A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Paper proposes using LSTM for LSH-based sequence alignment.
Sequence-to-sequence text-to-speech (TTS) is dominated by soft-attention-based methods. Recently, hard-attention-based methods have been proposed to prevent fatal alignment errors, but their sampling method of discrete alignment is poorly investigated. This research investigates various combinations of sampling methods…
Traditional pairwise sequence alignment is based on matching individual samples from two sequences, under time monotonicity constraints. However, in many application settings matching subsequences (segments) instead of individual samples may bring in additional robustness to noise or local non-causal perturbations. Thi…
A new framework improves ASR alignment accuracy via optimal transport.
We present a probabilistic model for unsupervised alignment of high-dimensional time-warped sequences based on the Dirichlet Process Mixture Model (DPMM). We follow the approach introduced in (Kazlauskaite, 2018) of simultaneously representing each data sequence as a composition of a true underlying function and a time…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly. Alignment-free methods, on the other hand, are based on abstract string comparisons …
New approach speeds up DNA sequence alignment.
The goal of temporal alignment is to establish time correspondence between two sequences, which has many applications in a variety of areas such as speech processing, bioinformatics, computer vision, and computer graphics. In this paper, we propose a novel temporal alignment method called least-squares dynamic time war…
NTW aligns multiple time-series data efficiently using neural networks.
We investigate the integration of a planning mechanism into sequence-to-sequence models using attention. We develop a model which can plan ahead in the future when it computes its alignments between input and output sequences, constructing a matrix of proposed future alignments and a commitment vector that governs whet…
Align-RUDDER improves reinforcement learning with few demonstrations by redistributing rewards.
The paper approaches the task of handwritten text recognition (HTR) with attentional encoder-decoder networks trained on sequences of characters, rather than words. We experiment on lines of text from popular handwriting datasets and compare different activation functions for the attention mechanism used for aligning i…
Pair Hidden Markov Models (PHMMs) are probabilistic models used for pairwise sequence alignment, a quintessential problem in bioinformatics. PHMMs include three types of hidden states: match, insertion and deletion. Most previous studies have used one or two hidden states for each PHMM state type. However, few studies …
We present a model that can automatically learn alignments between high-dimensional data in an unsupervised manner. Our proposed method casts alignment learning in a framework where both alignment and data are modelled simultaneously. Further, we automatically infer groupings of different types of sequences within the …
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 …
Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate computational tools for transcript reconstruction, this technology may also become us…
We propose a novel framework for combining datasets via alignment of their intrinsic geometry. This alignment can be used to fuse data originating from disparate modalities, or to correct batch effects while preserving intrinsic data structure. Importantly, we do not assume any pointwise correspondence between datasets…
Study SGD dynamics in sequence models, revealing training phases and influence of sequence length.
A new method estimates protein evolutionary fields and couplings from alignments.
Despite some empirical success at correcting exposure bias in machine translation, scheduled sampling algorithms suffer from a major drawback: they incorrectly assume that words in the reference translations and in sampled sequences are aligned at each time step. Our new differentiable sampling algorithm addresses this…
The application of machine learning to bioinformatics problems is well established. Less well understood is the application of bioinformatics techniques to machine learning and, in particular, the representation of non-biological data as biosequences. The aim of this paper is to explore the effects of giving amino acid…
Bayesian HMM for protein alignment state estimation.
Regularization effect found in neural feature alignment.
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for understanding function. Existing approaches for detecting structural similarity between prot…
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…
Improved speech recognition with language model integration in sequence-to-sequence models.
Consider an imitation learning problem that the imitator and the expert have different dynamics models. Most of the current imitation learning methods fail because they focus on imitating actions. We propose a novel state alignment-based imitation learning method to train the imitator to follow the state sequences in e…
Paper shows equivalence between two alignment methods and introduces a new algorithm.
B-cos transforms improve neural network interpretability by aligning weights.
Conformer encoder reverses sequence in time dimension, affecting decoder training.
Unified model integrates text and time series for financial forecasting.
Rapid progress in deep learning has spurred its application to bioinformatics problems including protein structure prediction and design. In classic machine learning problems like computer vision, progress has been driven by standardized data sets that facilitate fair assessment of new methods and lower the barrier to …
Viral sequence classification is an important task in pathogen detection, epidemiological surveys and evolutionary studies. Statistical learning methods are widely used to classify and identify viral sequences in samples from environments. These methods face several challenges associated with the nature and properties …
New statistical model improves protein alignment accuracy.
Paper proposes AXE loss for non-autoregressive machine translation, improving performance.
Parametric spatial transformation models have been successfully applied to image registration tasks. In such models, the transformation of interest is parameterized by a fixed set of basis functions as for example B-splines. Each basis function is located on a fixed regular grid position among the image domain, because…
Improved neural transducer model outperforms attention model on longer sequences.
In this paper, we propose a deep learning approach to tackle the automatic summarization tasks by incorporating topic information into the convolutional sequence-to-sequence (ConvS2S) model and using self-critical sequence training (SCST) for optimization. Through jointly attending to topics and word-level alignment, o…
In this paper, we study the problem of locating a predefined sequence of patterns in a time series. In particular, the studied scenario assumes a theoretical model is available that contains the expected locations of the patterns. This problem is found in several contexts, and it is commonly solved by first synthesizin…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does not have a close match in the database. In addition, each comparison can be costly…
Sequence-to-sequence models with soft attention have been successfully applied to a wide variety of problems, but their decoding process incurs a quadratic time and space cost and is inapplicable to real-time sequence transduction. To address these issues, we propose Monotonic Chunkwise Attention (MoChA), which adaptiv…
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,…
Learning a good distance measure for distance-based classification in time series leads to significant performance improvement in many tasks. Specifically, it is critical to effectively deal with variations and temporal dependencies in time series. However, existing metric learning approaches focus on tackling variatio…
FedGTEA learns new tasks in federated learning with task embeddings and alignment.
The celebrated Sequence to Sequence learning (Seq2Seq) technique and its numerous variants achieve excellent performance on many tasks. However, many machine learning tasks have inputs naturally represented as graphs; existing Seq2Seq models face a significant challenge in achieving accurate conversion from graph form …
AbDiffuser generates full-atom antibodies with sequence and structure fidelity.
In this paper, we present Neural Phrase-based Machine Translation (NPMT). Our method explicitly models the phrase structures in output sequences using Sleep-WAke Networks (SWAN), a recently proposed segmentation-based sequence modeling method. To mitigate the monotonic alignment requirement of SWAN, we introduce a new …
We explore models for translating abstract musical ideas (scores, rhythms) into expressive performances using Seq2Seq and recurrent Variational Information Bottleneck (VIB) models. Though Seq2Seq models usually require painstakingly aligned corpora, we show that it is possible to adapt an approach from the Generative A…