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Researcher profile

Ali Ghodsi

Ali Ghodsi contributes to research discovery and scholarly infrastructure.

ResearcherAffiliation not importedOpen to collaborate
Machine LearningComputer VisionComputation and LanguageBiomoleculesDistributed, Parallel, and Cluster Computingeess.IVNeural and Evolutionary Computingphysics.data-anPopulations and Evolution

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Published work

16 published item(s)

preprint2026arXiv

GraphPI: Efficient Protein Inference with Graph Neural Networks

The integration of deep learning approaches in biomedical research has been transformative, enabling breakthroughs in various applications. Despite these strides, its application in protein inference is impeded by the scarcity of extensively labeled datasets, a challenge compounded by the high costs and complexities of accurate protein annotation. In this study, we introduce GraphPI, a novel framework that treats protein inference as a node classification problem. We treat proteins as interconnected nodes within a protein-peptide-PSM graph, utilizing a Graph Neural Network-based architecture to elucidate their interrelations. To address label scarcity, we train the model on a set of unlabeled public protein datasets with pseudo-labels derived from an existing protein inference algorithm, enhanced by self-training to iteratively refine labels based on confidence scores. Contrary to prevalent methodologies necessitating dataset-specific training, our research illustrates that GraphPI, due to the well normalized nature of Percolator features, exhibits universal applicability without dataset-specific fine-tuning, a feature that not only mitigates the risk of overfitting but also enhances computational efficiency. Our empirical experiments reveal notable performance on various test datasets and deliver significantly reduced computation times compared to common protein inference algorithms.

0 citations0 reviewsNo code linkedOpen access
preprint2025arXiv

Orchid: Flexible and Data-Dependent Convolution for Sequence Modeling

In the rapidly evolving field of deep learning, the demand for models that are both expressive and computationally efficient has never been more critical. This paper introduces Orchid, a novel architecture designed to address the quadratic complexity of traditional attention mechanisms without compromising the ability to capture long-range dependencies and in-context learning. At the core of this architecture lies a new data-dependent global convolution layer, which contextually adapts its kernel conditioned on input sequence using a dedicated conditioning neural network. We design two simple conditioning networks that maintain shift equivariance in our data-dependent convolution operation. The dynamic nature of the proposed convolution kernel grants Orchid high expressivity while maintaining quasilinear scalability for long sequences. We evaluate the proposed model across multiple domains, including language modeling and image classification, to highlight its performance and generality. Our experiments demonstrate that this architecture not only outperforms traditional attention-based architectures such as BERT and Vision Transformers with smaller model sizes, but also extends the feasible sequence length beyond the limitations of the dense attention layers. This achievement represents a significant step towards more efficient and scalable deep learning models for sequence modeling. The code is available at https://github.com/Karami-m/orchid.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Factor Analysis, Probabilistic Principal Component Analysis, Variational Inference, and Variational Autoencoder: Tutorial and Survey

This is a tutorial and survey paper on factor analysis, probabilistic Principal Component Analysis (PCA), variational inference, and Variational Autoencoder (VAE). These methods, which are tightly related, are dimensionality reduction and generative models. They assume that every data point is generated from or caused by a low-dimensional latent factor. By learning the parameters of distribution of latent space, the corresponding low-dimensional factors are found for the sake of dimensionality reduction. For their stochastic and generative behaviour, these models can also be used for generation of new data points in the data space. In this paper, we first start with variational inference where we derive the Evidence Lower Bound (ELBO) and Expectation Maximization (EM) for learning the parameters. Then, we introduce factor analysis, derive its joint and marginal distributions, and work out its EM steps. Probabilistic PCA is then explained, as a special case of factor analysis, and its closed-form solutions are derived. Finally, VAE is explained where the encoder, decoder and sampling from the latent space are introduced. Training VAE using both EM and backpropagation are explained.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Laplacian-Based Dimensionality Reduction Including Spectral Clustering, Laplacian Eigenmap, Locality Preserving Projection, Graph Embedding, and Diffusion Map: Tutorial and Survey

This is a tutorial and survey paper for nonlinear dimensionality and feature extraction methods which are based on the Laplacian of graph of data. We first introduce adjacency matrix, definition of Laplacian matrix, and the interpretation of Laplacian. Then, we cover the cuts of graph and spectral clustering which applies clustering in a subspace of data. Different optimization variants of Laplacian eigenmap and its out-of-sample extension are explained. Thereafter, we introduce the locality preserving projection and its kernel variant as linear special cases of Laplacian eigenmap. Versions of graph embedding are then explained which are generalized versions of Laplacian eigenmap and locality preserving projection. Finally, diffusion map is introduced which is a method based on Laplacian of data and random walks on the data graph.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Restricted Boltzmann Machine and Deep Belief Network: Tutorial and Survey

This is a tutorial and survey paper on Boltzmann Machine (BM), Restricted Boltzmann Machine (RBM), and Deep Belief Network (DBN). We start with the required background on probabilistic graphical models, Markov random field, Gibbs sampling, statistical physics, Ising model, and the Hopfield network. Then, we introduce the structures of BM and RBM. The conditional distributions of visible and hidden variables, Gibbs sampling in RBM for generating variables, training BM and RBM by maximum likelihood estimation, and contrastive divergence are explained. Then, we discuss different possible discrete and continuous distributions for the variables. We introduce conditional RBM and how it is trained. Finally, we explain deep belief network as a stack of RBM models. This paper on Boltzmann machines can be useful in various fields including data science, statistics, neural computation, and statistical physics.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Spectral, Probabilistic, and Deep Metric Learning: Tutorial and Survey

This is a tutorial and survey paper on metric learning. Algorithms are divided into spectral, probabilistic, and deep metric learning. We first start with the definition of distance metric, Mahalanobis distance, and generalized Mahalanobis distance. In spectral methods, we start with methods using scatters of data, including the first spectral metric learning, relevant methods to Fisher discriminant analysis, Relevant Component Analysis (RCA), Discriminant Component Analysis (DCA), and the Fisher-HSIC method. Then, large-margin metric learning, imbalanced metric learning, locally linear metric adaptation, and adversarial metric learning are covered. We also explain several kernel spectral methods for metric learning in the feature space. We also introduce geometric metric learning methods on the Riemannian manifolds. In probabilistic methods, we start with collapsing classes in both input and feature spaces and then explain the neighborhood component analysis methods, Bayesian metric learning, information theoretic methods, and empirical risk minimization in metric learning. In deep learning methods, we first introduce reconstruction autoencoders and supervised loss functions for metric learning. Then, Siamese networks and its various loss functions, triplet mining, and triplet sampling are explained. Deep discriminant analysis methods, based on Fisher discriminant analysis, are also reviewed. Finally, we introduce multi-modal deep metric learning, geometric metric learning by neural networks, and few-shot metric learning.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Stochastic Neighbor Embedding with Gaussian and Student-t Distributions: Tutorial and Survey

Stochastic Neighbor Embedding (SNE) is a manifold learning and dimensionality reduction method with a probabilistic approach. In SNE, every point is consider to be the neighbor of all other points with some probability and this probability is tried to be preserved in the embedding space. SNE considers Gaussian distribution for the probability in both the input and embedding spaces. However, t-SNE uses the Student-t and Gaussian distributions in these spaces, respectively. In this tutorial and survey paper, we explain SNE, symmetric SNE, t-SNE (or Cauchy-SNE), and t-SNE with general degrees of freedom. We also cover the out-of-sample extension and acceleration for these methods.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

The Sky Above The Clouds

Technology ecosystems often undergo significant transformations as they mature. For example, telephony, the Internet, and PCs all started with a single provider, but in the United States each is now served by a competitive market that uses comprehensive and universal technology standards to provide compatibility. This white paper presents our view on how the cloud ecosystem, barely over fifteen years old, could evolve as it matures.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Theoretical Connection between Locally Linear Embedding, Factor Analysis, and Probabilistic PCA

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 look at the linear reconstruction step from a stochastic perspective where it is assumed that every data point is conditioned on its linear reconstruction weights as latent factors. The stochastic linear reconstruction of LLE is solved using expectation maximization. We show that there is a theoretical connection between three fundamental dimensionality reduction methods, i.e., LLE, factor analysis, and probabilistic Principal Component Analysis (PCA). The stochastic linear reconstruction of LLE is formulated similar to the factor analysis and probabilistic PCA. It is also explained why factor analysis and probabilistic PCA are linear and LLE is a nonlinear method. This work combines and makes a bridge between two broad approaches of dimensionality reduction, i.e., the spectral and probabilistic algorithms.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

Unified Framework for Spectral Dimensionality Reduction, Maximum Variance Unfolding, and Kernel Learning By Semidefinite Programming: Tutorial and Survey

This is a tutorial and survey paper on unification of spectral dimensionality reduction methods, kernel learning by Semidefinite Programming (SDP), Maximum Variance Unfolding (MVU) or Semidefinite Embedding (SDE), and its variants. We first explain how the spectral dimensionality reduction methods can be unified as kernel Principal Component Analysis (PCA) with different kernels. This unification can be interpreted as eigenfunction learning or representation of kernel in terms of distance matrix. Then, since the spectral methods are unified as kernel PCA, we say let us learn the best kernel for unfolding the manifold of data to its maximum variance. We first briefly introduce kernel learning by SDP for the transduction task. Then, we explain MVU in detail. Various versions of supervised MVU using nearest neighbors graph, by class-wise unfolding, by Fisher criterion, and by colored MVU are explained. We also explain out-of-sample extension of MVU using eigenfunctions and kernel mapping. Finally, we introduce other variants of MVU including action respecting embedding, relaxed MVU, and landmark MVU for big data.

0 citations0 reviewsNo code linkedOpen access
preprint2022arXiv

When Chosen Wisely, More Data Is What You Need: A Universal Sample-Efficient Strategy For Data Augmentation

Data Augmentation (DA) is known to improve the generalizability of deep neural networks. Most existing DA techniques naively add a certain number of augmented samples without considering the quality and the added computational cost of these samples. To tackle this problem, a common strategy, adopted by several state-of-the-art DA methods, is to adaptively generate or re-weight augmented samples with respect to the task objective during training. However, these adaptive DA methods: (1) are computationally expensive and not sample-efficient, and (2) are designed merely for a specific setting. In this work, we present a universal DA technique, called Glitter, to overcome both issues. Glitter can be plugged into any DA method, making training sample-efficient without sacrificing performance. From a pre-generated pool of augmented samples, Glitter adaptively selects a subset of worst-case samples with maximal loss, analogous to adversarial DA. Without altering the training strategy, the task objective can be optimized on the selected subset. Our thorough experiments on the GLUE benchmark, SQuAD, and HellaSwag in three widely used training setups including consistency training, self-distillation and knowledge distillation reveal that Glitter is substantially faster to train and achieves a competitive performance, compared to strong baselines.

0 citations0 reviewsNo code linkedOpen access
preprint2021arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access
preprint2020arXiv

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.

0 citations0 reviewsNo code linkedOpen access