arXiv research

Paper uses genome Markov structure for outlier detection and read classification.

Metagenomic studies have increasingly utilized sequencing technologies in order to analyze DNA fragments found in environmental samples.One important step in this analysis is the taxonomic classification of the DNA fragments. Conventional read classification methods require large databases and vast amounts of memory to…

In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs converted to 1D-signals. We noticed that specific signal patterns occur in each r…

Recurrent Neural Networks (RNN) are a type of statistical model designed to handle sequential data. The model reads a sequence one symbol at a time. Each symbol is processed based on information collected from the previous symbols. With existing RNN architectures, each symbol is processed using only information from th…

Recurrent neural networks (RNNs) can model natural language by sequentially 'reading' input tokens and outputting a distributed representation of each token. Due to the sequential nature of RNNs, inference time is linearly dependent on the input length, and all inputs are read regardless of their importance. Efforts to…

We address the problem of graph classification based only on structural information. Inspired by natural language processing techniques (NLP), our model sequentially embeds information to estimate class membership probabilities. Besides, we experiment with NLP-like variational regularization techniques, making the mode…

With an aging and growing population, the number of women requiring either screening or symptomatic mammograms is increasing. To reduce the number of mammograms that need to be read by a radiologist while keeping the diagnostic accuracy the same or better than current clinical practice, we develop Man and Machine Mammo…

A real-world dataset is provided from a pulp-and-paper manufacturing industry. The dataset comes from a multivariate time series process. The data contains a rare event of paper break that commonly occurs in the industry. The data contains sensor readings at regular time-intervals (x's) and the event label (y). The pri…

Aggregates diverse zero-shot LLM outputs for better corporate disclosure classification.

Dead-Direction Signatures (DDS) provide a cheap, closed-form spectral reading of a network's singular complexity.

Book teaches how Lagrangian torus fibration base geometry can be read off.

In this paper we explore continuous silent speech recognition using electroencephalography (EEG) signals. We implemented a connectionist temporal classification (CTC) automatic speech recognition (ASR) model to translate EEG signals recorded in parallel while subjects were reading English sentences in their mind withou…

Metagenomics characterizes the taxonomic diversity of microbial communities by sequencing DNA directly from an environmental sample. One of the main challenges in metagenomics data analysis is the binning step, where each sequenced read is assigned to a taxonomic clade. Due to the large volume of metagenomics datasets,…

The key contribution of this paper is to propose a classification into two dimensions of the load forecasting studies to decide which forecasting tools to use in which case. This classification aims to provide a synthetic view of the relevant forecasting techniques and methodologies by forecasting problem. In addition,…

Many Machine Reading and Natural Language Understanding tasks require reading supporting text in order to answer questions. For example, in Question Answering, the supporting text can be newswire or Wikipedia articles; in Natural Language Inference, premises can be seen as the supporting text and hypotheses as question…

Literary critics often attempt to uncover meaning in a single work of literature through careful reading and analysis. Applying natural language processing methods to aid in such literary analyses remains a challenge in digital humanities. While most previous work focuses on "distant reading" by algorithmically discove…

Batteryless or so called passive wearables are providing new and innovative methods for human activity recognition (HAR), especially in healthcare applications for older people. Passive sensors are low cost, lightweight, unobtrusive and desirably disposable; attractive attributes for healthcare applications in hospital…

Shannon's mathematical theory of communication defines fundamental limits on how much information can be transmitted between the different components of any man-made or biological system. This paper is an informal but rigorous introduction to the main ideas implicit in Shannon's theory. An annotated reading list is pro…

We present a graphical criterion for reading dependencies from the minimal directed independence map G of a graphoid p when G is a polytree and p satisfies composition and weak transitivity. We prove that the criterion is sound and complete. We argue that assuming composition and weak transitivity is not too restrictiv…

One out of four children in India are leaving grade eight without basic reading skills. Measuring the reading levels in a vast country like India poses significant hurdles. Recent advances in machine learning opens up the possibility of automating this task. However, the datasets of children's speech are not only rare …

New approach speeds up DNA sequence alignment.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following …

High predictive performance and ease of use and interpretability are important requirements for the applicability of a computer-aided diagnosis (CAD) to human reading studies. We propose a CAD system specifically designed to be more comprehensible to the radiologist reviewing screening breast MRI studies. Multiparametr…

Most work in machine reading focuses on question answering problems where the answer is directly expressed in the text to read. However, many real-world question answering problems require the reading of text not because it contains the literal answer, but because it contains a recipe to derive an answer together with …

This paper is an introduction to rational tangles, rational knots and links and their applications to DNA. The paper can be read as an introduction to our more technical papers on rational tangles (math.GT/0311499) and on rational knots (math.GT/0212011). The present paper includes a self-contained account of the tangl…

Bi-directional LSTMs are a powerful tool for text representation. On the other hand, they have been shown to suffer various limitations due to their sequential nature. We investigate an alternative LSTM structure for encoding text, which consists of a parallel state for each word. Recurrent steps are used to perform lo…

Neural network optimizes learning sequence for reading words.

Many recent papers address reading comprehension, where examples consist of (question, passage, answer) tuples. Presumably, a model must combine information from both questions and passages to predict corresponding answers. However, despite intense interest in the topic, with hundreds of published papers vying for lead…

Data annotation is an essential stage in supervised learning. However, the annotation process is exhaustive and time consuming, specially for large datasets. Activities of Daily Living (ADL) recognition is an example of systems that exploit very large raw sensor data readings. In such systems, sensor readings are colle…

Survey analyzes economic research on cryptocurrencies using hybrid methods.

We show how the rotation and translation fields of a surface, introduced by G. Darboux, may be used to obtain short proofs of a well-known theorem (that reads that the total mean curvature of a surface is stationary under an infinitesimal bending) and a new theorem (that reads that every infinitesimal flex of any simpl…

With the arrival of the big data era, more and more data are becoming readily available in various real-world applications and those data are usually highly heterogeneous. Taking computational medicine as an example, we have both Electronic Health Records (EHR) and medical images for each patient. For complicated disea…

Typical large-scale recommender systems use deep learning models that are stored on a large amount of DRAM. These models often rely on embeddings, which consume most of the required memory. We present Bandana, a storage system that reduces the DRAM footprint of embeddings, by using Non-volatile Memory (NVM) as the prim…

Single Molecule Real-Time (SMRT) sequencing is a recent advancement of Next Gen technology developed by Pacific Bio (PacBio). It comes with an explosion of long and noisy reads demanding cutting edge research to get most out of it. To deal with the high error probability of SMRT data, a novel contextual Locality Sensit…

In this paper, we propose to apply object detection methods from the vision domain on the speech recognition domain, by treating audio fragments as objects. More specifically, we present SpeechYOLO, which is inspired by the YOLO algorithm for object detection in images. The goal of SpeechYOLO is to localize boundaries …

Study prenatal PM2.5 exposure and 4th grade reading scores, identifying critical windows of susceptibility.

As automotive electronics continue to advance, cars are becoming more and more reliant on sensors to perform everyday driving operations. These sensors are omnipresent and help the car navigate, reduce accidents, and provide comfortable rides. However, they can also be used to learn about the drivers themselves. In thi…

The covariance graph (aka bi-directed graph) of a probability distribution $p$ is the undirected graph $G$ where two nodes are adjacent iff their corresponding random variables are marginally dependent in $p$. In this paper, we present a graphical criterion for reading dependencies from $G$, under the assumption that $…

Three-dimensional smooth, compact toric varieties (SCTV), when viewed as real six-dimensional manifolds, can admit G-structures rendering them suitable for internal manifolds in supersymmetric flux compactifications. We develop techniques which allow us to systematically construct G-structures on SCTV and read off thei…

FEM improves attention mechanisms by applying value-driven log-linear tilts.

We consider a scenario where an artificial agent is reading a stream of text composed of a set of narrations, and it is informed about the identity of some of the individuals that are mentioned in the text portion that is currently being read. The agent is expected to learn to follow the narrations, thus disambiguating…

New classifiers account for context-specific independences.

Because it is not feasible to collect training data for every language, there is a growing interest in cross-lingual transfer learning. In this paper, we systematically explore zero-shot cross-lingual transfer learning on reading comprehension tasks with a language representation model pre-trained on multi-lingual corp…

This work investigates how context should be taken into account when performing continuous authentication of a smartphone user based on touchscreen and accelerometer readings extracted from swipe gestures. The study is conducted on the publicly available HMOG dataset consisting of 100 study subjects performing pre-defi…

We present a memory augmented neural network for natural language understanding: Neural Semantic Encoders. NSE is equipped with a novel memory update rule and has a variable sized encoding memory that evolves over time and maintains the understanding of input sequences through read}, compose and write operations. NSE c…

Memory networks are neural networks with an explicit memory component that can be both read and written to by the network. The memory is often addressed in a soft way using a softmax function, making end-to-end training with backpropagation possible. However, this is not computationally scalable for applications which …

Standard accuracy metrics indicate that modern reading comprehension systems have achieved strong performance in many question answering datasets. However, the extent these systems truly understand language remains unknown, and existing systems are not good at distinguishing distractor sentences, which look related but…

Proposes a framework to adjust quotes for informational risk in markets with informed traders and price-revealing quotes.