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Hamidreza Mahyar

Publications and source records attributed to Hamidreza Mahyar.

At least 19 recordsLinked to original sources
arXiv2026

ChEmbed: Enhancing Chemical Literature Search Through Domain-Specific Text Embeddings

Retrieval-Augmented Generation (RAG) systems in chemistry heavily depend on accurate and relevant retrieval of chemical literature. However, general-purpose text embedding models frequently fail to adequately represent complex chemical terminologies, resulting in suboptimal retrieval quality. Existing embedding models for chemistry are outdated, and none is tailored to chemical literature retrieval, leaving a substantial performance gap. To address this challenge, we introduce ChEmbed, the first purpose-built family of domain-adapted text embedding models engineered for chemical literature retrieval. These models are fine-tuned via contrastive learning on a dataset comprising chemistry-specific text from the PubChem, Semantic Scholar, and ChemRxiv corpora. To create effective training data, we employ large language models to synthetically generate queries, resulting in approximately 1.7 million high-quality query-passage pairs. Additionally, we augment the tokenizer by adding 900 chemically specialized tokens to previously unused slots, which reduces the fragmentation of chemical entities, such as IUPAC names. ChEmbed also maintains an 8192-token context length, enabling retrieval of longer passages than many open-source embedding models allow. Evaluated on our newly introduced ChemRxiv Retrieval benchmark, ChEmbed outperforms state-of-the-art general embedding models, raising MRR@10 from 0.781 to 0.882 (+10.1 pp). It also substantially outperforms domain-specific embedding models such as Chemical-BERT, improving MRR@10 from 0.096 to 0.882. A role-based retrieval analysis using PubChem descriptions and ChEBI annotations shows that the improvement extends to chemical-role queries. ChEmbed represents a practical, lightweight, and reproducible embedding solution that effectively improves chemical literature retrieval.

cs.IR↗
arXiv2026

ChemCLIR-Bench: Benchmarking Cross-Lingual Information Retrieval in Multilingual Chemical Patents

Cross-lingual information retrieval (CLIR) is increasingly important in multi-national industries, where critical technical evidence may exist in a different language than the query. However, existing benchmarks do not adequately capture domain-specific cross-lingual retrieval or the retrieval-depth and recoverability failures that aggregate recall hides. In this work, we benchmark CLIR in the chemical domain, with a focus on patent data. We construct a multilingual dataset from Google Patents and the European Patent Office (EPO) data, spanning five languages (covering major Eastern and Western languages) and reflecting the diversity and complexity of real-world industrial documentation. Using this dataset, we systematically evaluate eight state-of-the-art embedding models for cross-lingual retrieval. Our results show a substantial performance gap between monolingual and cross-lingual settings: for the best-performing model, Recall@10 drops from 0.72 to 0.53 in cross-lingual setting. Retrieval depth also degrades significantly, with relevant documents ranked lower across languages in cross-lingual scenarios. Furthermore, some multilingual embedding models that perform strongly in monolingual settings exhibit sharp declines when queries and documents are in different languages, providing practical insights for model selection in cross-lingual use cases. These findings highlight critical limitations of current approaches and emphasize the need for more robust cross-lingual retrieval methods in domain-specific settings. Our benchmark provides actionable insights for model selection and establishes a controlled diagnostic evaluation framework for CLIR over industrial technical text. Data and code are publicly available at https://github.com/MohammadKhodadad/Multi-Lingual-QAC.

cs.CL↗
arXiv2026

When Iterative RAG Beats Ideal Evidence: A Diagnostic Study in Scientific Multi-hop Question Answering

Retrieval-Augmented Generation (RAG) extends large language models (LLMs) beyond parametric knowledge, yet it is unclear when iterative retrieval-reasoning loops meaningfully outperform static RAG, particularly in scientific domains requiring multi-hop reasoning over sparse, heterogeneous evidence. We provide the first controlled, mechanism-level diagnostic evaluation of whether synchronized iterative retrieval and reasoning can surpass even an idealized static upper bound (Gold Context) RAG. We benchmark eleven state-of-the-art LLMs under three regimes: (i) No Context, measuring reliance on parametric memory; (ii) Gold Context, where all oracle evidence is supplied at once; and (iii) Iterative RAG, a training-free controller that alternates retrieval, hypothesis refinement, and evidence-aware stopping. Using the chemistry-focused ChemKGMultiHopQA dataset, we isolate questions requiring genuine retrieval and analyze retrieval coverage gaps, anchor carry drop, query quality, composition fidelity, and control calibration. Iterative RAG consistently outperforms Gold Context, with gains up to 25.6 percentage points, especially for non-reasoning fine-tuned models. Staged retrieval reduces late-hop failures, mitigates context overload, and enables dynamic correction of early hypothesis drift, but failure modes remain, including incomplete hop coverage, distractor latch trajectories, early stopping miscalibration, and high composition failure rates even with perfect retrieval. Overall, the process of staged retrieval is often more influential than the mere presence of ideal evidence. We provide practical guidance for deploying and diagnosing RAG in specialized scientific settings. Code and evaluation results are available at https://github.com/Matroid1998/Iterative-rag

cs.CL↗
arXiv2026

GraphWalk: Enabling Reasoning in Large Language Models through Tool-Based Graph Navigation

The use of knowledge graphs for grounding agents in real-world Q&A applications has become increasingly common. Answering complex queries often requires multi-hop reasoning and the ability to navigate vast relational structures. Standard approaches rely on prompting techniques that steer large language models to reason over raw graph context, or retrieval-augmented generation pipelines where relevant subgraphs are injected into the context. These, however, face severe limitations with enterprise-scale KGs that cannot fit in even the largest context windows available today. We present GraphWalk, a problem-agnostic, training-free, tool-based framework that allows off-the-shelf LLMs to reason through sequential graph navigation, dramatically increasing performance across different tasks. Unlike task-specific agent frameworks that encode domain knowledge into specialized tools, GraphWalk equips the LLM with a minimal set of orthogonal graph operations sufficient to traverse any graph structure. We evaluate whether models equipped with GraphWalk can compose these operations into correct multi-step reasoning chains, where each tool call represents a verifiable step creating a transparent execution trace. We first demonstrate our approach on maze traversal, a problem non-reasoning models are completely unable to solve, then present results on graphs resembling real-world enterprise knowledge graphs. To isolate structural reasoning from world knowledge, we evaluate on entirely synthetic graphs with random, non-semantic labels. Our benchmark spans 12 query templates from basic retrieval to compound first-order logic queries. Results show that tool-based traversal yields substantial and consistent gains over in-context baselines across all model families tested, with gains becoming more pronounced as scale increases, precisely where in-context approaches fail catastrophically.

cs.AI↗
arXiv2025

Evaluating Multi-Hop Reasoning in Large Language Models: A Chemistry-Centric Case Study

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated a fully automated pipeline, verified by subject matter experts, to facilitate this task. Our approach integrates OpenAI reasoning models with named entity recognition (NER) systems to extract chemical entities from recent literature, which are then augmented with external knowledge bases to form a comprehensive knowledge graph. By generating multi-hop questions across these graphs, we assess LLM performance in both context-augmented and non-context augmented settings. Our experiments reveal that even state-of-the-art models face significant challenges in multi-hop compositional reasoning. The results reflect the importance of augmenting LLMs with document retrieval, which can have a substantial impact on improving their performance. However, even perfect retrieval accuracy with full context does not eliminate reasoning errors, underscoring the complexity of compositional reasoning. This work not only benchmarks and highlights the limitations of current LLMs but also presents a novel data generation pipeline capable of producing challenging reasoning datasets across various domains. Overall, this research advances our understanding of reasoning in computational linguistics.

cs.CL↗
arXiv2025

Towards Domain Specification of Embedding Models in Medicine

Medical text embedding models are foundational to a wide array of healthcare applications, ranging from clinical decision support and biomedical information retrieval to medical question answering, yet they remain hampered by two critical shortcomings. First, most models are trained on a narrow slice of medical and biological data, beside not being up to date in terms of methodology, making them ill suited to capture the diversity of terminology and semantics encountered in practice. Second, existing evaluations are often inadequate: even widely used benchmarks fail to generalize across the full spectrum of real world medical tasks. To address these gaps, we leverage MEDTE, a GTE model extensively fine-tuned on diverse medical corpora through self-supervised contrastive learning across multiple data sources, to deliver robust medical text embeddings. Alongside this model, we propose a comprehensive benchmark suite of 51 tasks spanning classification, clustering, pair classification, and retrieval modeled on the Massive Text Embedding Benchmark (MTEB) but tailored to the nuances of medical text. Our results demonstrate that this combined approach not only establishes a robust evaluation framework but also yields embeddings that consistently outperform state of the art alternatives in different tasks.

cs.CL↗
arXiv2025

ChemTEB: Chemical Text Embedding Benchmark, an Overview of Embedding Models Performance & Efficiency on a Specific Domain

Recent advancements in language models have started a new era of superior information retrieval and content generation, with embedding models playing an important role in optimizing data representation efficiency and performance. While benchmarks like the Massive Text Embedding Benchmark (MTEB) have standardized the evaluation of general domain embedding models, a gap remains in specialized fields such as chemistry, which require tailored approaches due to domain-specific challenges. This paper introduces a novel benchmark, the Chemical Text Embedding Benchmark (ChemTEB), designed specifically for the chemical sciences. ChemTEB addresses the unique linguistic and semantic complexities of chemical literature and data, offering a comprehensive suite of tasks on chemical domain data. Through the evaluation of 34 open-source and proprietary models using this benchmark, we illuminate the strengths and weaknesses of current methodologies in processing and understanding chemical information. Our work aims to equip the research community with a standardized, domain-specific evaluation framework, promoting the development of more precise and efficient NLP models for chemistry-related applications. Furthermore, it provides insights into the performance of generic models in a domain-specific context. ChemTEB comes with open-source code and data, contributing further to its accessibility and utility.

cs.CL↗
arXiv2023

Deep Learning Approaches on Image Captioning: A Review

Image captioning is a research area of immense importance, aiming to generate natural language descriptions for visual content in the form of still images. The advent of deep learning and more recently vision-language pre-training techniques has revolutionized the field, leading to more sophisticated methods and improved performance. In this survey paper, we provide a structured review of deep learning methods in image captioning by presenting a comprehensive taxonomy and discussing each method category in detail. Additionally, we examine the datasets commonly employed in image captioning research, as well as the evaluation metrics used to assess the performance of different captioning models. We address the challenges faced in this field by emphasizing issues such as object hallucination, missing context, illumination conditions, contextual understanding, and referring expressions. We rank different deep learning methods' performance according to widely used evaluation metrics, giving insight into the current state of the art. Furthermore, we identify several potential future directions for research in this area, which include tackling the information misalignment problem between image and text modalities, mitigating dataset bias, incorporating vision-language pre-training methods to enhance caption generation, and developing improved evaluation tools to accurately measure the quality of image captions.

cs.CV↗
arXiv2023

SMGRL: Scalable Multi-resolution Graph Representation Learning

Graph convolutional networks (GCNs) allow us to learn topologically-aware node embeddings, which can be useful for classification or link prediction. However, they are unable to capture long-range dependencies between nodes without adding additional layers -- which in turn leads to over-smoothing and increased time and space complexity. Further, the complex dependencies between nodes make mini-batching challenging, limiting their applicability to large graphs. We propose a Scalable Multi-resolution Graph Representation Learning (SMGRL) framework that enables us to learn multi-resolution node embeddings efficiently. Our framework is model-agnostic and can be applied to any existing GCN model. We dramatically reduce training costs by training only on a reduced-dimension coarsening of the original graph, then exploit self-similarity to apply the resulting algorithm at multiple resolutions. The resulting multi-resolution embeddings can be aggregated to yield high-quality node embeddings that capture both long- and short-range dependencies. Our experiments show that this leads to improved classification accuracy, without incurring high computational costs.

cs.LG↗
arXiv2023

Deep Learning Approaches in Pavement Distress Identification: A Review

This paper presents a comprehensive review of recent advancements in image processing and deep learning techniques for pavement distress detection and classification, a critical aspect in modern pavement management systems. The conventional manual inspection process conducted by human experts is gradually being superseded by automated solutions, leveraging machine learning and deep learning algorithms to enhance efficiency and accuracy. The ability of these algorithms to discern patterns and make predictions based on extensive datasets has revolutionized the domain of pavement distress identification. The paper investigates the integration of unmanned aerial vehicles (UAVs) for data collection, offering unique advantages such as aerial perspectives and efficient coverage of large areas. By capturing high-resolution images, UAVs provide valuable data that can be processed using deep learning algorithms to detect and classify various pavement distresses effectively. While the primary focus is on 2D image processing, the paper also acknowledges the challenges associated with 3D images, such as sensor limitations and computational requirements. Understanding these challenges is crucial for further advancements in the field. The findings of this review significantly contribute to the evolution of pavement distress detection, fostering the development of efficient pavement management systems. As automated approaches continue to mature, the implementation of deep learning techniques holds great promise in ensuring safer and more durable road infrastructure for the benefit of society.

cs.CV↗
arXiv2023

MLGCN: An Ultra Efficient Graph Convolution Neural Model For 3D Point Cloud Analysis

The analysis of 3D point clouds has diverse applications in robotics, vision and graphics. Processing them presents specific challenges since they are naturally sparse, can vary in spatial resolution and are typically unordered. Graph-based networks to abstract features have emerged as a promising alternative to convolutional neural networks for their analysis, but these can be computationally heavy as well as memory inefficient. To address these limitations we introduce a novel Multi-level Graph Convolution Neural (MLGCN) model, which uses Graph Neural Networks (GNN) blocks to extract features from 3D point clouds at specific locality levels. Our approach employs precomputed graph KNNs, where each KNN graph is shared between GCN blocks inside a GNN block, making it both efficient and effective compared to present models. We demonstrate the efficacy of our approach on point cloud based object classification and part segmentation tasks on benchmark datasets, showing that it produces comparable results to those of state-of-the-art models while requiring up to a thousand times fewer floating-point operations (FLOPs) and having significantly reduced storage requirements. Thus, our MLGCN model could be particular relevant to point cloud based 3D shape analysis in industrial applications when computing resources are scarce.

cs.CV↗
arXiv2023

A Triplet-loss Dilated Residual Network for High-Resolution Representation Learning in Image Retrieval

Content-based image retrieval is the process of retrieving a subset of images from an extensive image gallery based on visual contents, such as color, shape or spatial relations, and texture. In some applications, such as localization, image retrieval is employed as the initial step. In such cases, the accuracy of the top-retrieved images significantly affects the overall system accuracy. The current paper introduces a simple yet efficient image retrieval system with a fewer trainable parameters, which offers acceptable accuracy in top-retrieved images. The proposed method benefits from a dilated residual convolutional neural network with triplet loss. Experimental evaluations show that this model can extract richer information (i.e., high-resolution representations) by enlarging the receptive field, thus improving image retrieval accuracy without increasing the depth or complexity of the model. To enhance the extracted representations' robustness, the current research obtains candidate regions of interest from each feature map and applies Generalized-Mean pooling to the regions. As the choice of triplets in a triplet-based network affects the model training, we employ a triplet online mining method. We test the performance of the proposed method under various configurations on two of the challenging image-retrieval datasets, namely Revisited Paris6k (RPar) and UKBench. The experimental results show an accuracy of 94.54 and 80.23 (mean precision at rank 10) in the RPar medium and hard modes and 3.86 (recall at rank 4) in the UKBench dataset, respectively.

cs.CV↗
arXiv2023

Autonomous Vehicles: Open-Source Technologies, Considerations, and Development

Autonomous vehicles are the culmination of advances in many areas such as sensor technologies, artificial intelligence (AI), networking, and more. This paper will introduce the reader to the technologies that build autonomous vehicles. It will focus on open-source tools and libraries for autonomous vehicle development, making it cheaper and easier for developers and researchers to participate in the field. The topics covered are as follows. First, we will discuss the sensors used in autonomous vehicles and summarize their performance in different environments, costs, and unique features. Then we will cover Simultaneous Localization and Mapping (SLAM) and algorithms for each modality. Third, we will review popular open-source driving simulators, a cost-effective way to train machine learning models and test vehicle software performance. We will then highlight embedded operating systems and the security and development considerations when choosing one. After that, we will discuss Vehicle-to-Vehicle (V2V) and Internet-of-Vehicle (IoV) communication, which are areas that fuse networking technologies with autonomous vehicles to extend their functionality. We will then review the five levels of vehicle automation, commercial and open-source Advanced Driving Assistance Systems, and their features. Finally, we will touch on the major manufacturing and software companies involved in the field, their investments, and their partnerships. These topics will give the reader an understanding of the industry, its technologies, active research, and the tools available for developers to build autonomous vehicles.

cs.RO↗
arXiv2023

Contour Completion using Deep Structural Priors

Humans can easily perceive illusory contours and complete missing forms in fragmented shapes. This work investigates whether such capability can arise in convolutional neural networks (CNNs) using deep structural priors computed directly from images. In this work, we present a framework that completes disconnected contours and connects fragmented lines and curves. In our framework, we propose a model that does not even need to know which regions of the contour are eliminated. We introduce an iterative process that completes an incomplete image and we propose novel measures that guide this to find regions it needs to complete. Our model trains on a single image and fills in the contours with no additional training data. Our work builds a robust framework to achieve contour completion using deep structural priors and extensively investigate how such a model could be implemented.

cs.CV↗
arXiv2022

D-CryptO: Deep learning-based analysis of colon organoid morphology from brightfield images

Stem cell-derived organoids are a promising tool to model native human tissues as they resemble human organs functionally and structurally compared to traditional monolayer cell-based assays. For instance, colon organoids can spontaneously develop crypt-like structures similar to those found in the native colon. While analyzing the structural development of organoids can be a valuable readout, using traditional image analysis tools makes it challenging because of the heterogeneities and the abstract nature of organoid morphologies. To address this limitation, we developed and validated a deep learning-based image analysis tool, named D-CryptO, for the classification of organoid morphology. D-CryptO can automatically assess the crypt formation and opacity of colorectal organoids from brightfield images to determine the extent of organoid structural maturity. To validate this tool, changes in organoid morphology were analyzed during organoid passaging and short-term forskolin stimulation. To further demonstrate the potential of D-CryptO for drug testing, organoid structures were analyzed following treatments with a panel of chemotherapeutic drugs. With D-CryptO, subtle variations in how colon organoids responded to the different chemotherapeutic drugs were detected, which suggest potentially distinct mechanisms of action. This tool could be expanded to other organoid types, like intestinal organoids, to facilitate 3D tissue morphological analysis.

q-bio.QM↗
arXiv2022

Multiple Sclerosis Lesions Segmentation using Attention-Based CNNs in FLAIR Images

Objective: Multiple Sclerosis (MS) is an autoimmune, and demyelinating disease that leads to lesions in the central nervous system. This disease can be tracked and diagnosed using Magnetic Resonance Imaging (MRI). Up to now a multitude of multimodality automatic biomedical approaches is used to segment lesions which are not beneficial for patients in terms of cost, time, and usability. The authors of the present paper propose a method employing just one modality (FLAIR image) to segment MS lesions accurately. Methods: A patch-based Convolutional Neural Network (CNN) is designed, inspired by 3D-ResNet and spatial-channel attention module, to segment MS lesions. The proposed method consists of three stages: (1) the contrast-limited adaptive histogram equalization (CLAHE) is applied to the original images and concatenated to the extracted edges in order to create 4D images; (2) the patches of size 80 * 80 * 80 * 2 are randomly selected from the 4D images; and (3) the extracted patches are passed into an attention-based CNN which is used to segment the lesions. Finally, the proposed method was compared to previous studies of the same dataset. Results: The current study evaluates the model, with a test set of ISIB challenge data. Experimental results illustrate that the proposed approach significantly surpasses existing methods in terms of Dice similarity and Absolute Volume Difference while the proposed method use just one modality (FLAIR) to segment the lesions. Conclusions: The authors have introduced an automated approach to segment the lesions which is based on, at most, two modalities as an input. The proposed architecture is composed of convolution, deconvolution, and an SCA-VoxRes module as an attention module. The results show, the proposed method outperforms well compare to other methods.

eess.IV↗
arXiv2021

Medial Spectral Coordinates for 3D Shape Analysis

In recent years there has been a resurgence of interest in our community in the shape analysis of 3D objects represented by surface meshes, their voxelized interiors, or surface point clouds. In part, this interest has been stimulated by the increased availability of RGBD cameras, and by applications of computer vision to autonomous driving, medical imaging, and robotics. In these settings, spectral coordinates have shown promise for shape representation due to their ability to incorporate both local and global shape properties in a manner that is qualitatively invariant to isometric transformations. Yet, surprisingly, such coordinates have thus far typically considered only local surface positional or derivative information. In the present article, we propose to equip spectral coordinates with medial (object width) information, so as to enrich them. The key idea is to couple surface points that share a medial ball, via the weights of the adjacency matrix. We develop a spectral feature using this idea, and the algorithms to compute it. The incorporation of object width and medial coupling has direct benefits, as illustrated by our experiments on object classification, object part segmentation, and surface point correspondence.

cs.CV↗
arXiv2021

A Matrix Factorization Model for Hellinger-based Trust Management in Social Internet of Things

The Social Internet of Things (SIoT), integration of the Internet of Things and Social Networks paradigms, has been introduced to build a network of smart nodes that are capable of establishing social links. In order to deal with misbehaving service provider nodes, service requestor nodes must evaluate their trustworthiness levels. In this paper, we propose a novel trust management mechanism in the SIoT to predict the most reliable service providers for each service requestor, which leads to reduce the risk of being exposed to malicious nodes. We model the SIoT with a flexible bipartite graph (containing two sets of nodes: service providers and service requestors), then build a social network among the service requestor nodes, using the Hellinger distance. Afterward, we develop a social trust model using nodes' centrality and similarity measures to extract trust behaviors among the social network nodes. Finally, a matrix factorization technique is designed to extract latent features of SIoT nodes, find trustworthy nodes, and mitigate the data sparsity and cold start problems. We analyze the effect of parameters in the proposed trust prediction mechanism on prediction accuracy. The results indicate that feedbacks from the neighboring nodes of a specific service requestor with high Hellinger similarity in our mechanism outperforms the best existing methods. We also show that utilizing the social trust model, which only considers a similarity measure, significantly improves the accuracy of the prediction mechanism. Furthermore, we evaluate the effectiveness of the proposed trust management system through a real-world SIoT use case. Our results demonstrate that the proposed mechanism is resilient to different types of network attacks, and it can accurately find the most proper and trustworthy service provider.

cs.LG↗