Related papers: Y-Trim: Evidence-gated Adaptase tail trimming for …
Btrim is a fast and lightweight software to trim adapters and low quality regions in reads from ultra high-throughput next-generation sequencing machines. It also can reliably identify barcodes and assign the reads to the original samples.…
DNA-based data storage systems face practical challenges due to the high cost of DNA synthesis. A strategy to address the problem entails encoding data via topological modifications of the DNA sugar-phosphate backbone. The DNA Punchcards…
Syntax-guided synthesis (SyGuS) is a recently proposed framework for program synthesis problems. The SyGuS problem is to find an expression or program generated by a given grammar that meets a correctness specification. Correctness…
Text-to-image flow matching transformers degrade sharply in long-tail settings: tail-class outputs collapse in fidelity and diversity, limiting their value as synthetic augmentation for rare conditions. We trace this to low head-versus-tail…
We propose a novel approach for detecting change points in high-dimensional linear regression models. Unlike previous research that relied on strict Gaussian/sub-Gaussian error assumptions and had prior knowledge of change points, we…
This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…
Supervised learning is well-known to fail at generalization under distribution shifts. In typical clinical settings, the source data is inaccessible and the target distribution is represented with a handful of samples: adaptation can only…
We study long-context balanced entropic optimal transport (OT) attention on TPU hardware through a stopped-base, fixed-depth tail-refinement surrogate. After a stopped $T$-step Sinkhorn solve, we unroll a short refinement tail and…
Discrete biological sequence optimization requires iterative refinement under strict syntactic constraints. Diffusion models offer progressive refinement but do not naturally expose controllable discrete edit operations, while…
Sequence-directed assembly processes - such as protein folding - allow the assembly of a large number of structures with high accuracy from only a small handful of fundamental building blocks. We aim to explore how efficiently sequence…
Reliable brain tumor segmentation in MRI is indispensable for treatment planning and outcome monitoring, yet models trained on curated benchmarks often fail under domain shifts arising from scanner and protocol variability as well as…
Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Inferring spatially resolved gene expression from histology images offers a cost-effective complement to spatial transcriptomics (ST). However, existing methods reduce this task to a simple morphology-to-expression mapping, where visual…
Tail-biting convolutional codes extend the classical zero-termination convolutional codes: Both encoding schemes force the equality of start and end states, but under the tail-biting each state is a valid termination. This paper proposes a…
Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…
Test-Time Adaptation aims to adapt source domain model to testing data at inference stage with success demonstrated in adapting to unseen corruptions. However, these attempts may fail under more challenging real-world scenarios. Existing…
Computational cytology faces two major challenges: i) instance-level labels are unreliable and prohibitively costly to obtain, ii) witness rates are extremely low. We propose SLAM-AGS, a Slide-Label-Aware Multitask pretraining framework…
Test-Time Adaptation (TTA) offers a practical solution for deploying image segmentation models under domain shift without accessing source data or retraining. Among existing TTA strategies, pseudo-label-based methods have shown promising…
We study multivariate tail-dependence compatibility for complete and partial signed tail families, treating lower-tail, upper-tail, and mixed configurations in one geometric witness representation indexed by active coordinate sets and sign…