GeNet classifies metagenomic sequences with less memory and comparable recall to state-of-the-art methods.
problem Classifying metagenomic sequences from raw DNA sequences.
method Exploits hierarchical structure between labels for training, using deep representations.
result GeNet achieves competitive precision and good recall with less memory requirements.
ε-shotgun optimizes expensive function evaluations in parallel.
problem Optimizing expensive black-box functions efficiently.
method ε-greedy batch Bayesian optimisation.
result ε-shotgun outperforms state-of-the-art batch methods.
ShotgunCSP predicts crystal structures using machine learning, achieving high accuracy with minimal computation.
problem Predicting stable or metastable crystal structures of large systems.
method Noniterative screening using transfer learning and generative models.
result ShotgunCSP achieves 93.3% accuracy in benchmark tests with 90 different crystal structures.
Liquid chromatography coupled with tandem mass spectrometry, also known as shotgun proteomics, is a widely-used high-throughput technology for identifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by a typical shotgun proteomics experiment begins by assi…
We present a generic framework for parallel coordinate descent (CD) algorithms that includes, as special cases, the original sequential algorithms Cyclic CD and Stochastic CD, as well as the recent parallel Shotgun algorithm. We introduce two novel parallel algorithms that are also special cases---Thread-Greedy CD and …
Bayesian model selection of vine copulas: a loss-based perspective
problem Efficient model selection and estimation in Bayesian vine methodology
method Combines loss-based model priors with shotgun stochastic search strategy
result Promotes sparsity and enables fast and effective structure selection
New method corrects correlation bias in feature importance.
problem Correlations between features in high-dimensional data bias statistical and machine learning models.
method Pairwise Permutation Algorithm (PPA)
result PPA corrects correlation bias, identifying biological relevant biomarkers.
Large-scale L1-regularized loss minimization problems arise in high-dimensional applications such as compressed sensing and high-dimensional supervised learning, including classification and regression problems. High-performance algorithms and implementations are critical to efficiently solving these problems. Building…
Exploratory analysis over network data is often limited by the ability to efficiently calculate graph statistics, which can provide a model-free understanding of the macroscopic properties of a network. We introduce a framework for estimating the graphlet count---the number of occurrences of a small subgraph motif (e.g…
Bayesian learning for forests and trees improves graph detection and structure learning.
problem Learning graph structures in non-decomposable graphs.
method Adapted MCMC and SSS algorithms for forests and trees, using the Chow-Liu algorithm and Matrix Tree Theorem.
result SSS with trees or forests outperforms SSS with decomposable graphs in certain cases.
A novel sequence-to-sequence model predicts missing sensor data.
problem Missing sensor data in sequences.
method Formulated a novel sequence-to-sequence model using forward and backward RNNs.
result The model produces the lowest errors in 12% more cases than the current state-of-the-art.
Classifies intrinsically linked tournaments by their score sequences.
problem Classifying intrinsically linked tournaments using their score sequences.
method Examining the score sequences of tournaments and identifying linkless sequences.
result The vast majority of score sequences for 8-vertex tournaments are linkless.
Paper tackles embedding attributed sequences in unsupervised learning.
problem Mining tasks over attributed sequences with dependencies between sequences and attributes.
method Proposes a deep multimodal learning framework, NAS, for unsupervised learning of attributed sequences.
result NAS produces task-independent embeddings for various mining tasks on real-world datasets.
Paper defines and evaluates attention mechanisms for sequence to sequence tasks.
problem Improving sequence to sequence mapping tasks.
method Mathematical definition and evaluation of attention mechanisms in sequence to sequence models.
result Models using greater attention perform better and converge faster.
Study Thompson Sampling in adversarial bit prediction, finding regret bounds and optimal sequences.
problem Adversarial bit prediction with varying error weights.
method Thompson Sampling, analyzing sequences with largest and smallest regret.
result Regret bounds for adversarial bit prediction sequences, including optimal and worst-case scenarios.
Enhances sequence memory capacity in neural networks.
problem Limited sequence capacity in Hopfield-like neural networks.
method Introducing a nonlinear interaction term and a generalized pseudoinverse rule.
result Significantly increased sequence capacity with novel scaling laws.
Deep generative models have been successfully used to learn representations for high-dimensional discrete spaces by representing discrete objects as sequences and employing powerful sequence-based deep models. Unfortunately, these sequence-based models often produce invalid sequences: sequences which do not represent a…
Equivalent condition found for q-holonomic sequences.
problem Characterizing q-holonomic sequences.
method Elimination property for subsets of variables.
result Proved equivalence of q-holonomicity and elimination property.
Paper presents a new framework for sequence classification.
problem Sequence classification in real-world applications.
method Reference-based sequence classification framework.
result New sequence classification algorithms achieve comparable accuracy.
The abstract discusses a spectral sequence for Lie algebroids.
problem The abstract tackles the spectral sequence of Lie algebroids.
method The abstract presents a spectral sequence for Lie algebroids, generalizing classical constructions.
result The spectral sequence converges to Lie algebroid cohomology for wide Lie subalgebroids and to formal Lie algebroid cohomology for Lie subalgebroids over proper submanifolds.
Many machine learning tasks can be expressed as the transformation---or \emph{transduction}---of input sequences into output sequences: speech recognition, machine translation, protein secondary structure prediction and text-to-speech to name but a few. One of the key challenges in sequence transduction is learning to …
Paper proposes using LSTM for LSH-based sequence alignment.
problem Sequence alignment using deep learning models.
method Deep bidirectional LSTM for feature learning and LSH-based sequence alignment.
result Higher accuracy achieved with LSTM-based model.
Study on continuous sequence classification with distribution uncertainty.
problem Classifying continuous sequences with varying distribution uncertainty.
method Proposes distribution-free tests for three test designs: fixed-length, sequential, and two-phase tests.
result Error probabilities decay exponentially fast for all test designs.
A new mechanism for GANs improves text generation by evaluating sub-sequences.
problem Exposure bias and mode collapse in GANs for text generation.
method Segmenting the sequence into sub-sequences and evaluating them individually.
result Significant improvement in text generation models on benchmark data.
Deep learning models optimize protein sequences.
problem Optimizing protein properties through sequence design.
method Deep generative models guided by machine learning.
result Improved protein sequence generation from prior knowledge.
Unified approach for generating sequences from undirected models.
problem Generating sequences directly from undirected models like BERT.
method Generalized model of sequence generation unifying decoding in directed and undirected models.
result Adapted decoding algorithms for undirected models achieve competitive results.
Transformers can approximate any sequence-to-sequence function, surprising given their complexity.
problem Understanding the expressive power of Transformer models for sequence-to-sequence functions.
method Established that Transformers are universal approximators of continuous permutation equivariant sequence-to-sequence functions with compact support, and extended this to arbitrary functions using positional encodings.
result Transformers are universal approximators of arbitrary continuous sequence-to-sequence functions on a compact domain.
Unimodal sequences of moves connect 3-manifold triangulations.
problem Understanding the structure of sequences of bistellar flips.
method Examined unimodal sequences of moves that increase and decrease triangulation size.
result Proved that any two one-vertex triangulations are connected by a unimodal sequence of moves.
This paper presents a novel end-to-end approach to program repair based on sequence-to-sequence learning. We devise, implement, and evaluate a system, called SequenceR, for fixing bugs based on sequence-to-sequence learning on source code. This approach uses the copy mechanism to overcome the unlimited vocabulary probl…
This work compresses sequences by treating them as continuous-time processes, enabling efficient discretization.
problem Efficient compression of sequences, especially with deep learning models that scale with sequence length.
method Treat sequences as continuous-time processes, learn efficient discretization, and decode at different time intervals.
result Automatic bit rate reductions in video and motion capture sequences using learned discretization.
Characterizes sequences from two-component link diagrams.
problem Understanding information from non-self crossing sequences of link diagrams.
method Investigated and characterized pairs of non-self OU sequences of two-component link diagrams.
result Completely characterized pairs of non-self OU sequences of diagrams of two-component links.
In order to study large variations or fluctuations of finite or infinite sequences (time series), we bring to light an 1868 paper of Crofton and the (Cauchy-)Crofton theorem. After surveying occurrences of this result in the literature, we introduce the inconstancy of a sequence and we show why it seems more pertinent …
SVM and N-best algorithm classify microbial marker clades from genome sequences.
problem Classifying microbial clades from genome sequences, especially new species.
method Support vector machine (SVM) with N-best algorithm, time series feature extraction, random fragment generation, k-mer size selection.
result Recognition accuracy rates above 28% in top-1 candidate, above 91% in top-10 candidate.
Researchers develop flexible kernels for biological sequences with guaranteed reliability.
problem Challenges in applying machine learning to biological sequences, including unreliable methods.
method Theoretical analysis and development of modified kernels to ensure reliability and accuracy.
result Developed kernels that are universal, characteristic, and metrize the space of distributions for biological sequences.
A convolutional sequence to sequence non-intrusive load monitoring model is proposed in this paper. Gated linear unit convolutional layers are used to extract information from the sequences of aggregate electricity consumption. Residual blocks are also introduced to refine the output of the neural network. The partiall…
Using sequence to sequence algorithms for query expansion has not been explored yet in Information Retrieval literature nor in Question-Answering's. We tried to fill this gap in the literature with a custom Query Expansion engine trained and tested on open datasets. Starting from open datasets, we built a Query Expansi…
New method maps protein sequences to embeddings encoding structural information.
problem Inferring structural properties from amino acid sequences when structures are unknown.
method Representation learning using bidirectional LSTM models with structural similarity and residue contact maps.
result Trained embeddings improve structural similarity prediction and transfer to other tasks.
P3BO optimizes biological sequence design by combining multiple methods.
problem Variability in performance of black-box optimization methods for biological sequence design.
method Population-Based Black-Box Optimization (P3BO) that samples sequences from an ensemble of methods, weighting by past performance.
result P3BO outperforms individual methods, proposing higher quality and more diverse sequences.
Study on spectral sequence of Iwasawa manifold and its deformations.
problem Properties of Frölicher spectral sequence on Iwasawa manifold and its deformations.
method Determination of successive pages of the Frölicher spectral sequence.
result New examples and counterexamples on spectral sequence properties.
This research explores various sampling methods and probability distributions for hard alignment in sequence-to-sequence TTS synthesis.
problem Improving alignment accuracy in sequence-to-sequence text-to-speech synthesis.
method Investigated various sampling methods (greedy, beam, random) and probability distributions (Bernoulli, Concrete) for hard alignment.
result Deterministic search is more preferable than stochastic search for natural alignment transition.
New concordance invariant from spectral sequence on Khovanov homology.
problem Concordance invariants from spectral sequences.
method Constructing from E(−1) spectral sequence on Khovanov homology. result Provides a bound on the nonorientable slice genus.
The availability of large amounts of time series data, paired with the performance of deep-learning algorithms on a broad class of problems, has recently led to significant interest in the use of sequence-to-sequence models for time series forecasting. We provide the first theoretical analysis of this time series forec…
nTreeClus clusters categorical sequences using tree-based learners and k-mers.
problem Challenges in clustering categorical and sequential data.
method nTreeClus uses Tree-based Learners, k-mers, and autoregressive models for categorical time series.
result nTreeClus outperformed baseline methods in various validation metrics.
New sequences prove some link diagrams can't be transformed by specific moves.
problem Proving some link diagrams can't be transformed by specific sequences of Reidemeister moves.
method Proved the existence of I-generalized ordered sequences to create simple transformations.
result Some link diagrams cannot be transformed by sequences of moves that increase, then decrease crossings.
Sequence-to-Sequence (seq2seq) modeling has rapidly become an important general-purpose NLP tool that has proven effective for many text-generation and sequence-labeling tasks. Seq2seq builds on deep neural language modeling and inherits its remarkable accuracy in estimating local, next-word distributions. In this work…
Existence of an infinite sequence of harmonic maps between spheres of certain dimensions was proven by Bizon and Chmaj. This sequence shares many features of the Bartnik-McKinnon sequence of solutions to the Einstein-Yang-Mills equations as well as sequences of solutions that have arisen in other physical models. We ap…
A GAN variant synthesizes missing MRI sequences from available ones.
problem Missing MRI sequences due to various constraints.
method Multi-modal Generative Adversarial Network (GAN) that combines multiple available sequences to synthesize missing ones.
result The proposed GAN method outperforms competing approaches in synthesizing missing MRI sequences.
The study compares different scRNA sequencing methods using a high-dimensional dataset.
problem To identify unique characteristics of different scRNA sequencing methods.
method Quantitative comparison through clustering analysis of a high-dimensional dataset.
result Identifies unique characteristics associated with different scRNA sequencing methods.