Genomics and Phylogenetic Studies

Latest papers

• string2string Studio: An Interactive, In-Browser Platform for String-to-String Algorithms

  Mirac Suzgun, James Zou, Stuart M. Shieber, Dan Jurafsky · 5 August 2026

  We present string2string Studio, an interactive in-browser platform for string-to-string analysis across natural language processing, computational biology, and the digital humanities. The system integrates six main modules (alignment, distance, similarity, search, generation metrics, and BLAST homo…

• Evolutionary Curriculum Learning Improves Biological Sequence Modeling

  Richard Zhu, Kento Nishi · 4 August 2026

  Variational autoencoders (VAEs) trained on multiple sequence alignments (MSAs) have emerged as powerful generative models for biological sequences, with applications ranging from disease variant prediction to functional RNA design. However, standard biological VAE training treats all sequences as ex…

• Approximating SPR Distance Between Phylogenetic Trees with Graph Neural Networks

  Renata Martins Castanheira, Miguel Bugalho, C\'atia Vaz · 22 July 2026

  Comparing phylogenetic tree topologies is essential for understanding epidemic dynamics, yet biologically meaningful distances such as the Subtree Prune and Regraft (SPR) distance are NP-hard to compute and intractable on large datasets. We investigate whether a Graph Neural Network (GNN) can approx…

• Morphology-Aware Multimodal Representation Learning for Insect Phylogenetic Reconstruction

  Zixuan Liu, Kaijie Yu, Chun He, Xiaoxu Cai, Xinhai Ye, Haishuai Wang, Gongyin Ye, Jiajun Bu · 23 June 2026

  Morphological traits provide important evidence for phylogenetic reconstruction and evolutionary relationship analysis. Recent image-based approaches have introduced deep learning, particularly convolutional models, to derive morphological features from specimen images, but these methods generally r…

• Flexible Flows for Biological Sequence Design

  Yogesh Verma, Dani Korpela, Harri L\"ahdesm\"aki, Vikas Garg · 10 June 2026

  Designing functional biological sequences requires navigating vast discrete spaces under strict evolutionary and biophysical constraints. Discrete Flow Matching (DFM) offers a generative framework over such spaces, but existing approaches rely on biologically uninformative couplings and offer limite…

• CRANE: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models

  Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Ernest Zhang, Can Firtina · 21 May 2026

  Nanopore sequencing can read substantially longer sequences of nucleic acid molecules, called reads, than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the raw electrical signal reads that nanopore sequencing generates…

• Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models

  Weimin Wu, Xuefeng Song, Yibo Wen, Qinjie Lin, Zhihan Zhou, Jerry Yao-Chieh Hu, Zhong Wang, Han Liu · 18 May 2026

  We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection, model tuning, inference, benchmarking, and interpretability.…

• Tree-Conditioned Edit Flows for Ancestral Sequence Reconstruction

  Emil Sharafutdinov, Ingemar Andr\'e · 7 May 2026

  Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely independently and handle insertions and deletions only weakl…

• CRC-Screen: Certified DNA-Synthesis Hazard Screening Under Taxonomic Shift

  Najmul Hasan · 4 May 2026

  DNA-synthesis providers screen incoming orders by searching the requested sequence against curated hazard lists. We show that this baseline collapses to a 100% false-flag rate when the hazardous sequence comes from a taxonomic family absent from the reference set: under Conformal Risk Control's cert…

• CERN: Correcting Errors in Raw Nanopore Signals Using Hidden Markov Models

  Simon Ambrozak, Ulysse McConnell, Bhargav Srinivasan, Burak Ozkan, Can Firtina · 24 March 2026

  Nanopore sequencing can read substantially longer sequences of nucleic acid molecules than other sequencing methods, which has led to advances in genomic analysis such as the gapless human genome assembly. By analyzing the raw electrical signal reads that nanopore sequencing generates from molecules…

• SDSR: A Spectral Divide-and-Conquer Approach for Species Tree Reconstruction

  Ortal Reshef (Hebrew University of Jerusalem), Ofer Glassman (Weizmann Institute of Science), Or Zuk (Hebrew University of Jerusalem), Yariv Aizenbud (Tel Aviv University), Boaz Nadler (Weizmann Institute of Science), Ariel Jaffe (Hebrew University of Jerusalem) · 12 March 2026

  Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance between the evolutionary history of individual genes and that…

• LLM DNA: Tracing Model Evolution via Functional Representations

  Zhaomin Wu, Haodong Zhao, Ziyang Wang, Jizhou Guo, Qian Wang, Bingsheng He · 17 February 2026

  The explosive growth of large language models (LLMs) has created a vast but opaque landscape: millions of models exist, yet their evolutionary relationships through fine-tuning, distillation, or adaptation are often undocumented or unclear, complicating LLM management. Existing methods are limited b…

• A Comparison of Polynomial-Based Tree Clustering Methods

  Pengyu Liu, Mariel V\'azquez, Nata\v{s}a Jonoska · 22 January 2026

  Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of non-coding RNAs. Recent developments in sequencing technology and …

• DNATokenizer: A GPU-First Byte-to-Identifier Tokenizer for High-Throughput DNA Language Models

  Eliatan Niktab, Hardip Patel · 12 January 2026

  Tokenization sits at the boundary between high-throughput genomic input and GPU compute, posing challenges in both algorithm design and system throughput. Overlapping k-mer tokenization can introduce information leakage under masked language modeling (MLM) and may degrade downstream accuracy. Single…

• BarcodeMamba+: Advancing State-Space Models for Fungal Biodiversity Research

  Tiancheng Gao, Scott C. Lowe, Brendan Furneaux, Angel X Chang, Graham W. Taylor · 19 December 2025

  Accurate taxonomic classification from DNA barcodes is a cornerstone of global biodiversity monitoring, yet fungi present extreme challenges due to sparse labelling and long-tailed taxa distributions. Conventional supervised learning methods often falter in this domain, struggling to generalize to u…

• Murmur2Vec: A Hashing Based Solution For Embedding Generation Of COVID-19 Spike Sequences

  Sarwan Ali, Taslim Murad · 12 December 2025

  Early detection and characterization of coronavirus disease (COVID-19), caused by SARS-CoV-2, remain critical for effective clinical response and public-health planning. The global availability of large-scale viral sequence data presents significant opportunities for computational analysis; however,…

• On the Approximation of Phylogenetic Distance Functions by Artificial Neural Networks

  Benjamin K. Rosenzweig, Matthew W. Hahn · 3 December 2025

  Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by Bayesian and maximum likelihood search procedures based on compl…

• AGNES: Adaptive Graph Neural Network and Dynamic Programming Hybrid Framework for Real-Time Nanopore Seed Chaining

  Jahidul Arafat, Sanjaya Poudel · 5 November 2025

  Nanopore sequencing enables real-time long-read DNA sequencing with reads exceeding 10 kilobases, but inherent error rates of 12-15 percent present significant computational challenges for read alignment. The critical seed chaining step must connect exact k-mer matches between reads and reference ge…

• JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model

  Qihao Duan, Bingding Huang, Zhenqiao Song, Irina Lehmann, Lei Gu, Roland Eils, Benjamin Wild · 29 October 2025

  Large language models (LLMs) have revolutionized natural language processing and are increasingly applied to other sequential data types, including genetic sequences. However, adapting LLMs to genomics presents significant challenges. Capturing complex genomic interactions requires modeling long-ran…