arXiv subjects

Elham Dolatabadi

Publications and source records attributed to Elham Dolatabadi.

30 records · Page 2Linked to original sources

arXiv2025

A Shared Encoder Approach to Multimodal Representation Learning

Multimodal representation learning has demonstrated remarkable potential in enabling models to process and integrate diverse data modalities, such as text and images, for improved understanding and performance. While the medical domain can benefit significantly from this paradigm, the scarcity of paired multimodal data and reliance on proprietary or pretrained encoders pose significant challenges. In this work, we present a shared encoder framework for multimodal representation learning tailored to the medical domain. Our approach employs a single set of encoder parameters shared across modalities, augmented with learnable modality features. Empirical results demonstrate that our shared encoder idea achieves superior performance compared to separate modality-specific encoders, demonstrating improved generalization in data-constrained settings. Notably, the performance gains are more pronounced with fewer training examples, underscoring the efficiency of our shared encoder framework for real-world medical applications with limited data. Our code and experiment setup are available at https://github.com/VectorInstitute/shared_encoder.

cs.CV↗

arXiv2025

Academic case reports lack diversity: Assessing the presence and diversity of sociodemographic and behavioral factors related to Post COVID-19 Condition

Understanding the prevalence, disparities, and symptom variations of Post COVID-19 Condition (PCC) for vulnerable populations is crucial to improving care and addressing intersecting inequities. This study aims to develop a comprehensive framework for integrating social determinants of health (SDOH) into PCC research by leveraging NLP techniques to analyze disparities and variations in SDOH representation within PCC case reports. Following construction of a PCC Case Report Corpus, comprising over 7,000 case reports from the LitCOVID repository, a subset of 709 reports were annotated with 26 core SDOH-related entity types using pre-trained named entity recognition (NER) models, human review, and data augmentation to improve quality, diversity and representation of entity types. An NLP pipeline integrating NER, natural language inference (NLI), trigram and frequency analyses was developed to extract and analyze these entities. Both encoder-only transformer models and RNN-based models were assessed for the NER objective. Fine-tuned encoder-only BERT models outperformed traditional RNN-based models in generalizability to distinct sentence structures and greater class sparsity. Exploratory analysis revealed variability in entity richness, with prevalent entities like condition, age, and access to care, and underrepresentation of sensitive categories like race and housing status. Trigram analysis highlighted frequent co-occurrences among entities, including age, gender, and condition. The NLI objective (entailment and contradiction analysis) showed attributes like "Experienced violence or abuse" and "Has medical insurance" had high entailment rates (82.4%-80.3%), while attributes such as "Is female-identifying," "Is married," and "Has a terminal condition" exhibited high contradiction rates (70.8%-98.5%).

cs.CL↗

arXiv2025

FAIIR: Building Toward A Conversational AI Agent Assistant for Youth Mental Health Service Provision

The world's healthcare systems and mental health agencies face both a growing demand for youth mental health services, alongside a simultaneous challenge of limited resources. Here, we focus on frontline crisis support, where Crisis Responders (CRs) engage in conversations for youth mental health support and assign an issue tag to each conversation. In this study, we develop FAIIR (Frontline Assistant: Issue Identification and Recommendation), an advanced tool leveraging an ensemble of domain-adapted and fine-tuned transformer models trained on a large conversational dataset comprising 780,000 conversations. The primary aim is to reduce the cognitive burden on CRs, enhance the accuracy of issue identification, and streamline post-conversation administrative tasks. We evaluate FAIIR on both retrospective and prospective conversations, emphasizing human-in-the-loop design with active CR engagement for model refinement, consensus-building, and overall assessment. Our results indicate that FAIIR achieves an average AUCROC of 94%, a sample average F1-score of 64%, and a sample average recall score of 81% on the retrospective test set. We also demonstrate the robustness and generalizability of the FAIIR tool during the silent testing phase, with less than a 2% drop in all performance metrics. Notably, CRs' responses exhibited an overall agreement of 90.9% with FAIIR's predictions. Furthermore, expert agreement with FAIIR surpassed their agreement with the original labels. To conclude, our findings indicate that assisting with the identification of issues of relevance helps reduce the burden on CRs, ensuring that appropriate resources can be provided and that active rescues and mandatory reporting can take place in critical situations requiring immediate de-escalation.

cs.AI↗

arXiv2024

Exploring Bias and Prediction Metrics to Characterise the Fairness of Machine Learning for Equity-Centered Public Health Decision-Making: A Narrative Review

Background: The rapid advancement of Machine Learning (ML) represents novel opportunities to enhance public health research, surveillance, and decision-making. However, there is a lack of comprehensive understanding of algorithmic bias, systematic errors in predicted population health outcomes, resulting from the public health application of ML. The objective of this narrative review is to explore the types of bias generated by ML and quantitative metrics to assess these biases. Methods : We performed search on PubMed, MEDLINE, IEEE (Institute of Electrical and Electronics Engineers), ACM (Association for Computing Machinery) Digital Library, Science Direct, and Springer Nature. We used keywords to identify studies describing types of bias and metrics to measure these in the domain of ML and public and population health published in English between 2008 and 2023, inclusive. Results: A total of 72 articles met the inclusion criteria. Our review identified the commonly described types of bias and quantitative metrics to assess these biases from an equity perspective. Conclusion : The review will help formalize the evaluation framework for ML on public health from an equity perspective.

cs.LG↗

arXiv2024

Practical Guide for Causal Pathways and Sub-group Disparity Analysis

In this study, we introduce the application of causal disparity analysis to unveil intricate relationships and causal pathways between sensitive attributes and the targeted outcomes within real-world observational data. Our methodology involves employing causal decomposition analysis to quantify and examine the causal interplay between sensitive attributes and outcomes. We also emphasize the significance of integrating heterogeneity assessment in causal disparity analysis to gain deeper insights into the impact of sensitive attributes within specific sub-groups on outcomes. Our two-step investigation focuses on datasets where race serves as the sensitive attribute. The results on two datasets indicate the benefit of leveraging causal analysis and heterogeneity assessment not only for quantifying biases in the data but also for disentangling their influences on outcomes. We demonstrate that the sub-groups identified by our approach to be affected the most by disparities are the ones with the largest ML classification errors. We also show that grouping the data only based on a sensitive attribute is not enough, and through these analyses, we can find sub-groups that are directly affected by disparities. We hope that our findings will encourage the adoption of such methodologies in future ethical AI practices and bias audits, fostering a more equitable and fair technological landscape.

cs.CY↗

arXiv2024

Benchmarking Vision-Language Contrastive Methods for Medical Representation Learning

We perform a comprehensive benchmarking of contrastive frameworks for learning multimodal representations in the medical domain. Through this study, we aim to answer the following research questions: (i) How transferable are general-domain representations to the medical domain? (ii) Is multimodal contrastive training sufficient, or does it benefit from unimodal training as well? (iii) What is the impact of feature granularity on the effectiveness of multimodal medical representation learning? To answer these questions, we investigate eight contrastive learning approaches under identical training setups, and train them on 2.8 million image-text pairs from four datasets, and evaluate them on 25 downstream tasks, including classification (zero-shot and linear probing), image-to-text and text-to-image retrieval, and visual question-answering. Our findings suggest a positive answer to the first question, a negative answer to the second question, and the benefit of learning fine-grained features. Finally, we make our code publicly available.

cs.CV↗

arXiv2024

FAIR Enough: How Can We Develop and Assess a FAIR-Compliant Dataset for Large Language Models' Training?

The rapid evolution of Large Language Models (LLMs) highlights the necessity for ethical considerations and data integrity in AI development, particularly emphasizing the role of FAIR (Findable, Accessible, Interoperable, Reusable) data principles. While these principles are crucial for ethical data stewardship, their specific application in the context of LLM training data remains an under-explored area. This research gap is the focus of our study, which begins with an examination of existing literature to underline the importance of FAIR principles in managing data for LLM training. Building upon this, we propose a novel framework designed to integrate FAIR principles into the LLM development lifecycle. A contribution of our work is the development of a comprehensive checklist intended to guide researchers and developers in applying FAIR data principles consistently across the model development process. The utility and effectiveness of our framework are validated through a case study on creating a FAIR-compliant dataset aimed at detecting and mitigating biases in LLMs. We present this framework to the community as a tool to foster the creation of technologically advanced, ethically grounded, and socially responsible AI models.

cs.CL↗

arXiv2023

MLHOps: Machine Learning for Healthcare Operations

Machine Learning Health Operations (MLHOps) is the combination of processes for reliable, efficient, usable, and ethical deployment and maintenance of machine learning models in healthcare settings. This paper provides both a survey of work in this area and guidelines for developers and clinicians to deploy and maintain their own models in clinical practice. We cover the foundational concepts of general machine learning operations, describe the initial setup of MLHOps pipelines (including data sources, preparation, engineering, and tools). We then describe long-term monitoring and updating (including data distribution shifts and model updating) and ethical considerations (including bias, fairness, interpretability, and privacy). This work therefore provides guidance across the full pipeline of MLHOps from conception to initial and ongoing deployment.

cs.LG↗

arXiv2023

Bringing the State-of-the-Art to Customers: A Neural Agent Assistant Framework for Customer Service Support

Building Agent Assistants that can help improve customer service support requires inputs from industry users and their customers, as well as knowledge about state-of-the-art Natural Language Processing (NLP) technology. We combine expertise from academia and industry to bridge the gap and build task/domain-specific Neural Agent Assistants (NAA) with three high-level components for: (1) Intent Identification, (2) Context Retrieval, and (3) Response Generation. In this paper, we outline the pipeline of the NAA's core system and also present three case studies in which three industry partners successfully adapt the framework to find solutions to their unique challenges. Our findings suggest that a collaborative process is instrumental in spurring the development of emerging NLP models for Conversational AI tasks in industry. The full reference implementation code and results are available at \url{https://github.com/VectorInstitute/NAA}

cs.CL↗

arXiv2020

An Experimental Evaluation of Transformer-based Language Models in the Biomedical Domain

With the growing amount of text in health data, there have been rapid advances in large pre-trained models that can be applied to a wide variety of biomedical tasks with minimal task-specific modifications. Emphasizing the cost of these models, which renders technical replication challenging, this paper summarizes experiments conducted in replicating BioBERT and further pre-training and careful fine-tuning in the biomedical domain. We also investigate the effectiveness of domain-specific and domain-agnostic pre-trained models across downstream biomedical NLP tasks. Our finding confirms that pre-trained models can be impactful in some downstream NLP tasks (QA and NER) in the biomedical domain; however, this improvement may not justify the high cost of domain-specific pre-training.

cs.CL↗

arXiv2020

A Computer Vision Approach to Combat Lyme Disease

Lyme disease is an infectious disease transmitted to humans by a bite from an infected Ixodes species (blacklegged ticks). It is one of the fastest growing vector-borne illness in North America and is expanding its geographic footprint. Lyme disease treatment is time-sensitive, and can be cured by administering an antibiotic (prophylaxis) to the patient within 72 hours after a tick bite by the Ixodes species. However, the laboratory-based identification of each tick that might carry the bacteria is time-consuming and labour intensive and cannot meet the maximum turn-around-time of 72 hours for an effective treatment. Early identification of blacklegged ticks using computer vision technologies is a potential solution in promptly identifying a tick and administering prophylaxis within a crucial window period. In this work, we build an automated detection tool that can differentiate blacklegged ticks from other ticks species using advanced deep learning and computer vision approaches. We demonstrate the classification of tick species using Convolution Neural Network (CNN) models, trained end-to-end from tick images directly. Advanced knowledge transfer techniques within teacher-student learning frameworks are adopted to improve the performance of classification of tick species. Our best CNN model achieves 92% accuracy on test set. The tool can be integrated with the geography of exposure to determine the risk of Lyme disease infection and need for prophylaxis treatment.

cs.CV↗

arXiv2020

Evaluating Knowledge Transfer in Neural Network for Medical Images

Deep learning and knowledge transfer techniques have permeated the field of medical imaging and are considered as key approaches for revolutionizing diagnostic imaging practices. However, there are still challenges for the successful integration of deep learning into medical imaging tasks due to a lack of large annotated imaging data. To address this issue, we propose a teacher-student learning framework to transfer knowledge from a carefully pre-trained convolutional neural network (CNN) teacher to a student CNN. In this study, we explore the performance of knowledge transfer in the medical imaging setting. We investigate the proposed network's performance when the student network is trained on a small dataset (target dataset) as well as when teacher's and student's domains are distinct. The performances of the CNN models are evaluated on three medical imaging datasets including Diabetic Retinopathy, CheXpert, and ChestX-ray8. Our results indicate that the teacher-student learning framework outperforms transfer learning for small imaging datasets. Particularly, the teacher-student learning framework improves the area under the ROC Curve (AUC) of the CNN model on a small sample of CheXpert (n=5k) by 4% and on ChestX-ray8 (n=5.6k) by 9%. In addition to small training data size, we also demonstrate a clear advantage of the teacher-student learning framework in the medical imaging setting compared to transfer learning. We observe that the teacher-student network holds a great promise not only to improve the performance of diagnosis but also to reduce overfitting when the dataset is small.

eess.IV↗