Maryam Abbasi

Dr. Maryam Abbasi

orcid

Research Focus & Metrics

Academic Career Length

14Years (2013-Present)

(Calculated once Scilit publication data is synced: current year − year of first publication + 1)

Representative Publications

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26 June 2022 in Journal of Cheminformatics
Verified
Journal Article
Open access
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MAMaryam Abbasi
Maryam Abbasi
BSBeatriz P. Santos
Beatriz P. Santos
TPTiago C. Pereira
Tiago C. Pereira
RSRaul Sofia
Raul Sofia
NMNelson Monteiro
Nelson Monteiro
JAJoel P. Arrais
Joel P. Arrais
Drug design is an important area of study for pharmaceutical businesses. However, low efficacy, off-target delivery, time consumption, and high cost are challenges and can create barriers that impact this process. Deep Learning models are emerging as a promising solution to perform de novo drug design, i.e., to generate drug-like molecules tailored to specific needs. However, stereochemistry was not explicitly considered in the generated molecules, which is inevitable in targeted-oriented molecules. This paper proposes a framework based on Feedback Generative Adversarial Network (GAN) that includes optimization strategy by incorporating Encoder–Decoder, GAN, and Predictor deep models interconnected with a feedback loop. The Encoder–Decoder converts the string notations of molecules into latent space vectors, effectively creating a new type of molecular representation. At the same time, the GAN can learn and replicate the training data distribution and, therefore, generate new compounds. The feedback loop is designed to incorporate and evaluate the generated molecules according to the multiobjective desired property at every epoch of training to ensure a steady shift of the generated distribution towards the space of the targeted properties. Moreover, to develop a more precise set of molecules, we also incorporate a multiobjective optimization selection technique based on a non-dominated sorting genetic algorithm. The results demonstrate that the proposed framework can generate realistic, novel molecules that span the chemical space. The proposed Encoder–Decoder model correctly reconstructs 99% of the datasets, including stereochemical information. The model’s ability to find uncharted regions of the chemical space was successfully shown by optimizing the unbiased GAN to generate molecules with a high binding affinity to the Kappa Opioid and Adenosine $$A_ {2a}$$ A 2 a receptor. Furthermore, the generated compounds exhibit high internal and external diversity levels 0.88 and 0.94, respectively, and uniqueness.

21 May 2025 in Cryptography
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Journal Article
Open access
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MAMaryam Abbasi
Maryam Abbasi
FCFilipe Gonçalves Cardoso
Filipe Gonçalves Cardoso
PVPaulo Vaz
Paulo Vaz
JSJosé Silva
José Silva
PMPedro Martins
Pedro Martins
The emergence of large-scale quantum computing presents an imminent threat to contemporary public-key cryptosystems, with quantum algorithms such as Shor’s algorithm capable of efficiently breaking RSA and elliptic curve cryptography (ECC). This vulnerability has catalyzed accelerated standardization efforts for post-quantum cryptography (PQC) by the U.S. National Institute of Standards and Technology (NIST) and global security stakeholders. While theoretical security analysis of these quantum-resistant algorithms has advanced considerably, comprehensive real-world performance benchmarks spanning diverse computing environments—from high-performance cloud infrastructure to severely resource-constrained IoT devices—remain insufficient for informed deployment planning. This paper presents the most extensive cross-platform empirical evaluation to date of NIST-selected PQC algorithms, including CRYSTALS-Kyber and NTRU for key encapsulation mechanisms (KEMs), alongside BIKE as a code-based alternative, and CRYSTALS-Dilithium and Falcon for digital signatures. Our systematic benchmarking framework measures computational latency, memory utilization, key sizes, and protocol overhead across multiple security levels (NIST Levels 1, 3, and 5) in three distinct hardware environments and various network conditions. Results demonstrate that contemporary server architectures can implement these algorithms with negligible performance impact (<5% additional latency), making immediate adoption feasible for cloud services. In contrast, resource-constrained devices experience more significant overhead, with computational demands varying by up to 12× between algorithms at equivalent security levels, highlighting the importance of algorithm selection for edge deployments. Beyond standalone algorithm performance, we analyze integration challenges within existing security protocols, revealing that naive implementation of PQC in TLS 1.3 can increase handshake size by up to 7× compared to classical approaches. To address this, we propose and evaluate three optimization strategies that reduce bandwidth requirements by 40–60% without compromising security guarantees. Our investigation further encompasses memory-constrained implementation techniques, side-channel resistance measures, and hybrid classical-quantum approaches for transitional deployments. Based on these comprehensive findings, we present a risk-based migration framework and algorithm selection guidelines tailored to specific use cases, including financial transactions, secure firmware updates, vehicle-to-infrastructure communications, and IoT fleet management. This practical roadmap enables organizations to strategically prioritize systems for quantum-resistant upgrades based on data sensitivity, resource constraints, and technical feasibility. Our results conclusively demonstrate that PQC is deployment-ready for most applications, provided that implementations are carefully optimized for the specific performance characteristics and security requirements of target environments. We also identify several remaining research challenges for the community, including further optimization for ultra-constrained devices, standardization of hybrid schemes, and hardware acceleration opportunities.

9 March 2021 in Journal of Cheminformatics
Verified
Journal Article
Open access
PDF file
TPTiago Pereira
Tiago Pereira
MAMaryam Abbasi
Maryam Abbasi
Bernardete RibeiroBernardete Ribeiro
Bernardete Ribeiro
JAJoel P. Arrais
Joel P. Arrais
In this work, we explore the potential of deep learning to streamline the process of identifying new potential drugs through the computational generation of molecules with interesting biological properties. Two deep neural networks compose our targeted generation framework: the Generator, which is trained to learn the building rules of valid molecules employing SMILES strings notation, and the Predictor which evaluates the newly generated compounds by predicting their affinity for the desired target. Then, the Generator is optimized through Reinforcement Learning to produce molecules with bespoken properties. The innovation of this approach is the exploratory strategy applied during the reinforcement training process that seeks to add novelty to the generated compounds. This training strategy employs two Generators interchangeably to sample new SMILES: the initially trained model that will remain fixed and a copy of the previous one that will be updated during the training to uncover the most promising molecules. The evolution of the reward assigned by the Predictor determines how often each one is employed to select the next token of the molecule. This strategy establishes a compromise between the need to acquire more information about the chemical space and the need to sample new molecules, with the experience gained so far. To demonstrate the effectiveness of the method, the Generator is trained to design molecules with an optimized coefficient of partition and also high inhibitory power against the Adenosine $$A_{2A}$$ A 2 A and $$\kappa$$ κ opioid receptors. The results reveal that the model can effectively adjust the newly generated molecules towards the wanted direction. More importantly, it was possible to find promising sets of unique and diverse molecules, which was the main purpose of the newly implemented strategy.

Verified
Journal Article
Open access
PDF file
EPEduardo Pina
Eduardo Pina
JRJosé Afonso de Almeida Ramos
José Afonso de Almeida Ramos
HJHenrique Jorge
Henrique Jorge
PVPaulo Vaz
Paulo Vaz
JSJosé Silva
José Silva
PMPedro Martins
Pedro Martins
Data privacy and ethical considerations ensure the security of databases by respecting individual rights while upholding ethical considerations when collecting, managing, and using information. Nowadays, despite having regulations that help to protect citizens and organizations, we have been presented with thousands of instances of data breaches, unauthorized access, and misuse of data related to such individuals and organizations. In this paper, we propose ethical considerations and best practices associated with critical data and the role of the database administrator who helps protect data. First, we suggest best practices for database administrators regarding data minimization, anonymization, pseudonymization and encryption, access controls, data retention guidelines, and stakeholder communication. Then, we present a case study that illustrates the application of these ethical implementations and best practices in a real-world scenario, showing the approach in action and the benefits of privacy. Finally, the study highlights the importance of a comprehensive approach to deal with data protection challenges and provides valuable insights for future research and developments in this field.

19 February 2025 in Applied Sciences
Verified
Journal Article
Open access
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MAMaryam Abbasi
Maryam Abbasi
PVPaulo Vaz
Paulo Vaz
JSJosé Silva
José Silva
PMPedro Martins
Pedro Martins
This paper conducts a comprehensive experimental comparison of two widely used additive manufacturing (AM) processes, Fused Deposition Modeling (FDM) and Stereolithography (SLA), under standardized conditions using the same test geometries and protocols. FDM parts were printed with both Polylactic Acid (PLA) and Acrylonitrile Butadiene Styrene (ABS) filaments, while SLA used a general-purpose photopolymer resin. Quantitative evaluations included surface roughness, dimensional accuracy, tensile properties, production cost, and energy consumption. Additionally, environmental considerations and process reliability were assessed by examining waste streams, recyclability, and failure rates. The results indicate that SLA achieves superior surface quality (Ra≈2μm vs. 12–13μm) and dimensional tolerances (±0.05mm vs. ±0.15–0.20mm), along with higher tensile strength (up to 70MPa). However, FDM provides notable advantages in cost (approximately 60% lower on a per-part basis), production speed, and energy efficiency. Moreover, from an environmental perspective, FDM is more favorable when using biodegradable PLA or recyclable ABS, whereas SLA resin waste is hazardous. Overall, the study highlights that no single process is universally superior. FDM offers a rapid, cost-effective solution for prototyping, while SLA excels in precision and surface finish. By presenting a detailed, data-driven comparison, this work guides engineers, product designers, and researchers in choosing the most suitable AM technology for their specific needs.

25 January 2025 in Applied Sciences
Verified
Journal Article
Open access
PDF file
MAMaryam Abbasi
Maryam Abbasi
PVPaulo Vaz
Paulo Vaz
JSJosé Silva
José Silva
PMPedro Martins
Pedro Martins
The rise of deepfakes—synthetic media generated using artificial intelligence—threatens digital content authenticity, facilitating misinformation and manipulation. However, deepfakes can also depict real or entirely fictitious individuals, leveraging state-of-the-art techniques such as generative adversarial networks (GANs) and emerging diffusion-based models. Existing detection methods face challenges with generalization across datasets and vulnerability to adversarial attacks. This study focuses on subsets of frames extracted from the DeepFake Detection Challenge (DFDC) and FaceForensics++ videos to evaluate three convolutional neural network architectures—XCeption, ResNet, and VGG16—for deepfake detection. Performance metrics include accuracy, precision, F1-score, AUC-ROC, and Matthews Correlation Coefficient (MCC), combined with an assessment of resilience to adversarial perturbations via the Fast Gradient Sign Method (FGSM). Among the tested models, XCeption achieves the highest accuracy (89.2% on DFDC), strong generalization, and real-time suitability, while VGG16 excels in precision and ResNet provides faster inference. However, all models exhibit reduced performance under adversarial conditions, underscoring the need for enhanced resilience. These findings indicate that robust detection systems must consider advanced generative approaches, adversarial defenses, and cross-dataset adaptation to effectively counter evolving deepfake threats.