511 research outputs found
Improving the Caenorhabditis elegans Genome Annotation Using Machine Learning
For modern biology, precise genome annotations are of prime importance, as they allow the accurate definition of genic regions. We employ state-of-the-art machine learning methods to assay and improve the accuracy of the genome annotation of the nematode Caenorhabditis elegans. The proposed machine learning system is trained to recognize exons and introns on the unspliced mRNA, utilizing recent advances in support vector machines and label sequence learning. In 87% (coding and untranslated regions) and 95% (coding regions only) of all genes tested in several out-of-sample evaluations, our method correctly identified all exons and introns. Notably, only 37% and 50%, respectively, of the presently unconfirmed genes in the C. elegans genome annotation agree with our predictions, thus we hypothesize that a sizable fraction of those genes are not correctly annotated. A retrospective evaluation of the Wormbase WS120 annotation [1] of C. elegans reveals that splice form predictions on unconfirmed genes in WS120 are inaccurate in about 18% of the considered cases, while our predictions deviate from the truth only in 10%–13%. We experimentally analyzed 20 controversial genes on which our system and the annotation disagree, confirming the superiority of our predictions. While our method correctly predicted 75% of those cases, the standard annotation was never completely correct. The accuracy of our system is further corroborated by a comparison with two other recently proposed systems that can be used for splice form prediction: SNAP and ExonHunter. We conclude that the genome annotation of C. elegans and other organisms can be greatly enhanced using modern machine learning technology
Partial sequence labeling with structured Gaussian Processes
Existing partial sequence labeling models mainly focus on max-margin
framework which fails to provide an uncertainty estimation of the prediction.
Further, the unique ground truth disambiguation strategy employed by these
models may include wrong label information for parameter learning. In this
paper, we propose structured Gaussian Processes for partial sequence labeling
(SGPPSL), which encodes uncertainty in the prediction and does not need extra
effort for model selection and hyperparameter learning. The model employs
factor-as-piece approximation that divides the linear-chain graph structure
into the set of pieces, which preserves the basic Markov Random Field structure
and effectively avoids handling large number of candidate output sequences
generated by partially annotated data. Then confidence measure is introduced in
the model to address different contributions of candidate labels, which enables
the ground-truth label information to be utilized in parameter learning. Based
on the derived lower bound of the variational lower bound of the proposed
model, variational parameters and confidence measures are estimated in the
framework of alternating optimization. Moreover, weighted Viterbi algorithm is
proposed to incorporate confidence measure to sequence prediction, which
considers label ambiguity arose from multiple annotations in the training data
and thus helps improve the performance. SGPPSL is evaluated on several sequence
labeling tasks and the experimental results show the effectiveness of the
proposed model
Cascaded Scene Flow Prediction using Semantic Segmentation
Given two consecutive frames from a pair of stereo cameras, 3D scene flow
methods simultaneously estimate the 3D geometry and motion of the observed
scene. Many existing approaches use superpixels for regularization, but may
predict inconsistent shapes and motions inside rigidly moving objects. We
instead assume that scenes consist of foreground objects rigidly moving in
front of a static background, and use semantic cues to produce pixel-accurate
scene flow estimates. Our cascaded classification framework accurately models
3D scenes by iteratively refining semantic segmentation masks, stereo
correspondences, 3D rigid motion estimates, and optical flow fields. We
evaluate our method on the challenging KITTI autonomous driving benchmark, and
show that accounting for the motion of segmented vehicles leads to
state-of-the-art performance.Comment: International Conference on 3D Vision (3DV), 2017 (oral presentation
Automatic analysis of facial actions: a survey
As one of the most comprehensive and objective ways to describe facial expressions, the Facial Action Coding System (FACS) has recently received significant attention. Over the past 30 years, extensive research has been conducted by psychologists and neuroscientists on various aspects of facial expression analysis using FACS. Automating FACS coding would make this research faster and more widely applicable, opening up new avenues to understanding how we communicate through facial expressions. Such an automated process can also potentially increase the reliability, precision and temporal resolution of coding. This paper provides a comprehensive survey of research into machine analysis of facial actions. We systematically review all components of such systems: pre-processing, feature extraction and machine coding of facial actions. In addition, the existing FACS-coded facial expression databases are summarised. Finally, challenges that have to be addressed to make automatic facial action analysis applicable in real-life situations are extensively discussed. There are two underlying motivations for us to write this survey paper: the first is to provide an up-to-date review of the existing literature, and the second is to offer some insights into the future of machine recognition of facial actions: what are the challenges and opportunities that researchers in the field face
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