced to extract the facial dynamics by encoding the structural aspects. Afterwards, we employ the Temporal Attentive Pooling (TAP) approach to summarize the segment-level features for audio and video data. Finally, the multi-modal factorized bilinear pooling (MFB) strategy is applied to fuse the multi-modal features effectively. An extensive experimental study reveals that the proposed method outperforms state-of-the-art approaches.

In a hate speech detection model, we should consider two critical aspects in addition to detection performance–bias and explainability. Hate speech cannot be identified based solely on the presence of specific words; the model should be able to reason like humans and be explainable. To improve the performance concerning the two aspects, we propose Masked Rationale Prediction (MRP) as an intermediate task. MRP is a task to predict the masked human rationales–snippets of a sentence that are grounds for human judgment–by referring to surrounding tokens combined with their unmasked rationales. As the model learns its reasoning ability based on rationales by MRP, it performs hate speech detection robustly in terms of bias and explainability. The proposed method generally achieves state-of-the-art performance in various metrics, demonstrating its effectiveness for hate speech detection. Warning: This paper contains samples that may be upsetting.

Recent progress in deep learning-based models has improved photo-realistic (or perceptual) single-image super-resolution significantly. However, despite their powerful performance, many methods are difficult to apply to real-world applications because of the heavy computational requirements. To facilitate the use of a deep model under such demands, we focus on keeping the network efficient while maintaining its performance. In detail, we design an architecture that implements a cascading mechanism on a residual network to boost the performance with limited resources via multi-level feature fusion. In addition, our proposed model adopts group convolution and recursive schemes in order to achieve extreme efficiency. We further improve the perceptual quality of the output by employing the adversarial learning paradigm and a multi-scale discriminator approach. The performance of our method is investigated through extensive internal experiments and benchmarks using various datasets. Our results show that our models outperform the recent methods with similar complexity, for both traditional pixel-based and perception-based tasks.

In recent years, dynamic scene understanding has gained attention from researchers because of its widespread applications. The main important factor in successfully understanding the dynamic scenes lies in jointly representing the appearance and motion features to obtain an informative description. Numerous methods have been introduced to solve dynamic scene recognition problem, nevertheless, a few concerns still need to be investigated. In this article, we introduce a novel multi-modal network for dynamic scene understanding from video data, which captures both spatial appearance and temporal dynamics effectively. Furthermore, two-level joint tuning layers are proposed to integrate the global and local spatial features as well as spatial and temporal stream deep features. In order to extract the temporal information, we present a novel dynamic descriptor, namely, Volume Symmetric Gradient Local Graph Structure ( VSGLGS ), which generates temporal feature maps similar to optical flow maps. However, this approach overcomes the issues of optical flow maps. Additionally, Volume Local Directional Transition Pattern ( VLDTP ) based handcrafted spatiotemporal feature descriptor is also introduced, which extracts the directional information through exploiting edge responses. Lastly, a stacked Bidirectional Long Short-Term Memory ( Bi-LSTM ) network along with a temporal mixed pooling scheme is designed to achieve the dynamic information without noise interference. The extensive experimental investigation proves that the proposed multi-modal network outperforms most of the state-of-the-art approaches for dynamic scene understanding.

Alzheimer's disease (AD) is a progressive neurodegenerative brain disorder characterized by memory loss and cognitive decline. Early detection and accurate prognosis of AD is an important research topic, and numerous machine learning methods have been proposed to solve this problem. However, traditional machine learning models are facing challenges in effectively integrating longitudinal neuroimaging data and biologically meaningful structure and knowledge to build accurate and interpretable prognostic predictors. To bridge this gap, we propose an interpretable graph neural network (GNN) model for AD prognostic prediction based on longitudinal neuroimaging data while embracing the valuable knowledge of structural brain connectivity. In our empirical study, we demonstrate that 1) the proposed model outperforms several competing models (i.e., DNN, SVM) in terms of prognostic prediction accuracy, and 2) our model can capture neuroanatomical contribution to the prognostic predictor and yield biologically meaningful interpretation to facilitate better mechanistic understanding of the Alzheimer's disease. Source code is available at https://github.com/JaesikKim/temporal-GNN.

MOTIVATION: To better understand the molecular features of cancers, a comprehensive analysis using multi-omics data has been conducted. In addition, a pathway activity inference method has been developed to facilitate the integrative effects of multiple genes. In this respect, we have recently proposed a novel integrative pathway activity inference approach, iDRW and demonstrated the effectiveness of the method with respect to dichotomizing two survival groups. However, there were several limitations, such as a lack of generality. In this study, we designed a directed gene-gene graph using pathway information by assigning interactions between genes in multiple layers of networks. RESULTS: As a proof-of-concept study, it was evaluated using three genomic profiles of urologic cancer patients. The proposed integrative approach achieved improved outcome prediction performances compared with a single genomic profile alone and other existing pathway activity inference methods. The integrative approach also identified common/cancer-specific candidate driver pathways as predictive prognostic features in urologic cancers. Furthermore, it provides better biological insights into the prioritized pathways and genes in an integrated view using a multi-layered gene-gene network. Our framework is not specifically designed for urologic cancers and can be generally applicable for various datasets. AVAILABILITY AND IMPLEMENTATION: iDRW is implemented as the R software package. The source codes are available at https://github.com/sykim122/iDRW. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

MOTIVATION: Knowledge manipulation of Gene Ontology (GO) and Gene Ontology Annotation (GOA) can be done primarily by using vector representation of GO terms and genes. Previous studies have represented GO terms and genes or gene products in Euclidean space to measure their semantic similarity using an embedding method such as the Word2Vec-based method to represent entities as numeric vectors. However, this method has the limitation that embedding large graph-structured data in the Euclidean space cannot prevent a loss of information of latent hierarchies, thus precluding the semantics of GO and GOA from being captured optimally. On the other hand, hyperbolic spaces such as the Poincaré balls are more suitable for modeling hierarchies, as they have a geometric property in which the distance increases exponentially as it nears the boundary because of negative curvature. RESULTS: In this article, we propose hierarchical representations of GO and genes (HiG2Vec) by applying Poincaré embedding specialized in the representation of hierarchy through a two-step procedure: GO embedding and gene embedding. Through experiments, we show that our model represents the hierarchical structure better than other approaches and predicts the interaction of genes or gene products similar to or better than previous studies. The results indicate that HiG2Vec is superior to other methods in capturing the GO and gene semantics and in data utilization as well. It can be robustly applied to manipulate various biological knowledge. AVAILABILITYAND IMPLEMENTATION: https://github.com/JaesikKim/HiG2Vec. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The prevalent approach for unsupervised text style transfer is disentanglement between content and style.However, it is difficult to completely separate style information from the content.Other approaches allow the latent text representation to contain style and the target style to affect the generated output more than the latent representation does.In both approaches, however, it is impossible to adjust the strength of the style in the generated output.Moreover, those previous approaches typically perform both the sentence reconstruction and style control tasks in a single model, which complicates the overall architecture.In this paper, we address these issues by separating the model into a sentence reconstruction module and a style module.We use the Transformer-based autoencoder model for sentence reconstruction and the adaptive style embedding is learned directly in the style module.Because of this separation, each module can better focus on its own task.Moreover, we can vary the style strength of the generated sentence by changing the style of the embedding expression.Therefore, our approach not only controls the strength of the style, but also simplifies the model architecture.Experimental results show that our approach achieves better style transfer performance and content preservation than previous approaches.

Data augmentation is an effective way to improve the performance of deep networks. Unfortunately, current methods are mostly developed for high-level vision tasks (e.g., classification) and few are studied for low-level vision tasks (e.g., image restoration). In this paper, we provide a comprehensive analysis of the existing augmentation methods applied to the super-resolution task. We find that the methods discarding or manipulating the pixels or features too much hamper the image restoration, where the spatial relationship is very important. Based on our analyses, we propose CutBlur that cuts a low-resolution patch and pastes it to the corresponding high-resolution image region and vice versa. The key intuition of CutBlur is to enable a model to learn not only "how" but also "where" to super-resolve an image. By doing so, the model can understand "how much", instead of blindly learning to apply super-resolution to every given pixel. Our method consistently and significantly improves the performance across various scenarios, especially when the model size is big and the data is collected under real-world environments. We also show that our method improves other low-level vision tasks, such as denoising and compression artifact removal.

Generative adversarial networks (GANs) are well known both for being unstable to train and for the problem of mode collapse, particularly when trained on data collections containing a diverse set of visual objects. This study introduces an adaptive hyper-parameter learning procedure for GANs as an alternative to the existing static approach. The proposed procedure is designed to mitigate the impact of instability and saturation in the original by dynamically adjusting the ratio of the training steps of both the generator and discriminator. To accomplish this, we track and analyze stable training curves of relatively narrow datasets and use them as the target fitting lines when training more diverse data collections. Experimental results show that the proposed model improves the stability and generates more realistic images.

The multiple types of social media data have abundant information, but learning multi-modal social data is challenging due to data heterogeneity and noise in usergenerated data. To address this problem, we propose a multiview network-based clustering approach that is robust to noise and fully reflects the underlying structure of the comprehensive network. To demonstrate the proposed approach, we experimented with clustering challenging tagged images of landmarks. The results show that the proposed method outperforms other previously reported multi-view clustering algorithms and better utilizes the advantages of the network for each view. Furthermore, the tagged-image network constructed by the proposed method and the clustering results are extensively analyzed.

Document novelty detection is a concept learning problem wherein the system gains its knowledge only from the positive documents under a concept and with that limited knowledge it attempts to detect the negative cases. This work focuses on learning author style as a concept from the given set of do cuments, particularly emails. Since author attribution for shorter texts such as emails is more complex compared to larger documents, the techniques originally used for the large documents prove inefficient for short texts. To address this shortcoming of existing algorithms in detecting aberration in author style, we have proposed a graph-model based technique for feature set extraction from short documents. Given the extracted feature set, we have also developed two probability based text representation schemes that could best represent a text document to an underlying one-class SVM classifier. The proposed models have been compared and evaluated on the public Enron email dataset. Applying graph based feature set extraction technique in combination with the inclusive compound probability based text representation has proved to be very efficient. The generality of the proposed method allows the approach to be applicable to all kind of text documents including emails.

Electronic mails have increasingly replaced all written modes of communications for important correspondences including personal and business transactions. An e-mail is given equal significance as a signed document. Hence email impersonation through compromised accounts has become a major threat. In this paper, we have proposed an email style acquisition and classification model for authorship attribution that serves as an effective tool to prevent and detect email impersonation. The proposed model gains knowledge of the author's email style by being trained only with the sample email texts of the author and then identifies if a given email text is a legitimate email of the author or not. Extracting the significant features that represent an author's style from the available concise emails is a big challenge in email authorship attribution. We have proposed to use a graph-based model to precisely extract the unique feature set of the author. We have used one-class SVM classifier to deal with the single-class sample data that consists of only true positive samples. Two classification models have been designed and compared. The first one is a probability model which is based on the probability of occurrence of a feature in the specific email. The second technique is based on inclusive compound probability of a feature to appear in a sentence of an email. Both the models have been evaluated against the public Enron dataset.

The continuing growth of information overflow has made it hard to obtain valuable information on the web. In this trend, the need for effective Information Retrieval (IR) technique has been increased. Although document data contain much more abundant information, users can retrieve necessary information only from the title and description in conventional web services. In order to meet the demands for fast and accurate retrieval of valuable information, we propose a fast and effective content-based document information retrieval system that retrieves the information from the actual content of a document. The proposed method is based on a topic model of Latent Dirichlet Allocation that is used to extract major keywords for a given document. The main contributions of our system are the increased flexibility, effectiveness, and fast retrieval of information. Our system can easily communicate with existing web service through the standard JSON format. In addition, we increase the speed of information retrieval by using NoSQL based database system with inverted indexing and B-tree based indexing. We validate the performance of our system on real data collected from the SlideShare service. The proposed system shows better retrieval performance over the existing IR system.

Image spams have been annoying users everywhere and it has also been increasingly appearing in mobile phones these days. In accordance with more sophisticated spam filtering system, spams are being more intelligent and have caused severe social problems. However, there has not been effective solution for detecting mobile phone spam images yet. Due to the insufficient spam image data in mobile phones, training the predictive model is quite hard. To resolve this issue, we recently proposed a phone spam image filtering system using e-mail spam images and showed that using e-mail spam data is fairly meaningful in improving the performance of phone spam image detection. In this paper, we further investigate the effectiveness of utilizing the graph structure in e-mail spam data. Furthermore, the classification performance behavior depending on different image descriptors of Pyramid Histogram of Visual Words (PHOW) and RGB histogram is explored extensively.

MOTIVATION: Genome-wide mapping of chromatin states is essential for defining regulatory elements and inferring their activities in eukaryotic genomes. A number of hidden Markov model (HMM)-based methods have been developed to infer chromatin state maps from genome-wide histone modification data for an individual genome. To perform a principled comparison of evolutionarily distant epigenomes, we must consider species-specific biases such as differences in genome size, strength of signal enrichment and co-occurrence patterns of histone modifications. RESULTS: Here, we present a new Bayesian non-parametric method called hierarchically linked infinite HMM (hiHMM) to jointly infer chromatin state maps in multiple genomes (different species, cell types and developmental stages) using genome-wide histone modification data. This flexible framework provides a new way to learn a consistent definition of chromatin states across multiple genomes, thus facilitating a direct comparison among them. We demonstrate the utility of this method using synthetic data as well as multiple modENCODE ChIP-seq datasets. CONCLUSION: The hierarchical and Bayesian non-parametric formulation in our approach is an important extension to the current set of methodologies for comparative chromatin landscape analysis. AVAILABILITY AND IMPLEMENTATION: Source codes are available at https://github.com/kasohn/hiHMM. Chromatin data are available at http://encode-x.med.harvard.edu/data_sets/chromatin/.

OBJECTIVE: Cancer can involve gene dysregulation via multiple mechanisms, so no single level of genomic data fully elucidates tumor behavior due to the presence of numerous genomic variations within or between levels in a biological system. We have previously proposed a graph-based integration approach that combines multi-omics data including copy number alteration, methylation, miRNA, and gene expression data for predicting clinical outcome in cancer. However, genomic features likely interact with other genomic features in complex signaling or regulatory networks, since cancer is caused by alterations in pathways or complete processes. METHODS: Here we propose a new graph-based framework for integrating multi-omics data and genomic knowledge to improve power in predicting clinical outcomes and elucidate interplay between different levels. To highlight the validity of our proposed framework, we used an ovarian cancer dataset from The Cancer Genome Atlas for predicting stage, grade, and survival outcomes. RESULTS: Integrating multi-omics data with genomic knowledge to construct pre-defined features resulted in higher performance in clinical outcome prediction and higher stability. For the grade outcome, the model with gene expression data produced an area under the receiver operating characteristic curve (AUC) of 0.7866. However, models of the integration with pathway, Gene Ontology, chromosomal gene set, and motif gene set consistently outperformed the model with genomic data only, attaining AUCs of 0.7873, 0.8433, 0.8254, and 0.8179, respectively. CONCLUSIONS: Integrating multi-omics data and genomic knowledge to improve understanding of molecular pathogenesis and underlying biology in cancer should improve diagnostic and prognostic indicators and the effectiveness of therapies.

MOTIVATION: Many complex disease syndromes such as asthma consist of a large number of highly related, rather than independent, clinical phenotypes, raising a new technical challenge in identifying genetic variations associated simultaneously with correlated traits. Although a causal genetic variation may influence a group of highly correlated traits jointly, most of the previous association analyses considered each phenotype separately, or combined results from a set of single-phenotype analyses. RESULTS: We propose a new statistical framework called graph-guided fused lasso to address this issue in a principled way. Our approach represents the dependency structure among the quantitative traits explicitly as a network, and leverages this trait network to encode structured regularizations in a multivariate regression model over the genotypes and traits, so that the genetic markers that jointly influence subgroups of highly correlated traits can be detected with high sensitivity and specificity. While most of the traditional methods examined each phenotype independently, our approach analyzes all of the traits jointly in a single statistical method to discover the genetic markers that perturb a subset of correlated traits jointly rather than a single trait. Using simulated datasets based on the HapMap consortium data and an asthma dataset, we compare the performance of our method with the single-marker analysis, and other sparse regression methods that do not use any structural information in the traits. Our results show that there is a significant advantage in detecting the true causal single nucleotide polymorphisms when we incorporate the correlation pattern in traits using our proposed methods. AVAILABILITY: Software for GFlasso is available at http://www.sailing.cs.cmu.edu/gflasso.html.

Uncovering the haplotypes of single nucleotide polymorphisms and their population demography is essential for many biological and medical applications. Methods for haplotype inference developed thus far---including methods based on coalescence, finite and infinite mixtures, and maximal parsimony---ignore the underlying population structure in the genotype data. As noted by Pritchard (2001), different populations can share certain portion of their genetic ancestors, as well as have their own genetic components through migration and diversification. In this paper, we address the problem of multi-population haplotype inference. We capture cross-population structure using a nonparametric Bayesian prior known as the hierarchical Dirichlet process (HDP) (Teh et al., 2006), conjoining this prior with a recently developed Bayesian methodology for haplotype phasing known as DP-Haplotyper (Xing et al., 2004). We also develop an efficient sampling algorithm for the HDP based on a two-level nested Pólya urn scheme. We show that our model outperforms extant algorithms on both simulated and real biological data.

We present a new statistical framework called hidden Markov Dirichlet process (HMDP) to jointly model the genetic recombinations among possibly infinite number of founders and the coalescence-with-mutation events in the resulting genealogies. The HMDP posits that a haplotype of genetic markers is generated by a sequence of recombination events that select an ancestor for each locus from an unbounded set of founders according to a 1st-order Markov transition process. Conjoining this process with a mutation model, our method accommodates both between-lineage recombination and within-lineage sequence variations, and leads to a compact and natural interpretation of the population structure and inheritance process underlying haplotype data. We have developed an efficient sampling algo rithm for HMDP based on a two-level nested Polya urn scheme. On both simulated and real SNP haplotype data, our method performs competitively or significantly better than extant methods in uncovering the recombination hotspots along chromosomal loci; and in addition it also infers the ancestral genetic patterns and offers a highly accurate map of ancestral compositions of modern populations.

Many face database and recognition systems have been constructed in specially designed studios with various illuminations, poses, and expressions. However, none of these databases yet satisfies a large variation of poses and illuminations that permit the study of systematic 3D human face information, which results in an unsatisfactory success rate. It is caused primarily by the difficulty of data collection of facial images to satisfy the large variation of poses and illuminations to fully represent the 3D characteristics of human faces. We present how computer-generated database can be used for face recognition experiment focused on multiview face recognition/descriptor. We show multiview face data collection using rendering of 3D models. We also illustrate our approach how to build a face descriptor containing 3D information of human face using multiview concepts. This multiview face recognition descriptor is a 3D descriptor using the concept how much powerful a view influences over nearby views, so called as "quasiview " size.

We present an algorithm for computing the distance between two free-form surfaces. Using line geometry, the distance computation is reformulated as a simple instance of a surface-surface intersection problem, which leads to low-dimensional root finding in a system of equations. This approach produces an efficient algorithm for computing the distance between two ellipsoids, where the problem is reduced to finding a specific solution in a system of two equations in two variables. Similar algorithms can be designed for computing the distance between an ellipsoid and a simple surface (such as cylinder cone, or torus). In an experimental implementation (on a 500 MHz Windows PC), the distance between two ellipsoids was computed in less than 0.3 msec on average; and the distance between an ellipsoid and a simple convex surface was computed in less than 0.15 msec on average.