We propose non-parametric estimators for the average run length (ARL) and average detection delay (ADD) in quickest changepoint detection (QCD) under finite and irregular sequence lengths. Although ARL and ADD are widely used as optimality criteria in theoretical and simulation studies, their application to real-world datasets is hindered by limited and irregular sequence lengths. To address this issue, we propose non-parametric estimators for the ARL and ADD, termed KM-ARL and KM-ADD, by drawing an analogy between QCD and survival analysis to model detection probabilities under sequence truncation. We derive estimation bias bounds and prove that they are asymptotically unbiased unless extrapolation is required. Experiments on simulated and real-world datasets demonstrate their practical utility, enhancing robustness against limited and irregular sequence lengths, improving interpretability, and facilitating empirical, intuitive model selection. Our Python code is provided at https://github.com/TaikiMiyagawa/Kaplan-Meier-Average-Run-Length, offering ready-to-use implementations for practitioners.

The ability to maintain and manipulate information over time is a fundamental aspect of living beings and Artificial Intelligence. While modern models have achieved remarkable success in tasks like natural language processing, evaluating the capacity of novel architectures to process sequential information remains computationally expensive and time-consuming. Testing a new architecture often requires scaling up to massive datasets and models, leading to vast computational costs and slow iteration cycles. In this paper, we propose CogScale, a benchmark of 14 scalable synthetic tasks designed to isolate and evaluate specific cognitive and memory abilities at different parametrizable scales. By providing a standardized, lightweight framework, CogScale allows researchers to rapidly validate architectural innovations before committing to large-scale training. To establish a solid baseline, we evaluate seven distinct architectures: Gated Recurrent Unit (GRU), Long Short-Term Memory (LSTM), xLSTM, Echo State Network (ESN), Mamba, Transformer Decoder, and Transformer Encoder-Decoder. These evaluations are conducted under strict parameter budgets (1k, 10k, and 100k) and across different difficulty levels and scales. Our results show that while classical RNNs and Echo State Networks excel at basic retention within strict parameter budgets, only attention mechanisms and modern state-space models consistently maintain high performance as reasoning complexity and task difficulty scale.

Similar to natural language models, researchers have proposed foundation models in genomics to learn generalizable features from unlabeled genome data that can then be fine-tuned for downstream tasks such as identifying regulatory elements. Due to the quadratic scaling of attention, previous Transformer-based genomic models have used 512 to 4k tokens as context (<0.001% of the human genome), significantly limiting the modeling of long-range interactions in DNA. In addition, these methods rely on tokenizers or fixed k-mers to aggregate meaningful DNA units, losing single nucleotide resolution (i.e. DNA "characters") where subtle genetic variations can completely alter protein function via single nucleotide polymorphisms (SNPs). Recently, Hyena, a large language model based on implicit convolutions was shown to match attention in quality while allowing longer context lengths and lower time complexity.

Proteomics is the interdisciplinary field focusing on the large-scale study of proteins. Proteins essentially organize and execute all functions within organisms. Today, the bottom-up analysis approach is the most commonly used workflow, where proteins are digested into peptides and subsequently analyzed using Tandem Mass Spectrometry (MS/MS). MS-based proteomics has transformed various fields in life sciences, such as drug discovery and biomarker identification. Today, proteomics is entering a phase where it is helpful for clinical decision-making. Computational methods are vital in turning large amounts of acquired raw MS data into information and, ultimately, knowledge.

We introduce new methods for 1) accelerating and 2) stabilizing training for large language-vision models.

We follow [21] and implement our image compression models as "VQGANs". More specifically, we use the official implementation provided at https://github.com/CompVis/ For FFHQ, we train such a compression model from scratch. See Tab. 4 for an overview. As some of the codebook entries remain unused after training, we shrink the codebook to its effective size when training a generative model on top of it.