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Paul Horton, Readings in Computational Biology 2024

Course Overview

Papers Presented

  • The Precision-Recall Plot is more Informative than the ROC when evaluating binary classifiers on Imbalanced Datasets
    Takaya Saito & Marc Rehmsmeier
    PLoS ONE, 10:(3), e0118432, 2015.
  • BasicVSR: The Search for Essential Components in Video Super-Resolution and Beyond
    Kelvin C.K. Chan, Xintao Wang, Ke Yu, Chao Dong, Chen Change Loy
    arXiv:2012.02181, 2021.
  • Is artificial data useful for biomedical natural language processing algorithms
    Zixu Wang, Julia Ive, Sumithra Velupillai & Lucia Specia
    Proceedings of the 18th BioNLP Workshop and Shared Task, 2019.
  • A linear space algorithm for computing maximal common subsequences
    Hirschberg, D. S.
    Communications of the ACM,, 18(6), 341–343, 1975.
  • Computing Longest Common Subsequence for Multiple Sequences
    Chinmay Bepery, Sk. Abdullah-Al-Mamum & M Sohel Rahman
    2nd International Conference on EICT, 2015.
  • Basic local alignment search tool
    Stephen F. Altschul, Warren Gish, Webb Miller, Eugene W. Myers & David Lipman
    Journal of molecular biology,215(3):403-10, 1990.
  • A Fast UPGMA Algorithm With Multiple Graphics Processing Units Using NCCL
    Guan-Jie Hua, Che-Lun Hung, Chun-Yuan Lin, Fu-Che Wu, Yu-Wei Chan & Chuan Yi Tang
    Evol Bioinform Online 13:1176934317734220, 2017.
  • nnU-Net: Self-adapting Framework for U-Net-Based Medical Image Segmentation
    Fabian Isensee, Paul F. Jaeger, Simon A. A. Kohl, Jens Petersen & Klaus H. Maier-Hein Nature Methods, 18, 203–211 2021.
  • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    Ben Langmead, Cole Trapnell, Mihai Pop & Steven L Salzberg
    Genome Biology, 10, R25. 2009.
  • Automatic Task-Level Thinking Steps Help Large Language Models for Challenging Classification Tasks
    Chunhui Du, Jidong Tian, Haoran Liao, Jindou Chen, Hao He & Yaohui Jin
    Conference on Empirical Methods in Natural Language Processing, 2023.
  • Scaling Vision Transformers to Gigapixel Images via Hierarchical Self-Supervised Learning
    Richard J. Chen, Chengkuan Chen, Yicong Li, Tiffany Y. Chen, Andrew D. Trister, Rahul G. Krishnan, Faisal Mahmood
    arXiv:2206.02647, 2022.
  • Sequence to Sequence Learning with Neural Networks
    Ilya Sutskever, Oriol Vinyals & Quoc V. Le
    Proceedings of the 27th International Conference on Neural Information Processing Systems, 2 3104–3112, 2014.
  • Language Models are Unsupervised Multitask Learners
    Alec Radford, Jeffrey Wu, Rewon Child, David Luan, Dario Amodei & Ilya Sutskever
    Preprint, 2019.
  • Deep Learning
    LeCun, Y., Bengio, Y. & Hinton, G.
    Nature, 521:436–444, 2015.
  • A Block-sorting Lossless Data Compression Algorithm
    Michael Burrow & David Wheeler
    Technical Report 124, Digital Equipment Corporation, SRC-RR-124, 1994
  • Massively Multilingual Sentence Embeddings for Zero-Shot Cross-Lingual Transfer and Beyond
    Mikel Artetxe & Holger Schwenk
    Transactions of the Association for Computational Linguistics, 7: 597–610, 2019.
  • The Paradoxical Success of Fuzzy Logic
    Charles Elkan
    Proc. AAAI'93, 1993.
  • Efficient Acceleration of the Pair-HMMs Forwarding Algorithms for GATK HaplotypeCaller on Graphics Processing Units
    Shanshan Ren, Koen Bertels & Zaid Al-Ars
    Evol Bioinform Online, 2018.
  • Neural Machine Translation by Jointly Learning to Align and Translate
    Dzmitry Bahdanau, Kyunghyun Cho & Yoshua Bengio
    Presented at ICLR 2015, arXiv:1409.0473, 2015.
  • GPU Accelerated API for Alignment of Genomes Sequencing Data
    Nauman Ahmed; Hamid Mushtaq; Koen Bertels; Zaid Al-Ars
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017.
  • Scaling accurate genetic variant discovery to tens of thousands of samples
    Ryan Poplin, Valentin Ruano-Rubio, Mark A. DePristo, ..., Eric Banks
    bioRxiv, doi:10.1101/201178, 2017.
  • Not All Demonstration Examples are Equally Beneficial
    Zhe Yang, Damai Dai, Peiyi Wang, and Zhifang Sui
    Findings of the Association for Computational Linguistics: EMNLP, 13209–13221, 2023.
  • Memorizing Normality to Detect Anomaly: Memory-augmented Deep Autoencoder for Unsupervised Anomaly Detection
    Dong Gong, ..., Anton van den Hengel
    Presented at ICCV 2019, arXiv:1904.02639v2, 2019.
  • BioREx: Improving biomedical relation extraction by leverage heterogeneous datasets
    Po-Ting Lai, Chih-Hsuan Wei, Ling Luo, Qingyu Chen, & Zhiyong Lua
    arXiv:2306.11189v1, 2019.
  • LOTUS: A single- and multitask machine-learning algorithm for the prediction of cancer driver genes
    Olivier Collier, Véronique Stoven, Jean-Philippe Vert
    PLoS Computational Biology, 15(9):e1007381, 2019.
  • Attention Is All You Need
    Ashish Vaswani, Noam Shazeer, Niki Parmar,..., Illia, Polosukhin
    Advances in Neural Information Processing Systems (NIPS), 30, 2017.
  • An Interpretable Neuro-Symbolic Reasoning Framework for Task-Oriented Dialogue Generation
    Shiquan Yang, Rui Zhang, Sarah M. Erfani, Jey Han Lau
    Association for Computational Linguistics (ACL) (1):4918-4935, 2022.
  • RoBERTa: A Robustly Optimized BERT Pretraining Approach
    Yinhan Liu, Myle Ott, Naman Goyal, ..., Veselin Stoyanov
    arXiv:1907.11692, 2019.
  • ImageNet Classification with Deep Convolutional Neural Networks
    Alex Krizhevsky, Ilya Sutskever, Geoffrey E. Hinton
    Advances in Neural Information Processing Systems 25 (NIPS), 2012.
  • AI and Memory Wall
    Amir Gholami, Zhewei Yao, Sehoon Kim, Coleman Hooper, Michael W. Mahoney, Kurt Keutzer
    IEEE Micro Journal, arXiv:2403.14123, 2024.
  • Improved GPU Implementation of the Pair-HMM Forward Algorithm
    Enliang Li, Subho S. Banerjee, Sitao Huang, Ravishankar K. Iyer, Deming Chen
    2021 IEEE 39th International Conference on Computer Design (ICCD) 2021.
  • Chaos Engineering
    Ali Basiri, Niosha Behnam, Ruud de Rooij, Lorin Hochstein, Luke Kosewski, Justin Reynolds & Casey Rosenthal
    IEEE Software, 33(3), 2016.
  • Distributed Cache Reduction Approach to DNA sequencing using a greedy algorithm for the shortest common superstring
    Ali Khalid, Anthony Enem & Eduardo Colmenares
    International Conference on Computational Science and Computational Intelligence (CSCI), 2018.
  • PLINK: A tool set for whole-genome association and population-based linkage analyses
    Shaun Purcell, Benjamin Neale, Kathe Todd-Brown, ..., Pak C. Sham
    American Journal of Human Genetics, 81(3), 559–575, 2007.
  • One Cannot Stand for Everyone! Leveraging Multiple User Simulators
    Yajiao Liu, Xin Jiang, Yichun Yin, Yasheng Wang, Fei Mi, Qun Liu, Xiang Wan, Benyou Wang
    61st Annual Meeting of the Association for Computational Linguistics, 1, 2023.
  • Applying hidden Markov models to keystroke pattern analysis for password verification
    W. Chen; W. Chang
    IEEE International Conference on Information Reuse and Integration, 2004.
  • MitoFates: Improved Prediction of Mitochondrial Targeting Sequences and Their Cleavage Sites
    Yoshinori Fukasawa, Junko Tsuji, Szu-Chin Fu, Kentaro Tomii, Paul Horton, Kenichiro Imai
    Mol Cell Proteomics, 14(4):1113-26, 2015.
  • A Hybrid Ensemble Learning Model for Short-Term Solar Irradiance Forecasting Using Historical Observations and Sky Images
    Zhongju Wang, Long Wang, Chao Huang & Xiong Luo
    IEEE/IAS Industrial and Commercial Power System Asia (I&CPS Asia), 2021.
  • Self-RAG: Learning to Retrieve, Generate, and Critique through Self-Reflection
    Akari Asai, Zeqiu Wu, Yizhong Wang, Avirup Sil, Hannaneh Hajishirzi
    arXiv:2310.11511, 2023.
  • Translating Hanja Historical Documents to Contemporary Korea and English
    Juhee Son, Jiho Jin, Haneul Yoo, JinYeong Bak, Kyunghyun Cho & Alice Oh
    Findings of the Association for Computational Linguistics: EMNLP, 1260–1272, 2022.
  • Defending Jailbreak Prompts via In-Context Adversarial Game
    Yujun Zhou, Yufei Han, Haomin Zhuang, Taicheng Guo, Kehan Guo, Zhenwen Liang, Hongyan Bao & Xiangliang Zhang
    arXiv:2402.13148, 2024.
  • Deep Residual Learning for Image Recognition
    Kaiming He, Xiangyu Zhang, Shaoqing Ren & Jian Sun
    arXiv:1512.03385, 2015.
  • Earliest Eligible Virtual Deadline First: A Flexible and Accurate Mechanism for Proportional Share Resource Allocation
    Ion Stoica, Hussein Abdel-Wahab
    Technical Report, 1995.
  • Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion
    Martin Christen Frølund Thomsen & Morten Nielsen
    Nucleic Acids Res. 40(Web Server issue):W281–287, 2012.
  • Parallel algorithm for indexing large DNA sequences using MapReduce on Hadoop
    F Kaniwa, O Dinakenyane & VM Kuthadi
    IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2017.
  • UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy
    Tom Smith, Andreas Heger & Ian Sudbery
    Genome Research, 27(3):491-499, 2017.
  • Cognitive Reframing of Negative Thoughts through Human-Language Model Interaction
    Ashish Sharma, Kevin Rushton, Inna Lin, David Wadden, Khendra Lucas, Adam Miner, Theresa Nguyen, Tim Althoff
    61st Annual Meeting of the Association for Computational Linguistics, 1, 2023.
  • Accelerating Genotyping Improving the performance of Masked PanGenie
    Hartmut Häntze & Paul Horton
    Bioinformatics, 39(Suppl 1):i213–221, 2023.
  • MedSAM: Segment anything in medical images
    Ma, J., He, Y., Li, F. et al.
    Nature Communications, 15654, 2024.
  • How to apply de Bruijn graphs to genome assembly
    Compeau, P., Pevzner, P. & Tesler, G.
    Nat Biotechnol 29, 987–991, 2011.
  • PROTLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training
    Le Zhuo, ..., Wentao Zhang
    Proceedings of the ACL, 2024.
  • Accurate brain tumor detection using deep convolutional neural network Md. Saikat Islam Khan, ..., Iman Dehzangig
    Comput Struct Biotechnol J. 20:4733–4745, 2022.
  • Seq2Image: Sequence Analysis using Visualization and Deep Convolution Neural Network
    Neda Tavakoli
    Annual International Computer Software and Applications Conference, 2020.
  • Development and Validation of a Deep Learning Algorithm for Detection of Diabetic Retinopathy in Retinal Fundus Photographs
    Varun Gulshan, ..., Dale R Webster
    JAMA, 316(22):2402-2410, 2016.