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In this work we develop and demonstrate a probabilistic generative model for phytoplankton communities. The proposed model takes counts of a set of phytoplankton taxa in a timeseries as its training data, and models communities by learning sparse co-occurrence structure between the taxa. Our model is probabilistic, where communities are represented by probability distributions over the species, and...
Trigger detection plays a key role in the extraction of biomedical events, so it will influence the results of biomedical events extraction directly. The traditional biomedical event trigger recognition method is based on artificial design features and construct feature vectors; Not only does it consume great amounts of manpower, it also lacks system generalization ability. Most of methods of trigger...
There are intensive computational efforts to discover large-scale microbial interactions from metagenomic abundance data, however, it is often difficult to validate such inferred interactions without a manually curated dataset. There are also a number of small-scale microbial interactions reported in massive literature with experimental confidence. Text mining can be employed to extract such microbial...
In biomedical research, events revealing complex relations between entities play an important role. Event trigger identification is a crucial and prerequisite step in the pipeline process of biomedical event extraction. There exist two main problems in the previous work: (1) Traditional feature-based methods often rely on human ingenuity, which is a time-consuming process. Though most representation-based...
In molecular biology, phenotypes are often described using complex semantics and diverse biomedical expressions, thereby facilitating the development of named entity recognition (NER). Here, we propose a novel approach of recognizing plant phenotypes by cascading word embedding to sentence embedding with a class label enhancement. We utilized a word embedding method to find high-frequency phenotypes...
Protein-DNA docking is an important computational technique for generating native or near-native complex models. A docking program typically generates a number of complex conformations and predicts the docking solution based on interaction energies. However, incomplete sampling and energy function deficiencies can result in false positive protein-DNA complex models, which hampers its application in...
Biomedical named entity recognition (Bio-NER) is an important preliminary step for many biomedical text mining tasks. The current mainstream methods for NER are based on the neural networks to avoid the complex hand-designed features derived from various linguistic analyses. However, the performance of these methods is always limited to exploring dependencies across output label and ignoring some...
Biomedical semantic indexing refers to annotating biomedical citations with Medical Subject Headings, which is crucial for texting mining, information retrieval and other researches in the field of bioinformatics. The traditional methods ignore the relations among labels and need complicated feature engineering. In this paper, we present a novel model with a deep serial multi-task learning structure,...
Motivation: Next-generation sequencing (NGS) technologies using DNA, RNA, or methylation sequencing are prevailing tools used in modern genome research. For DNA sequencing, whole genome sequencing (WGS) and whole exome sequencing (WES) are two typical applications with a different preference on the trade-off between sequencing depth and base coverage. Although sequencing costs have been greatly reduced,...
This paper introduces a novel approach for modeling visual relations between pairs of objects. We call relation a triplet of the form (subject; predicate; object) where the predicate is typically a preposition (eg. ’under’, ’in front of’) or a verb (’hold’, ’ride’) that links a pair of objects (subject; object). Learning such relations is challenging as the objects have different spatial configurations...
In this empirical study we develop forecasting models for electricity demand using publicly available data and three models based on machine learning algorithms. It compares accuracy of these models using different evaluation metrics. The data consist of several measurements and observations related to the electricity market in Turkey from 2011 to 2016. It is available in different time granularities...
Natural Language Processing (NLP) is a prominent subject which includes various subcategories such as text classification, error correction, machine translation, etc. Unlike other languages, there are limited number of Turkish NLP studies in literature. In this study, we apply text classification on Turkish documents by using n-gram features. Our algorithm applies different preprocessing techniques,...
In this paper, we propose a novel application of Generative Adversarial Networks (GAN) to the synthesis of cells imaged by fluorescence microscopy. Compared to natural images, cells tend to have a simpler and more geometric global structure that facilitates image generation. However, the correlation between the spatial pattern of different fluorescent proteins reflects important biological functions,...
We report an experimental study that involves understanding how display (conventional or ecological) and system mode (profiting, neutral or losing) affect financial trading performance and risk preference. Twenty-four undergraduate and graduate student participants interacted with a financial trading simulator in the playback of a real market. Each participant completed a conventional display scenario...
This innovative practice paper describes a one-year pilot program designed to intentionally develop intercultural competencies in undergraduate engineering students, without leaving campus. The design of the program was informed by theoretical frameworks about national cultural differences and development of intercultural competencies. The activities of the program included, but were not limited to,...
Most traditional soft sensor modeling requires the labeled training samples that contain both subsidiary and key variables. However, key variables are difficult to be obtained online due to lack of detection information or high measurement cost. In this paper, a novel semi-supervised learning algorithm, called cotraining-style kernel extreme learning machine, is proposed to exploit unlabeled training...
Cell Cycle Learn (CCL) is a learning game designed for undergraduate students in Biology to learn common knowledge about the cell-division cycle along with practical skills related with setting up an experiment and the scientific method in general. In CCL, learners are guided through the process of formulating hypotheses, conducting virtual experiments and analysing the results in order to validate...
In this paper an advanced iris-biometric comparator is presented. In the proposed scheme an analysis of bit-error patterns produced by Hamming distance-based iris-code comparisons is performed. The lengths of sequences of horizontal consecutive mis-matching bits are measured and a frequency distribution is estimated. The difference of the extracted frequency distribution to that of an average genuine...
An appreciable fraction of introns is thought to be involved in cellular functions, but there is no obvious way to predict which specific intron is likely to be functional. For each intron we are given a feature representation that is based on its evolutionary patterns. For a small subsets of introns we are also given an indication that they are functional. For all other introns it is not known whether...
The paper evaluates three variants of the Gated Recurrent Unit (GRU) in recurrent neural networks (RNNs) by retaining the structure and systematically reducing parameters in the update and reset gates. We evaluate the three variant GRU models on MNIST and IMDB datasets and show that these GRU-RNN variant models perform as well as the original GRU RNN model while reducing the computational expense...
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