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.
New task aligns molecular structure with gene expression changes.
Transcriptomics response of SK-N-AS cells to methamidophos (an acetylcholine esterase inhibitor) exposure was measured at 10 time points between 0.5 and 48 h. The data was analyzed using a combination of traditional statistical methods and novel machine learning algorithms for detecting anomalous behavior and infer cau…
Despite great advances, molecular cancer pathology is often limited to the use of a small number of biomarkers rather than the whole transcriptome, partly due to computational challenges. Here, we introduce a novel architecture of Deep Neural Networks (DNNs) that is capable of simultaneous inference of various properti…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult …
A novel criterion selects optimal distance metrics for cell profile analysis.
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…
End-to-end ASR error detection using audio-transcript entailment.
Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of nega…
Inverse Drum Machine separates drum mixes using transcription and synthesis.
Automatic music transcription is considered to be one of the hardest problems in music information retrieval, yet recent deep learning approaches have achieved substantial improvements on transcription performance. These approaches commonly employ supervised learning models that predict various time-frequency represent…
With different genomes available, unsupervised learning algorithms are essential in learning genome-wide biological insights. Especially, the functional characterization of different genomes is essential for us to understand lives. In this book chapter, we review the state-of-the-art unsupervised learning algorithms fo…
Motivation: Cell-biological processes are regulated through a complex network of interactions between genes and their products. The processes, their activating conditions, and the associated transcriptional responses are often unknown. Organism-wide modeling of network activation can reveal unique and shared mechanisms…
Case Law has a significant impact on the proceedings of legal cases. Therefore, the information that can be obtained from previous court cases is valuable to lawyers and other legal officials when performing their duties. This paper describes a methodology of applying discourse relations between sentences when processi…
Deep learning is at the core of recent spoken language understanding (SLU) related tasks. More precisely, deep neural networks (DNNs) drastically increased the performances of SLU systems, and numerous architectures have been proposed. In the real-life context of theme identification of telephone conversations, it is c…
TF-MoDISco (Transcription Factor Motif Discovery from Importance Scores) is an algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data. This technical note focuses on version v0.5.6.5. The implementation is available at https://github.com/kundajelab/tfmodisco/tree/v0.5.6…
Generative AI predicts economic activity from corporate transcripts.
Study detects SLI in children from spontaneous narrative transcripts.
In training a deep learning system to perform audio transcription, two practical problems may arise. Firstly, most datasets are weakly labelled, having only a list of events present in each recording without any temporal information for training. Secondly, deep neural networks need a very large amount of labelled train…
Model earnings call transcripts for better stock price prediction.
Standard ChIP-seq peak calling pipelines seek to differentiate biochemically reproducible signals of individual genomic elements from background noise. However, reproducibility alone does not imply functional regulation (e.g., enhancer activation, alternative splicing). Here we present a general-purpose, interpretable …
We advance the state of the art in polyphonic piano music transcription by using a deep convolutional and recurrent neural network which is trained to jointly predict onsets and frames. Our model predicts pitch onset events and then uses those predictions to condition framewise pitch predictions. During inference, we r…
The regulatory process of Drosophila is thoroughly studied for understanding a great variety of biological principles. While pattern-forming gene networks are analysed in the transcription step, post-transcriptional events (e.g. translation, protein processing) play an important role in establishing protein expression …
Many of the recent approaches to polyphonic piano note onset transcription require training a machine learning model on a large piano database. However, such approaches are limited by dataset availability; additional training data is difficult to produce, and proposed systems often perform poorly on novel recording con…
Study analyzes deep learning models for financial sentiment in earnings calls.
We investigate the problem of modeling symbolic sequences of polyphonic music in a completely general piano-roll representation. We introduce a probabilistic model based on distribution estimators conditioned on a recurrent neural network that is able to discover temporal dependencies in high-dimensional sequences. Our…
SnapMMD forecasts cell differentiation outcomes from snapshot data.
In this paper, we explore various approaches for semi supervised learning in an end to end automatic speech recognition (ASR) framework. The first step in our approach involves training a seed model on the limited amount of labelled data. Additional unlabelled speech data is employed through a data selection mechanism …
Hidden Markov Models (HMMs) are a ubiquitous tool to model time series data, and have been widely used in two main tasks of Automatic Music Transcription (AMT): note segmentation, i.e. identifying the played notes after a multi-pitch estimation, and sequential post-processing, i.e. correcting note segmentation using tr…
TransST improves spatial transcriptomics data analysis by identifying cell clusters and biomarkers.
Model predicts active and passive cosponsorship motivations in Congress.
This paper proposes a speech emotion recognition method based on speech features and speech transcriptions (text). Speech features such as Spectrogram and Mel-frequency Cepstral Coefficients (MFCC) help retain emotion-related low-level characteristics in speech whereas text helps capture semantic meaning, both of which…
This paper explores a variety of models for frame-based music transcription, with an emphasis on the methods needed to reach state-of-the-art on human recordings. The translation-invariant network discussed in this paper, which combines a traditional filterbank with a convolutional neural network, was the top-performin…
Study combines speaker verification and voice trigger detection in a single network.
Automatic Music Transcription (AMT) consists in automatically estimating the notes in an audio recording, through three attributes: onset time, duration and pitch. Probabilistic Latent Component Analysis (PLCA) has become very popular for this task. PLCA is a spectrogram factorization method, able to model a magnitude …
Anonymization reduces economic signal extraction from financial texts.
We use automatic speech recognition to assess spoken English learner pronunciation based on the authentic intelligibility of the learners' spoken responses determined from support vector machine (SVM) classifier or deep learning neural network model predictions of transcription correctness. Using numeric features produ…
Framework ranks sectors influenced by Indian Union Budgets.
Each year, roughly 30% of first-year students at US baccalaureate institutions do not return for their second year and over $9 billion is spent educating these students. Yet, little quantitative research has analyzed the causes and possible remedies for student attrition. Here, we describe initial efforts to model stud…
A method to produce personalized classification models to automatically review online dating profiles on Tinder is proposed, based on the user's historical preference. The method takes advantage of a FaceNet facial classification model to extract features which may be related to facial attractiveness. The embeddings fr…
Automated prediction of public speaking performance enables novel systems for tutoring public speaking skills. We use the largest open repository---TED Talks---to predict the ratings provided by the online viewers. The dataset contains over 2200 talk transcripts and the associated meta information including over 5.5 mi…
Profile entropy measures learnability and compressibility of discrete distributions.
A method to describe Riemann surfaces using graph profiles is proposed.
Automatic Music Transcription (AMT) is one of the oldest and most well-studied problems in the field of music information retrieval. Within this challenging research field, onset detection and instrument recognition take important places in transcription systems, as they respectively help to determine exact onset times…
In cheminformatics, compound-target binding profiles has been a main source of data for research. For data repositories that only provide positive profiles, a popular assumption is that unreported profiles are all negative. In this paper, we caution audience not to take this assumption for granted, and present empirica…
Large financial dataset tracks FOMC communications and their impact.
Method controls extrapolation in prediction profiles for statistical and machine learning models.
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction problem. However, such data can be limited in size and/or are expensive to acqu…
Background: While machine learning (ML) models are rapidly emerging as promising screening tools in critical care medicine, the identification of homogeneous subphenotypes within populations with heterogeneous conditions such as pediatric sepsis may facilitate attainment of high-predictive performance of these prognost…