publications | Md Toki Tahmid

2024

Nat. Commun. Biol.

TransBind allows precise detection of DNA-binding proteins and residues using language models and deep learning

Md. Toki Tahmid, A.K.M. Mehedi Hasan, and Md Shamsuzzoha Bayzid

Nature Communications Biology, Nov 2024

Accepted

@article{tahmid2024transbind,
  title = {TransBind allows precise detection of {DNA}-binding proteins and residues
                   using language models and deep learning},
  author = {Tahmid, Md. Toki and Hasan, A.K.M. Mehedi and Bayzid, Md Shamsuzzoha},
  journal = {Nature Communications Biology},
  year = {2024},
  month = nov,
  publisher = {Nature Publishing Group},
  note = {Accepted}
}

NeurIPS ENLSP

BiRNA-BERT: Adaptive Tokenization for Efficient RNA Language Modeling

Md Toki Tahmid, H.A.Z Sameen Sagir, Sazan Mahbub, and 2 more authors

In NeurIPS 2024 Workshop on Efficient Natural Language and Speech Processing, Sep 2024

\textbfSpotlight Paper · Under Major Revision at \textitNature Communications Biology · Collaboration: University of California, Riverside

Bib

@inproceedings{tahmid2024birnabertworkshop,
  title = {{BiRNA-BERT}: Adaptive Tokenization for Efficient {RNA} Language Modeling},
  author = {Tahmid, Md Toki and Sagir, H.A.Z Sameen and Mahbub, Sazan and Dong, Yue and Bayzid, Md Shamsuzzoha},
  booktitle = {NeurIPS 2024 Workshop on Efficient Natural Language and Speech Processing},
  year = {2024},
  month = sep,
  note = {\textbf{Spotlight Paper} · Under Major Revision at \textit{Nature Communications Biology} · Collaboration: University of California, Riverside},
}

NeurIPS

Structure Matters: Deciphering Neural Network’s Properties from its Structure

Shashata Sawmya, Md Toki Tahmid, Gourab Saha, and 3 more authors

In NeurIPS 2024 Workshop: Symmetry and Geometry in Neural Representations, Nov 2024

Joint Co-First Author · Collaboration: Computational Connectomics Lab, MIT

Bib

@inproceedings{sawmya2024structurematters,
  title = {Structure Matters: Deciphering Neural Network's Properties from its Structure},
  author = {Sawmya, Shashata and Tahmid, Md Toki and Saha, Gourab and Saha, Arpita and Shavit, Nir N and Mi, Lu},
  booktitle = {NeurIPS 2024 Workshop: Symmetry and Geometry in Neural Representations},
  year = {2024},
  month = nov,
  note = {Joint Co-First Author · Collaboration: Computational Connectomics Lab, MIT},
}

NeurIPS MLSB

TomoPicker: Annotation-Efficient Particle Picking in Cryo-Electron Tomograms

Mostofa Rafid Uddin, Ajmain Yasar Ahmed, Md Toki Tahmid, and 3 more authors

In NeurIPS 2024 Workshop on Machine Learning for Structural Biology, Nov 2024

Collaboration: XuLab, Carnegie Mellon University

Bib

@inproceedings{uddin2024tomopicker,
  title = {{TomoPicker}: Annotation-Efficient Particle Picking in Cryo-Electron Tomograms},
  author = {Uddin, Mostofa Rafid and Ahmed, Ajmain Yasar and Tahmid, Md Toki and Alam, Md Zarif Ul and Freyberg, Zachary and Xu, Min},
  booktitle = {NeurIPS 2024 Workshop on Machine Learning for Structural Biology},
  year = {2024},
  month = nov,
  note = {Collaboration: XuLab, Carnegie Mellon University},
}

NeurIPS MLSB

RNA-DCGen: Dual Constrained RNA Sequence Generation with LLM-Attack

Haz Sameen Shahgir^*, Md Rownok Zahan Ratul^*, Md Toki Tahmid^*, and 2 more authors

In NeurIPS 2024 Workshop on Machine Learning for Structural Biology, Sep 2024

Joint Co-First Author

Bib

@inproceedings{shahgir2024rnadcgen,
  title = {{RNA-DCGen}: Dual Constrained {RNA} Sequence Generation with {LLM-Attack}},
  author = {Shahgir, Haz Sameen and Ratul, Md Rownok Zahan and Tahmid, Md Toki and Sayeed, Khondker Salman and Rahman, Atif},
  booktitle = {NeurIPS 2024 Workshop on Machine Learning for Structural Biology},
  year = {2024},
  month = sep,
  note = {Joint Co-First Author},
}

NeurIPS MLSB

LOCAS: Multi-label mRNA Localization with Supervised Contrastive Learning

Abrar Rahman Abir^*, Md Toki Tahmid^*, and M Saifur Rahman

In NeurIPS 2024 Workshop on Machine Learning for Structural Biology, Sep 2024

Joint Co-First Author

Bib

@inproceedings{abir2024locas,
  title = {{LOCAS}: Multi-label {mRNA} Localization with Supervised Contrastive Learning},
  author = {Abir, Abrar Rahman and Tahmid, Md Toki and Rahman, M Saifur},
  booktitle = {NeurIPS 2024 Workshop on Machine Learning for Structural Biology},
  year = {2024},
  month = sep,
  note = {Joint Co-First Author},
}

NeurIPS SSL

EmbedSimScore: Advancing Protein Similarity Analysis with Structural and Contextual Embeddings

Gourab Saha^*, Md Toki Tahmid^*, and Md. Shamsuzzoha Bayzid

In NeurIPS 2024 Workshop: Self-Supervised Learning – Theory and Practice, Sep 2024

Joint Co-First Author

Bib

@inproceedings{saha2024embedsimscore,
  title = {{EmbedSimScore}: Advancing Protein Similarity Analysis with Structural and Contextual Embeddings},
  author = {Saha, Gourab and Tahmid, Md Toki and Bayzid, Md. Shamsuzzoha},
  booktitle = {NeurIPS 2024 Workshop: Self-Supervised Learning -- Theory and Practice},
  year = {2024},
  month = sep,
  note = {Joint Co-First Author},
}

bioRxiv

BioLLMNet: Enhancing RNA-Interaction Prediction with a Specialized Cross-LLM Transformation Network

Md Toki Tahmid, Abrar Rahman Abir, and Md Shamsuzzoha Bayzid

Sep 2024

Under Review at \textitBriefings in Bioinformatics

Bib

@misc{tahmid2024biollmnet,
  title = {{BioLLMNet}: Enhancing {RNA}-Interaction Prediction with a Specialized Cross-{LLM} Transformation Network},
  author = {Tahmid, Md Toki and Abir, Abrar Rahman and Bayzid, Md Shamsuzzoha},
  year = {2024},
  month = sep,
  note = {Under Review at \textit{Briefings in Bioinformatics}},
}

bioRxiv

DeepRNA-Twist: Language Model guided RNA Torsion Angle Prediction with Attention-Inception Network

Abrar Rahman Abir, Md Toki Tahmid, Rafiqul Islam Rayan, and 1 more author

Sep 2024

Under Review at \textitBriefings in Bioinformatics

Bib

@misc{abir2024deeprnatwist,
  title = {{DeepRNA-Twist}: Language Model guided {RNA} Torsion Angle Prediction with Attention-Inception Network},
  author = {Abir, Abrar Rahman and Tahmid, Md Toki and Rayan, Rafiqul Islam and Rahman, M Saifur},
  year = {2024},
  month = sep,
  note = {Under Review at \textit{Briefings in Bioinformatics}},
}

bioRxiv

wQFM-TREE: Highly accurate and scalable quartet-based species tree inference from gene trees

Abdur Rafi, Ahmed Mahir Sultan Rumi, Sheikh Azizul Hakim, and 6 more authors

Jul 2024

Under Review at \textitBioinformatics Advances

Bib

@misc{rafi2024wqfmtree,
  title = {{wQFM-TREE}: Highly accurate and scalable quartet-based species tree inference from gene trees},
  author = {Rafi, Abdur and Rumi, Ahmed Mahir Sultan and Hakim, Sheikh Azizul and Sohaib, Sohaib and Tahmid, Md Toki and Momin, Rabib Jahin Ibn and Zaman, Tanjeem Azwad and Reaz, Rezwana and Bayzid, Md Shamsuzzoha},
  year = {2024},
  month = jul,
  note = {Under Review at \textit{Bioinformatics Advances}},
}

bioRxiv

GraFusionNet: Integrating Node, Edge, and Semantic Features for Enhanced Graph Representations

Md Toki Tahmid, Tanjeem Azwad Zaman, and M. Saifur Rahman

Nov 2024

Preprint

Bib

@misc{tahmid2024grafusionnet,
  title = {{GraFusionNet}: Integrating Node, Edge, and Semantic Features for Enhanced Graph Representations},
  author = {Tahmid, Md Toki and Zaman, Tanjeem Azwad and Rahman, M. Saifur},
  year = {2024},
  month = nov,
  note = {Preprint},
}

bioRxiv

Advancing Noninvasive Mechanical Ventilation: Simulating Techniques for Improved Respiratory Care

Md Toki Tahmid and Mrinmoy Nandi Bappa

Nov 2024

Preprint

Bib

@misc{tahmid2024ventilation,
  title = {Advancing Noninvasive Mechanical Ventilation: Simulating Techniques for Improved Respiratory Care},
  author = {Tahmid, Md Toki and Bappa, Mrinmoy Nandi},
  year = {2024},
  month = nov,
  note = {Preprint},
}

bioRxiv

A Paradigm Shift in Mouza Map Vectorization: A Human-Machine Collaboration Approach

Mahir Shahriar Dhrubo, Samira Akter, Anwarul Bashir Shuaib, and 3 more authors

Jul 2024

Submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence

Bib

@misc{dhrubo2024mouza,
  title = {A Paradigm Shift in Mouza Map Vectorization: A Human-Machine Collaboration Approach},
  author = {Dhrubo, Mahir Shahriar and Akter, Samira and Shuaib, Anwarul Bashir and Tahmid, Md Toki and Hasan, Zahid and Islam, ABM},
  year = {2024},
  month = jul,
  note = {Submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence},
}

2023

IEEE JBHI

MD-CardioNet: A Multi-Dimensional Deep Neural Network for Cardiovascular Disease Diagnosis from Electrocardiogram

MT Tahmid, ME Kader, T Mahmud, and 1 more author

IEEE Journal of Biomedical and Health Informatics, Aug 2023

Bib

@article{tahmid2023mdcardionet,
  title = {{MD-CardioNet}: A Multi-Dimensional Deep Neural Network for Cardiovascular
                   Disease Diagnosis from Electrocardiogram},
  author = {Tahmid, MT and Kader, ME and Mahmud, T and Fattah, SA},
  journal = {IEEE Journal of Biomedical and Health Informatics},
  year = {2023},
  month = aug,
  publisher = {IEEE},
}

Sci. Rep.

A ubiquitous method for predicting underground petroleum deposits based on satellite data

S Newaz, MT Tahmid, N Al-Aboody, and 1 more author

Nature Scientific Reports, Apr 2023

Bib

@article{newaz2023petroleum,
  title = {A ubiquitous method for predicting underground petroleum deposits based on satellite data},
  author = {Newaz, S and Tahmid, MT and Al-Aboody, N and Islam, ABMAA},
  journal = {Nature Scientific Reports},
  volume = {13},
  number = {1},
  pages = {6638},
  year = {2023},
  month = apr,
  publisher = {Nature Publishing Group},
}

arXiv

Connecting the Dots: Leveraging Spatio-Temporal Graph Neural Networks for Accurate Bangla Sign Language Recognition

Haz Sameen Shahgir, Khondker Salman Sayeed, Md Toki Tahmid, and 2 more authors

Jul 2023

Preprint

Bib

@misc{shahgir2023banglasign,
  title = {Connecting the Dots: Leveraging Spatio-Temporal Graph Neural Networks for Accurate Bangla Sign Language Recognition},
  author = {Shahgir, Haz Sameen and Sayeed, Khondker Salman and Tahmid, Md Toki and Zaman, Tanjeem Azwad and Alam, Md Zarif Ul},
  year = {2023},
  month = jul,
  note = {Preprint},
}

2022

Heliyon

Escalating post-disaster rescue missions through ad-hoc victim localization exploiting Wi-Fi networks

TA Khan, TR Toha, SI Salim, and 2 more authors

Heliyon, May 2022

Bib

@article{khan2022postdisaster,
  title = {Escalating post-disaster rescue missions through ad-hoc victim localization
                   exploiting {Wi-Fi} networks},
  author = {Khan, TA and Toha, TR and Salim, SI and Tahmid, MT and Al Islam, ABMA},
  journal = {Heliyon},
  volume = {8},
  number = {5},
  year = {2022},
  month = may,
  publisher = {Elsevier},
}

ICTD

Long-Range Low-Cost Networking for Real-Time Monitoring of Rail Tracks in Developing Countries

Saiful Islam Salim, Uday Kamal, Adnan Quaium, and 5 more authors

In Proceedings of the 2022 International Conference on Information and Communication Technologies and Development, Jun 2022

Bib

@inproceedings{salim2022railtrack,
  title = {Long-Range Low-Cost Networking for Real-Time Monitoring of Rail Tracks in Developing Countries},
  author = {Salim, Saiful Islam and Kamal, Uday and Quaium, Adnan and Hossain, Mainul and Rahaman, Masfiqur and Sakib, Nazmul Hasan and Tahmid, Md Toki and Islam, ABM Alim Al},
  booktitle = {Proceedings of the 2022 International Conference on Information and Communication Technologies and Development},
  year = {2022},
  month = jun,
}

2021

Results Phys.

Forecasting COVID-19 cases: A comparative analysis between recurrent and convolutional neural networks

KN Nabi, MT Tahmid, A Rafi, and 2 more authors

Results in Physics, May 2021

74 citations

Bib

@article{nabi2021forecasting,
  title = {Forecasting {COVID-19} cases: A comparative analysis between recurrent and
                   convolutional neural networks},
  author = {Nabi, KN and Tahmid, MT and Rafi, A and Kader, ME and Haider, MA},
  journal = {Results in Physics},
  volume = {24},
  pages = {104137},
  year = {2021},
  month = may,
  publisher = {Elsevier},
  note = {74 citations}
}

IEEE SOLI

Artificial Intelligence Based Cybersecurity: Two-Step Suitability Test

Sajjad Waheed Shah Md Istiaque, Md Toki Tahmid, Asif Iqbal Khan, and 1 more author

In IEEE International Conference on Service Operations and Logistics, and Informatics (SOLI), Dec 2021

Bib

@inproceedings{istiaque2021cybersecurity,
  title = {Artificial Intelligence Based Cybersecurity: Two-Step Suitability Test},
  author = {Istiaque, Sajjad Waheed Shah Md and Tahmid, Md Toki and Khan, Asif Iqbal and Hassan, Zaber Al},
  booktitle = {IEEE International Conference on Service Operations and Logistics, and Informatics (SOLI)},
  year = {2021},
  month = dec,
}