arXiv subjects

Ali Ghodsi

Publications and source records attributed to Ali Ghodsi.

At least 55 records · Page 3Linked to original sources

arXiv2021

Uniform Manifold Approximation and Projection (UMAP) and its Variants: Tutorial and Survey

Uniform Manifold Approximation and Projection (UMAP) is one of the state-of-the-art methods for dimensionality reduction and data visualization. This is a tutorial and survey paper on UMAP and its variants. We start with UMAP algorithm where we explain probabilities of neighborhood in the input and embedding spaces, optimization of cost function, training algorithm, derivation of gradients, and supervised and semi-supervised embedding by UMAP. Then, we introduce the theory behind UMAP by algebraic topology and category theory. Then, we introduce UMAP as a neighbor embedding method and compare it with t-SNE and LargeVis algorithms. We discuss negative sampling and repulsive forces in UMAP's cost function. DensMAP is then explained for density-preserving embedding. We then introduce parametric UMAP for embedding by deep learning and progressive UMAP for streaming and out-of-sample data embedding.

cs.HC↗

arXiv2021

Johnson-Lindenstrauss Lemma, Linear and Nonlinear Random Projections, Random Fourier Features, and Random Kitchen Sinks: Tutorial and Survey

This is a tutorial and survey paper on the Johnson-Lindenstrauss (JL) lemma and linear and nonlinear random projections. We start with linear random projection and then justify its correctness by JL lemma and its proof. Then, sparse random projections with $\ell_1$ norm and interpolation norm are introduced. Two main applications of random projection, which are low-rank matrix approximation and approximate nearest neighbor search by random projection onto hypercube, are explained. Random Fourier Features (RFF) and Random Kitchen Sinks (RKS) are explained as methods for nonlinear random projection. Some other methods for nonlinear random projection, including extreme learning machine, randomly weighted neural networks, and ensemble of random projections, are also introduced.

stat.ML↗

arXiv2021

SymbolicGPT: A Generative Transformer Model for Symbolic Regression

Symbolic regression is the task of identifying a mathematical expression that best fits a provided dataset of input and output values. Due to the richness of the space of mathematical expressions, symbolic regression is generally a challenging problem. While conventional approaches based on genetic evolution algorithms have been used for decades, deep learning-based methods are relatively new and an active research area. In this work, we present SymbolicGPT, a novel transformer-based language model for symbolic regression. This model exploits the advantages of probabilistic language models like GPT, including strength in performance and flexibility. Through comprehensive experiments, we show that our model performs strongly compared to competing models with respect to the accuracy, running time, and data efficiency.

cs.LG↗

arXiv2021

Legendre Deep Neural Network (LDNN) and its application for approximation of nonlinear Volterra Fredholm Hammerstein integral equations

Various phenomena in biology, physics, and engineering are modeled by differential equations. These differential equations including partial differential equations and ordinary differential equations can be converted and represented as integral equations. In particular, Volterra Fredholm Hammerstein integral equations are the main type of these integral equations and researchers are interested in investigating and solving these equations. In this paper, we propose Legendre Deep Neural Network (LDNN) for solving nonlinear Volterra Fredholm Hammerstein integral equations (VFHIEs). LDNN utilizes Legendre orthogonal polynomials as activation functions of the Deep structure. We present how LDNN can be used to solve nonlinear VFHIEs. We show using the Gaussian quadrature collocation method in combination with LDNN results in a novel numerical solution for nonlinear VFHIEs. Several examples are given to verify the performance and accuracy of LDNN.

math.NA↗

arXiv2021

Reproducing Kernel Hilbert Space, Mercer's Theorem, Eigenfunctions, Nyström Method, and Use of Kernels in Machine Learning: Tutorial and Survey

This is a tutorial and survey paper on kernels, kernel methods, and related fields. We start with reviewing the history of kernels in functional analysis and machine learning. Then, Mercer kernel, Hilbert and Banach spaces, Reproducing Kernel Hilbert Space (RKHS), Mercer's theorem and its proof, frequently used kernels, kernel construction from distance metric, important classes of kernels (including bounded, integrally positive definite, universal, stationary, and characteristic kernels), kernel centering and normalization, and eigenfunctions are explained in detail. Then, we introduce types of use of kernels in machine learning including kernel methods (such as kernel support vector machines), kernel learning by semi-definite programming, Hilbert-Schmidt independence criterion, maximum mean discrepancy, kernel mean embedding, and kernel dimensionality reduction. We also cover rank and factorization of kernel matrix as well as the approximation of eigenfunctions and kernels using the Nystr{ö}m method. This paper can be useful for various fields of science including machine learning, dimensionality reduction, functional analysis in mathematics, and mathematical physics in quantum mechanics.

stat.ML↗

arXiv2021

Not Far Away, Not So Close: Sample Efficient Nearest Neighbour Data Augmentation via MiniMax

In Natural Language Processing (NLP), finding data augmentation techniques that can produce high-quality human-interpretable examples has always been challenging. Recently, leveraging kNN such that augmented examples are retrieved from large repositories of unlabelled sentences has made a step toward interpretable augmentation. Inspired by this paradigm, we introduce Minimax-kNN, a sample efficient data augmentation strategy tailored for Knowledge Distillation (KD). We exploit a semi-supervised approach based on KD to train a model on augmented data. In contrast to existing kNN augmentation techniques that blindly incorporate all samples, our method dynamically selects a subset of augmented samples that maximizes KL-divergence between the teacher and student models. This step aims to extract the most efficient samples to ensure our augmented data covers regions in the input space with maximum loss value. We evaluated our technique on several text classification tasks and demonstrated that Minimax-kNN consistently outperforms strong baselines. Our results show that Minimax-kNN requires fewer augmented examples and less computation to achieve superior performance over the state-of-the-art kNN-based augmentation techniques.

cs.CL↗

arXiv2021

Annealing Knowledge Distillation

Significant memory and computational requirements of large deep neural networks restrict their application on edge devices. Knowledge distillation (KD) is a prominent model compression technique for deep neural networks in which the knowledge of a trained large teacher model is transferred to a smaller student model. The success of knowledge distillation is mainly attributed to its training objective function, which exploits the soft-target information (also known as "dark knowledge") besides the given regular hard labels in a training set. However, it is shown in the literature that the larger the gap between the teacher and the student networks, the more difficult is their training using knowledge distillation. To address this shortcoming, we propose an improved knowledge distillation method (called Annealing-KD) by feeding the rich information provided by the teacher's soft-targets incrementally and more efficiently. Our Annealing-KD technique is based on a gradual transition over annealed soft-targets generated by the teacher at different temperatures in an iterative process, and therefore, the student is trained to follow the annealed teacher output in a step-by-step manner. This paper includes theoretical and empirical evidence as well as practical experiments to support the effectiveness of our Annealing-KD method. We did a comprehensive set of experiments on different tasks such as image classification (CIFAR-10 and 100) and NLP language inference with BERT-based models on the GLUE benchmark and consistently got superior results.

cs.CL↗

arXiv2021

Generative Locally Linear Embedding

Locally Linear Embedding (LLE) is a nonlinear spectral dimensionality reduction and manifold learning method. It has two main steps which are linear reconstruction and linear embedding of points in the input space and embedding space, respectively. In this work, we propose two novel generative versions of LLE, named Generative LLE (GLLE), whose linear reconstruction steps are stochastic rather than deterministic. GLLE assumes that every data point is caused by its linear reconstruction weights as latent factors. The proposed GLLE algorithms can generate various LLE embeddings stochastically while all the generated embeddings relate to the original LLE embedding. We propose two versions for stochastic linear reconstruction, one using expectation maximization and another with direct sampling from a derived distribution by optimization. The proposed GLLE methods are closely related to and inspired by variational inference, factor analysis, and probabilistic principal component analysis. Our simulations show that the proposed GLLE methods work effectively in unfolding and generating submanifolds of data.

stat.ML↗

arXiv2021

Fine-Tuning and Training of DenseNet for Histopathology Image Representation Using TCGA Diagnostic Slides

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

eess.IV↗

arXiv2020

Locally Linear Embedding and its Variants: Tutorial and Survey

This is a tutorial and survey paper for Locally Linear Embedding (LLE) and its variants. The idea of LLE is fitting the local structure of manifold in the embedding space. In this paper, we first cover LLE, kernel LLE, inverse LLE, and feature fusion with LLE. Then, we cover out-of-sample embedding using linear reconstruction, eigenfunctions, and kernel mapping. Incremental LLE is explained for embedding streaming data. Landmark LLE methods using the Nystrom approximation and locally linear landmarks are explained for big data embedding. We introduce the methods for parameter selection of number of neighbors using residual variance, Procrustes statistics, preservation neighborhood error, and local neighborhood selection. Afterwards, Supervised LLE (SLLE), enhanced SLLE, SLLE projection, probabilistic SLLE, supervised guided LLE (using Hilbert-Schmidt independence criterion), and semi-supervised LLE are explained for supervised and semi-supervised embedding. Robust LLE methods using least squares problem and penalty functions are also introduced for embedding in the presence of outliers and noise. Then, we introduce fusion of LLE with other manifold learning methods including Isomap (i.e., ISOLLE), principal component analysis, Fisher discriminant analysis, discriminant LLE, and Isotop. Finally, we explain weighted LLE in which the distances, reconstruction weights, or the embeddings are adjusted for better embedding; we cover weighted LLE for deformed distributed data, weighted LLE using probability of occurrence, SLLE by adjusting weights, modified LLE, and iterative LLE.

stat.ML↗

arXiv2020

Symbolically Solving Partial Differential Equations using Deep Learning

We describe a neural-based method for generating exact or approximate solutions to differential equations in the form of mathematical expressions. Unlike other neural methods, our system returns symbolic expressions that can be interpreted directly. Our method uses a neural architecture for learning mathematical expressions to optimize a customizable objective, and is scalable, compact, and easily adaptable for a variety of tasks and configurations. The system has been shown to effectively find exact or approximate symbolic solutions to various differential equations with applications in natural sciences. In this work, we highlight how our method applies to partial differential equations over multiple variables and more complex boundary and initial value conditions.

cs.LG↗

arXiv2020

A Neuro-Symbolic Method for Solving Differential and Functional Equations

When neural networks are used to solve differential equations, they usually produce solutions in the form of black-box functions that are not directly mathematically interpretable. We introduce a method for generating symbolic expressions to solve differential equations while leveraging deep learning training methods. Unlike existing methods, our system does not require learning a language model over symbolic mathematics, making it scalable, compact, and easily adaptable for a variety of tasks and configurations. As part of the method, we propose a novel neural architecture for learning mathematical expressions to optimize a customizable objective. The system is designed to always return a valid symbolic formula, generating a useful approximation when an exact analytic solution to a differential equation is not or cannot be found. We demonstrate through examples how our method can be applied on a number of differential equations, often obtaining symbolic approximations that are useful or insightful. Furthermore, we show how the system can be effortlessly generalized to find symbolic solutions to other mathematical tasks, including integration and functional equations.

cs.LG↗

arXiv2020

Multidimensional Scaling, Sammon Mapping, and Isomap: Tutorial and Survey

Multidimensional Scaling (MDS) is one of the first fundamental manifold learning methods. It can be categorized into several methods, i.e., classical MDS, kernel classical MDS, metric MDS, and non-metric MDS. Sammon mapping and Isomap can be considered as special cases of metric MDS and kernel classical MDS, respectively. In this tutorial and survey paper, we review the theory of MDS, Sammon mapping, and Isomap in detail. We explain all the mentioned categories of MDS. Then, Sammon mapping, Isomap, and kernel Isomap are explained. Out-of-sample embedding for MDS and Isomap using eigenfunctions and kernel mapping are introduced. Then, Nystrom approximation and its use in landmark MDS and landmark Isomap are introduced for big data embedding. We also provide some simulations for illustrating the embedding by these methods.

stat.ML↗

arXiv2020

Semi-Supervised Representation Learning based on Probabilistic Labeling

In this paper, we present a new algorithm for semi-supervised representation learning. In this algorithm, we first find a vector representation for the labels of the data points based on their local positions in the space. Then, we map the data to lower-dimensional space using a linear transformation such that the dependency between the transformed data and the assigned labels is maximized. In fact, we try to find a mapping that is as discriminative as possible. The approach will use Hilber-Schmidt Independence Criterion (HSIC) as the dependence measure. We also present a kernelized version of the algorithm, which allows non-linear transformations and provides more flexibility in finding the appropriate mapping. Use of unlabeled data for learning new representation is not always beneficial and there is no algorithm that can deterministically guarantee the improvement of the performance by exploiting unlabeled data. Therefore, we also propose a bound on the performance of the algorithm, which can be used to determine the effectiveness of using the unlabeled data in the algorithm. We demonstrate the ability of the algorithm in finding the transformation using both toy examples and real-world datasets.

cs.LG↗

arXiv2020

Segmentation Approach for Coreference Resolution Task

In coreference resolution, it is important to consider all members of a coreference cluster and decide about all of them at once. This technique can help to avoid losing precision and also in finding long-distance relations. The presented paper is a report of an ongoing study on an idea which proposes a new approach for coreference resolution which can resolve all coreference mentions to a given mention in the document in one pass. This has been accomplished by defining an embedding method for the position of all members of a coreference cluster in a document and resolving all of them for a given mention. In the proposed method, the BERT model has been used for encoding the documents and a head network designed to capture the relations between the embedded tokens. These are then converted to the proposed span position embedding matrix which embeds the position of all coreference mentions in the document. We tested this idea on CoNLL 2012 dataset and although the preliminary results from this method do not quite meet the state-of-the-art results, they are promising and they can capture features like long-distance relations better than the other approaches.

cs.CL↗

arXiv2020

Personalized workflow to identify optimal T-cell epitopes for peptide-based vaccines against COVID-19

Traditional vaccines against viruses are designed to target their surface proteins, i.e., antigens, which can trigger the immune system to produce specific antibodies to capture and neutralize the viruses. However, viruses often evolve quickly, and their antigens are prone to mutations to avoid recognition by the antibodies (antigenic drift). This limitation of the antibody-mediated immunity could be addressed by the T-cell mediated immunity, which is able to recognize conserved viral HLA peptides presented on virus-infected cells. Thus, by targeting conserved regions on the genome of a virus, T-cell epitope-based vaccines are less subjected to mutations and may work effectively on different strains of the virus. Here we propose a personalized workflow to identify an optimal set of T-cell epitopes based on the HLA alleles and the immunopeptidome of an individual person. Specifically, our workflow trains a machine learning model on the immunopeptidome and then predicts HLA peptides from conserved regions of a virus that are most likely to trigger responses from the person T cells. We applied the workflow to identify T-cell epitopes for the SARS-COV-2 virus, which has caused the recent COVID-19 pandemic in more than 100 countries across the globe.

q-bio.PE↗

arXiv2019

DeepNovoV2: Better de novo peptide sequencing with deep learning

Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from mass spectrometry data. In this paper we introduce DeepNovoV2, the state-of-the-art model for peptide sequencing. In DeepNovoV2, a spectrum is directly represented as a set of (m/z, intensity) pairs, therefore it does not suffer from the accuracy-speed/memory trade-off problem. The model combines an order invariant network structure (T-Net) and recurrent neural networks and provides a complete end-to-end training and prediction framework to sequence patterns of peptides. Our experiments on a wide variety of data from different species show that DeepNovoV2 outperforms previous state-of-the-art methods, achieving 13.01-23.95\% higher accuracy at the peptide level.

cs.LG↗

arXiv2018

Deep Variational Sufficient Dimensionality Reduction

We consider the problem of sufficient dimensionality reduction (SDR), where the high-dimensional observation is transformed to a low-dimensional sub-space in which the information of the observations regarding the label variable is preserved. We propose DVSDR, a deep variational approach for sufficient dimensionality reduction. The deep structure in our model has a bottleneck that represent the low-dimensional embedding of the data. We explain the SDR problem using graphical models and use the framework of variational autoencoders to maximize the lower bound of the log-likelihood of the joint distribution of the observation and label. We show that such a maximization problem can be interpreted as solving the SDR problem. DVSDR can be easily adopted to semi-supervised learning setting. In our experiment we show that DVSDR performs competitively on classification tasks while being able to generate novel data samples.

cs.LG↗