arXiv subjects

Arijit Sehanobish

Publications and source records attributed to Arijit Sehanobish.

29 records · Page 2Linked to original sources

arXiv2022

Explaining the Effectiveness of Multi-Task Learning for Efficient Knowledge Extraction from Spine MRI Reports

Pretrained Transformer based models finetuned on domain specific corpora have changed the landscape of NLP. However, training or fine-tuning these models for individual tasks can be time consuming and resource intensive. Thus, a lot of current research is focused on using transformers for multi-task learning (Raffel et al.,2020) and how to group the tasks to help a multi-task model to learn effective representations that can be shared across tasks (Standley et al., 2020; Fifty et al., 2021). In this work, we show that a single multi-tasking model can match the performance of task specific models when the task specific models show similar representations across all of their hidden layers and their gradients are aligned, i.e. their gradients follow the same direction. We hypothesize that the above observations explain the effectiveness of multi-task learning. We validate our observations on our internal radiologist-annotated datasets on the cervical and lumbar spine. Our method is simple and intuitive, and can be used in a wide range of NLP problems.

cs.LG↗

arXiv2022

Efficient Extraction of Pathologies from C-Spine Radiology Reports using Multi-Task Learning

Pretrained Transformer based models finetuned on domain specific corpora have changed the landscape of NLP. Generally, if one has multiple tasks on a given dataset, one may finetune different models or use task specific adapters. In this work, we show that a multi-task model can beat or achieve the performance of multiple BERT-based models finetuned on various tasks and various task specific adapter augmented BERT-based models. We validate our method on our internal radiologist's report dataset on cervical spine. We hypothesize that the tasks are semantically close and related and thus multitask learners are powerful classifiers. Our work opens the scope of using our method to radiologist's reports on various body parts.

cs.LG↗

arXiv2022

Hybrid Random Features

We propose a new class of random feature methods for linearizing softmax and Gaussian kernels called hybrid random features (HRFs) that automatically adapt the quality of kernel estimation to provide most accurate approximation in the defined regions of interest. Special instantiations of HRFs lead to well-known methods such as trigonometric (Rahimi and Recht, 2007) or (recently introduced in the context of linear-attention Transformers) positive random features (Choromanski et al., 2021). By generalizing Bochner's Theorem for softmax/Gaussian kernels and leveraging random features for compositional kernels, the HRF-mechanism provides strong theoretical guarantees - unbiased approximation and strictly smaller worst-case relative errors than its counterparts. We conduct exhaustive empirical evaluation of HRF ranging from pointwise kernel estimation experiments, through tests on data admitting clustering structure to benchmarking implicit-attention Transformers (also for downstream Robotics applications), demonstrating its quality in a wide spectrum of machine learning problems.

cs.LG↗

arXiv2021

Learning Full Configuration Interaction Electron Correlations with Deep Learning

In this report, we present a deep learning framework termed the Electron Correlation Potential Neural Network (eCPNN) that can learn succinct and compact potential functions. These functions can effectively describe the complex instantaneous spatial correlations among electrons in many--electron atoms. The eCPNN was trained in an unsupervised manner with limited information from Full Configuration Interaction (FCI) one--electron density functions within predefined limits of accuracy. Using the effective correlation potential functions generated by eCPNN, we can predict the total energies of each of the studied atomic systems with a remarkable accuracy when compared to FCI energies.

quant-ph↗

arXiv2021

Fine-tuning Vision Transformers for the Prediction of State Variables in Ising Models

Transformers are state-of-the-art deep learning models that are composed of stacked attention and point-wise, fully connected layers designed for handling sequential data. Transformers are not only ubiquitous throughout Natural Language Processing (NLP), but, recently, they have inspired a new wave of Computer Vision (CV) applications research. In this work, a Vision Transformer (ViT) is applied to predict the state variables of 2-dimensional Ising model simulations. Our experiments show that ViT outperform state-of-the-art Convolutional Neural Networks (CNN) when using a small number of microstate images from the Ising model corresponding to various boundary conditions and temperatures. This work opens the possibility of applying ViT to other simulations, and raises interesting research directions on how attention maps can learn about the underlying physics governing different phenomena.

cs.CV↗

arXiv2021

Permutation invariant networks to learn Wasserstein metrics

Understanding the space of probability measures on a metric space equipped with a Wasserstein distance is one of the fundamental questions in mathematical analysis. The Wasserstein metric has received a lot of attention in the machine learning community especially for its principled way of comparing distributions. In this work, we use a permutation invariant network to map samples from probability measures into a low-dimensional space such that the Euclidean distance between the encoded samples reflects the Wasserstein distance between probability measures. We show that our network can generalize to correctly compute distances between unseen densities. We also show that these networks can learn the first and the second moments of probability distributions.

cs.LG↗

arXiv2021

Learning Potentials of Quantum Systems using Deep Neural Networks

Attempts to apply Neural Networks (NN) to a wide range of research problems have been ubiquitous and plentiful in recent literature. Particularly, the use of deep NNs for understanding complex physical and chemical phenomena has opened a new niche of science where the analysis tools from Machine Learning (ML) are combined with the computational concepts of the natural sciences. Reports from this unification of ML have presented evidence that NNs can learn classical Hamiltonian mechanics. This application of NNs to classical physics and its results motivate the following question: Can NNs be endowed with inductive biases through observation as means to provide insights into quantum phenomena? In this work, this question is addressed by investigating possible approximations for reconstructing the Hamiltonian of a quantum system in an unsupervised manner by using only limited information obtained from the system's probability distribution.

cs.LG↗

arXiv2020

Gaining Insight into SARS-CoV-2 Infection and COVID-19 Severity Using Self-supervised Edge Features and Graph Neural Networks

A molecular and cellular understanding of how SARS-CoV-2 variably infects and causes severe COVID-19 remains a bottleneck in developing interventions to end the pandemic. We sought to use deep learning to study the biology of SARS-CoV-2 infection and COVID-19 severity by identifying transcriptomic patterns and cell types associated with SARS-CoV-2 infection and COVID-19 severity. To do this, we developed a new approach to generating self-supervised edge features. We propose a model that builds on Graph Attention Networks (GAT), creates edge features using self-supervised learning, and ingests these edge features via a Set Transformer. This model achieves significant improvements in predicting the disease state of individual cells, given their transcriptome. We apply our model to single-cell RNA sequencing datasets of SARS-CoV-2 infected lung organoids and bronchoalveolar lavage fluid samples of patients with COVID-19, achieving state-of-the-art performance on both datasets with our model. We then borrow from the field of explainable AI (XAI) to identify the features (genes) and cell types that discriminate bystander vs. infected cells across time and moderate vs. severe COVID-19 disease. To the best of our knowledge, this represents the first application of deep learning to identifying the molecular and cellular determinants of SARS-CoV-2 infection and COVID-19 severity using single-cell omics data.

cs.LG↗

arXiv2020

Self-supervised edge features for improved Graph Neural Network training

Graph Neural Networks (GNN) have been extensively used to extract meaningful representations from graph structured data and to perform predictive tasks such as node classification and link prediction. In recent years, there has been a lot of work incorporating edge features along with node features for prediction tasks. One of the main difficulties in using edge features is that they are often handcrafted, hard to get, specific to a particular domain, and may contain redundant information. In this work, we present a framework for creating new edge features, applicable to any domain, via a combination of self-supervised and unsupervised learning. In addition to this, we use Forman-Ricci curvature as an additional edge feature to encapsulate the local geometry of the graph. We then encode our edge features via a Set Transformer and combine them with node features extracted from popular GNN architectures for node classification in an end-to-end training scheme. We validate our work on three biological datasets comprising of single-cell RNA sequencing data of neurological disease, \textit{in vitro} SARS-CoV-2 infection, and human COVID-19 patients. We demonstrate that our method achieves better performance on node classification tasks over baseline Graph Attention Network (GAT) and Graph Convolutional Network (GCN) models. Furthermore, given the attention mechanism on edge and node features, we are able to interpret the cell types and genes that determine the course and severity of COVID-19, contributing to a growing list of potential disease biomarkers and therapeutic targets.

eess.IV↗

arXiv2020

Disease State Prediction From Single-Cell Data Using Graph Attention Networks

Single-cell RNA sequencing (scRNA-seq) has revolutionized biological discovery, providing an unbiased picture of cellular heterogeneity in tissues. While scRNA-seq has been used extensively to provide insight into both healthy systems and diseases, it has not been used for disease prediction or diagnostics. Graph Attention Networks (GAT) have proven to be versatile for a wide range of tasks by learning from both original features and graph structures. Here we present a graph attention model for predicting disease state from single-cell data on a large dataset of Multiple Sclerosis (MS) patients. MS is a disease of the central nervous system that can be difficult to diagnose. We train our model on single-cell data obtained from blood and cerebrospinal fluid (CSF) for a cohort of seven MS patients and six healthy adults (HA), resulting in 66,667 individual cells. We achieve 92 % accuracy in predicting MS, outperforming other state-of-the-art methods such as a graph convolutional network and a random forest classifier. Further, we use the learned graph attention model to get insight into the features (cell types and genes) that are important for this prediction. The graph attention model also allow us to infer a new feature space for the cells that emphasizes the differences between the two conditions. Finally we use the attention weights to learn a new low-dimensional embedding that can be visualized. To the best of our knowledge, this is the first effort to use graph attention, and deep learning in general, to predict disease state from single-cell data. We envision applying this method to single-cell data for other diseases.

q-bio.GN↗

arXiv2020

Using Chinese Glyphs for Named Entity Recognition

Most Named Entity Recognition (NER) systems use additional features like part-of-speech (POS) tags, shallow parsing, gazetteers, etc. Such kind of information requires external knowledge like unlabeled texts and trained taggers. Adding these features to NER systems have been shown to have a positive impact. However, sometimes creating gazetteers or taggers can take a lot of time and may require extensive data cleaning. In this paper for Chinese NER systems, we do not use these traditional features but we use lexicographic features of Chinese characters. Chinese characters are composed of graphical components called radicals and these components often have some semantic indicators. We propose CNN based models that incorporate this semantic information and use them for NER. Our models show an improvement over the baseline BERT-BiLSTM-CRF model. We set a new baseline score for Chinese OntoNotes v5.0 and show an improvement of +.64 F1 score. We present a state-of-the-art F1 score on Weibo dataset of 71.81 and show a competitive improvement of +0.72 over baseline on ResumeNER dataset.

cs.CL↗