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Jan 13

Binary BPE: A Family of Cross-Platform Tokenizers for Binary Analysis

Sequence models for binary analysis are bottlenecked by byte-level tokenization: raw bytes waste precious context window capacity for transformers and other neural network architectures, and many existing text-oriented tokenizers fail on arbitrary 0x00--0xFF sequences. To address this issue, we introduce the Binary BPE tokenizer family, a set of cross-platform Byte Pair Encoding (BPE) tokenizers for executables trained on a large corpus of binaries spanning multiple platforms, architectures, and operating systems, including Linux, Windows, macOS, Android, and malware sources. We release trained tokenizers with vocabularies of 4K, 8K, 16K, 32K, and 64K tokens, enabling both systematic scaling studies and practical deployment from resource-constrained edge devices to high-throughput datacenters. These tokenizers discover interpretable patterns (ELF/PE headers, instruction sequences, cross-platform strings) while yielding multi-byte compression per token. On representative uncompressed executables (e.g., ELF/PE/Mach-O rather than compressed APKs), the Binary BPE tokenizers typically allow for roughly 2-3x more binary content per fixed-length transformer context window than raw bytes, enabling more efficient research and practical deployment for content identification, malware detection, reverse engineering, and optimization. We release the trained Binary BPE tokenizers on HuggingFace, providing a drop-in, open-source foundation for binary-focused language models and context-efficient agentic tools.

  • 1 authors
·
Nov 14, 2025

Assemblage: Automatic Binary Dataset Construction for Machine Learning

Binary code is pervasive, and binary analysis is a key task in reverse engineering, malware classification, and vulnerability discovery. Unfortunately, while there exist large corpuses of malicious binaries, obtaining high-quality corpuses of benign binaries for modern systems has proven challenging (e.g., due to licensing issues). Consequently, machine learning based pipelines for binary analysis utilize either costly commercial corpuses (e.g., VirusTotal) or open-source binaries (e.g., coreutils) available in limited quantities. To address these issues, we present Assemblage: an extensible cloud-based distributed system that crawls, configures, and builds Windows PE binaries to obtain high-quality binary corpuses suitable for training state-of-the-art models in binary analysis. We have run Assemblage on AWS over the past year, producing 890k Windows PE and 428k Linux ELF binaries across 29 configurations. Assemblage is designed to be both reproducible and extensible, enabling users to publish "recipes" for their datasets, and facilitating the extraction of a wide array of features. We evaluated Assemblage by using its data to train modern learning-based pipelines for compiler provenance and binary function similarity. Our results illustrate the practical need for robust corpuses of high-quality Windows PE binaries in training modern learning-based binary analyses. Assemblage can be downloaded from https://assemblage-dataset.net

  • 8 authors
·
May 7, 2024

How Far Have We Gone in Stripped Binary Code Understanding Using Large Language Models

Binary code analysis plays a pivotal role in various software security applications, such as software maintenance, malware detection, software vulnerability discovery, patch analysis, etc. However, unlike source code, understanding binary code is challenging for reverse engineers due to the absence of semantic information. Therefore, automated tools are needed to assist human players in interpreting binary code. In recent years, two groups of technologies have shown promising prospects: (1) Deep learning-based technologies have demonstrated competitive results in tasks related to binary code understanding, furthermore, (2) Large Language Models (LLMs) have been extensively pre-trained at the source-code level for tasks such as code understanding and generation. This makes participants wonder about the ability of LLMs in binary code understanding. In this work, we propose a benchmark to evaluate the effectiveness of LLMs in real-world reverse engineering scenarios. The benchmark covers two key binary code understanding tasks, including function name recovery and binary code summarization. We gain valuable insights into their capabilities and limitations through extensive evaluations of popular LLMs using our benchmark. Our evaluations reveal that existing LLMs can understand binary code to a certain extent, thereby improving the efficiency of binary code analysis. Our results highlight the great potential of the LLMs in advancing the field of binary code understanding.

  • 9 authors
·
Apr 15, 2024

BanglishRev: A Large-Scale Bangla-English and Code-mixed Dataset of Product Reviews in E-Commerce

This work presents the BanglishRev Dataset, the largest e-commerce product review dataset to date for reviews written in Bengali, English, a mixture of both and Banglish, Bengali words written with English alphabets. The dataset comprises of 1.74 million written reviews from 3.2 million ratings information collected from a total of 128k products being sold in online e-commerce platforms targeting the Bengali population. It includes an extensive array of related metadata for each of the reviews including the rating given by the reviewer, date the review was posted and date of purchase, number of likes, dislikes, response from the seller, images associated with the review etc. With sentiment analysis being the most prominent usage of review datasets, experimentation with a binary sentiment analysis model with the review rating serving as an indicator of positive or negative sentiment was conducted to evaluate the effectiveness of the large amount of data presented in BanglishRev for sentiment analysis tasks. A BanglishBERT model is trained on the data from BanglishRev with reviews being considered labeled positive if the rating is greater than 3 and negative if the rating is less than or equal to 3. The model is evaluated by being testing against a previously published manually annotated dataset for e-commerce reviews written in a mixture of Bangla, English and Banglish. The experimental model achieved an exceptional accuracy of 94\% and F1 score of 0.94, demonstrating the dataset's efficacy for sentiment analysis. Some of the intriguing patterns and observations seen within the dataset and future research directions where the dataset can be utilized is also discussed and explored. The dataset can be accessed through https://huggingface.co/datasets/BanglishRev/bangla-english-and-code-mixed-ecommerce-review-dataset.

  • 4 authors
·
Dec 17, 2024

Binary Classifier Optimization for Large Language Model Alignment

Aligning Large Language Models (LLMs) to human preferences through preference optimization has been crucial but labor-intensive, necessitating for each prompt a comparison of both a chosen and a rejected text completion by evaluators. Recently, Kahneman-Tversky Optimization (KTO) has demonstrated that LLMs can be aligned using merely binary "thumbs-up" or "thumbs-down" signals on each prompt-completion pair. In this paper, we present theoretical foundations to explain the successful alignment achieved through these binary signals. Our analysis uncovers a new perspective: optimizing a binary classifier, whose logit is a reward, implicitly induces minimizing the Direct Preference Optimization (DPO) loss. In the process of this discovery, we identified two techniques for effective alignment: reward shift and underlying distribution matching. Consequently, we propose a new algorithm, Binary Classifier Optimization, that integrates the techniques. We validate our methodology in two settings: first, on a paired preference dataset, where our method performs on par with DPO and KTO; and second, on binary signal datasets simulating real-world conditions with divergent underlying distributions between thumbs-up and thumbs-down data. Our model consistently demonstrates effective and robust alignment across two base LLMs and three different binary signal datasets, showcasing the strength of our approach to learning from binary feedback.

  • 4 authors
·
Apr 6, 2024

Beyond Binary: Towards Fine-Grained LLM-Generated Text Detection via Role Recognition and Involvement Measurement

The rapid development of large language models (LLMs), like ChatGPT, has resulted in the widespread presence of LLM-generated content on social media platforms, raising concerns about misinformation, data biases, and privacy violations, which can undermine trust in online discourse. While detecting LLM-generated content is crucial for mitigating these risks, current methods often focus on binary classification, failing to address the complexities of real-world scenarios like human-LLM collaboration. To move beyond binary classification and address these challenges, we propose a new paradigm for detecting LLM-generated content. This approach introduces two novel tasks: LLM Role Recognition (LLM-RR), a multi-class classification task that identifies specific roles of LLM in content generation, and LLM Influence Measurement (LLM-IM), a regression task that quantifies the extent of LLM involvement in content creation. To support these tasks, we propose LLMDetect, a benchmark designed to evaluate detectors' performance on these new tasks. LLMDetect includes the Hybrid News Detection Corpus (HNDC) for training detectors, as well as DetectEval, a comprehensive evaluation suite that considers five distinct cross-context variations and two multi-intensity variations within the same LLM role. This allows for a thorough assessment of detectors' generalization and robustness across diverse contexts. Our empirical validation of 10 baseline detection methods demonstrates that fine-tuned PLM-based models consistently outperform others on both tasks, while advanced LLMs face challenges in accurately detecting their own generated content. Our experimental results and analysis offer insights for developing more effective detection models for LLM-generated content. This research enhances the understanding of LLM-generated content and establishes a foundation for more nuanced detection methodologies.

  • 5 authors
·
Oct 18, 2024

Efficient Massive Black Hole Binary parameter estimation for LISA using Sequential Neural Likelihood

The inspiral, merger, and ringdown of Massive Black Hole Binaries (MBHBs) is one the main sources of Gravitational Waves (GWs) for the future Laser Interferometer Space Antenna (LISA), an ESA-led mission in the implementation phase. It is expected that LISA will detect these systems throughout the entire observable universe. Robust and efficient data analysis algorithms are necessary to detect and estimate physical parameters for these systems. In this work, we explore the application of Sequential Neural Likelihood, a simulation-based inference algorithm, to detect and characterize MBHB GW signals in synthetic LISA data. We describe in detail the different elements of the method, their performance and possible alternatives that can be used to enhance the performance. Instead of sampling from the conventional likelihood function, which requires a forward simulation for each evaluation, this method constructs a surrogate likelihood that is ultimately described by a neural network trained from a dataset of simulations of the MBHB signals and noise. One important advantage of this method is that, given that the likelihood is independent of the priors, we can iteratively train models that target specific observations in a fraction of the time and computational cost that other traditional and machine learning-based strategies would require. Because of the iterative nature of the method, we are able to train models to obtain qualitatively similar posteriors with less than 2\% of the simulator calls that Markov Chain Monte Carlo methods would require. We compare these posteriors with those obtained from Markov Chain Monte Carlo techniques and discuss the differences that appear, in particular in relation with the important role that data compression has in the modular implementation of the method that we present. We also discuss different strategies to improve the performance of the algorithms.

  • 2 authors
·
Jun 1, 2024

A Multifaceted Analysis of Negative Bias in Large Language Models through the Lens of Parametric Knowledge

Negative bias refers to the tendency of large language models (LLMs) to excessively generate negative responses in binary decision tasks (e.g., yes-no question answering). Previous research has focused on detecting and addressing negative attention heads that induce negative bias. However, the underlying detailed factors influencing negative bias remain underexplored. In this paper, we demonstrate that LLMs exhibit format-level negative bias, meaning the prompt format more influences their responses than the semantics of the negative response. For the fine-grained study of the negative bias, we introduce a pipeline for constructing the evaluation set, which systematically categorizes the dataset into three subsets based on the model's parametric knowledge: correct, incorrect, and insufficient relevant knowledge. Through analysis of this evaluation set, we identify a shortcut behavior in which models tend to generate negative responses when they lack sufficient knowledge to answer a yes-no question, leading to negative bias. We further examine how negative bias changes under various prompting scenarios related to parametric knowledge. We observe that providing relevant context and offering an "I don't know" option generally reduces negative bias, whereas chain-of-thought prompting tends to amplify the bias. Finally, we demonstrate that the degree of negative bias can vary depending on the type of prompt, which influences the direction of the response. Our work reveals the various factors that influence negative bias, providing critical insights for mitigating it in LLMs.

  • 3 authors
·
Nov 13, 2025

Scaling Particle Collision Data Analysis

For decades, researchers have developed task-specific models to address scientific challenges across diverse disciplines. Recently, large language models (LLMs) have shown enormous capabilities in handling general tasks; however, these models encounter difficulties in addressing real-world scientific problems, particularly in domains involving large-scale numerical data analysis, such as experimental high energy physics. This limitation is primarily due to BPE tokenization's inefficacy with numerical data. In this paper, we propose a task-agnostic architecture, BBT-Neutron, which employs a binary tokenization method to facilitate pretraining on a mixture of textual and large-scale numerical experimental data. We demonstrate the application of BBT-Neutron to Jet Origin Identification (JoI), a critical categorization challenge in high-energy physics that distinguishes jets originating from various quarks or gluons. Our results indicate that BBT-Neutron achieves comparable performance to state-of-the-art task-specific JoI models. Furthermore, we examine the scaling behavior of BBT-Neutron's performance with increasing data volume, suggesting the potential for BBT-Neutron to serve as a foundational model for particle physics data analysis, with possible extensions to a broad spectrum of scientific computing applications for Big Science experiments, industrial manufacturing and spacial computing. The project code is available at https://github.com/supersymmetry-technologies/bbt-neutron.

  • 13 authors
·
Nov 28, 2024

The first measurements of carbon isotopic ratios in post-RGB stars: SZ Mon and DF Cyg. E-iSpec: A spectral analysis tool to derive elemental abundances and isotopic ratios for evolved stars

Dusty post-red giant branch (post-RGB) stars are low- and intermediate-mass stars where the RGB evolution was prematurely terminated by a poorly understood binary interaction. These binary stars are considered to be low-luminosity analogues of post-asymptotic giant branch (post-AGB) binary stars. In this study, we investigated the chemical composition of two dusty post-RGB binary stars, SZ Mon and DF Cyg, using multi-wavelength spectroscopic data from HERMES/Mercator (optical) and the APOGEE survey (near-infrared). Owing to challenges posed by existing spectral analysis tools for the study of evolved stars with complex atmospheres, we developed E-iSpec: a dedicated spectral analysis tool for evolved stars, to consistently determine atmospheric parameters, elemental abundances, and carbon isotopic ratios. Our abundance analysis revealed that observed depletion patterns and estimated depletion efficiencies resemble those found in post-AGB binary stars. However, the onset of chemical depletion in post-RGB targets occurs at higher condensation temperatures (T_{rm turn-off, post-RGB}approx1400 K), than in most post-AGB stars (T_{rm turn-off, post-AGB}approx1100 K). Additionally, our study resulted in the first estimates of carbon isotopic ratios for post-RGB stars (^{12}C/^{13}C_{rm SZ Mon}=8pm4, ^{12}C/^{13}C_{rm DF Cyg}=12pm3). We found that the observationally derived CNO abundances and the carbon isotopic ratios of our post-RGB binary targets are in good agreement with theoretical predictions from the ATON single star evolutionary models involving first dredge-up and moderately-deep extra mixing. This agreement emphasises that in post-RGB binary targets, the observed CNO abundances reflect the chemical composition expected from single star nucleosynthesis (i.e., convective and non-convective mixing processes) occurring during the RGB phase before it is terminated.

  • 7 authors
·
Mar 14, 2024

A Three-Phase Analysis of Synergistic Effects During Co-pyrolysis of Algae and Wood for Biochar Yield Using Machine Learning

Pyrolysis techniques have served to be a groundbreaking technique for effectively utilising natural and man-made biomass products like plastics, wood, crop residue, fruit peels etc. Recent advancements have shown a greater yield of essential products like biochar, bio-oil and other non-condensable gases by blending different biomasses in a certain ratio. This synergy effect of combining two pyrolytic raw materials i.e co-pyrolysis of algae and wood biomass has been systematically studied and grouped into 3 phases in this research paper-kinetic analysis of co-pyrolysis, correlation among proximate and ultimate analysis with bio-char yield and lastly grouping of different weight ratios based on biochar yield up to a certain percentage. Different ML and DL algorithms have been utilized for regression and classification techniques to give a comprehensive overview of the effect of the synergy of two different biomass materials on biochar yield. For the first phase, the best prediction of biochar yield was obtained by using a decision tree regressor with a perfect MSE score of 0.00, followed by a gradient-boosting regressor. The second phase was analyzed using both ML and DL techniques. Within ML, SVR proved to be the most convenient model with an accuracy score of 0.972 with DNN employed for deep learning technique. Finally, for the third phase, binary classification was applied to biochar yield with and without heating rate for biochar yield percentage above and below 40%. The best technique for ML was Support Vector followed by Random forest while ANN was the most suitable Deep Learning Technique.

  • 2 authors
·
May 20, 2024

Multi-Step Knowledge Interaction Analysis via Rank-2 Subspace Disentanglement

Natural Language Explanations (NLEs) describe how Large Language Models (LLMs) make decisions, drawing on both external Context Knowledge (CK) and Parametric Knowledge (PK) stored in model weights. Understanding their interaction is key to assessing the grounding of NLEs, yet it remains underexplored. Prior work has largely examined only single-step generation, typically the final answer, and has modelled PK and CK interaction only as a binary choice in a rank-1 subspace. This overlooks richer forms of interaction, such as complementary or supportive knowledge. We propose a novel rank-2 projection subspace that disentangles PK and CK contributions more accurately and use it for the first multi-step analysis of knowledge interactions across longer NLE sequences. Experiments on four QA datasets and three open-weight instruction-tuned LLMs show that diverse knowledge interactions are poorly represented in a rank-1 subspace but are effectively captured in our rank-2 formulation. Our multi-step analysis reveals that hallucinated NLEs align strongly with the PK direction, context-faithful ones balance PK and CK, and Chain-of-Thought prompting for NLEs shifts generated NLEs toward CK by reducing PK reliance. This work provides the first framework for systematic studies of multi-step knowledge interactions in LLMs through a richer rank-2 subspace disentanglement. Code and data: https://github.com/copenlu/pk-ck-knowledge-disentanglement.

  • 3 authors
·
Nov 3, 2025 1

DCT-HistoTransformer: Efficient Lightweight Vision Transformer with DCT Integration for histopathological image analysis

In recent years, the integration of advanced imaging techniques and deep learning methods has significantly advanced computer-aided diagnosis (CAD) systems for breast cancer detection and classification. Transformers, which have shown great promise in computer vision, are now being applied to medical image analysis. However, their application to histopathological images presents challenges due to the need for extensive manual annotations of whole-slide images (WSIs), as these models require large amounts of data to work effectively, which is costly and time-consuming. Furthermore, the quadratic computational cost of Vision Transformers (ViTs) is particularly prohibitive for large, high-resolution histopathological images, especially on edge devices with limited computational resources. In this study, we introduce a novel lightweight breast cancer classification approach using transformers that operates effectively without large datasets. By incorporating parallel processing pathways for Discrete Cosine Transform (DCT) Attention and MobileConv, we convert image data from the spatial domain to the frequency domain to utilize the benefits such as filtering out high frequencies in the image, which reduces computational cost. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets. Our proposed model achieves an accuracy of 96.00% pm 0.48% for binary classification and 87.85% pm 0.93% for multiclass classification, which is comparable to state-of-the-art models while significantly reducing computational costs. This demonstrates the potential of our approach to improve breast cancer classification in histopathological images, offering a more efficient solution with reduced reliance on extensive annotated datasets.

  • 4 authors
·
Oct 24, 2024

Phemenological Modelling of a Group of Eclipsing Binary Stars

Phenomenological modeling of variable stars allows determination of a set of the parameters, which are needed for classification in the "General Catalogue of Variable Stars" and similar catalogs. We apply a recent method NAV ("New Algol Variable") to eclipsing binary stars of different types. Although all periodic functions may be represented as Fourier series with an infinite number of coefficients, this is impossible for a finite number of the observations. Thus one may use a restricted Fourier series, i.e. a trigonometric polynomial (TP) of order s either for fitting the light curve, or to make a periodogram analysis. However, the number of parameters needed drastically increases with decreasing width of minimum. In the NAV algorithm, the special shape of minimum is used, so the number of parameters is limited to 10 (if the period and initial epoch are fixed) or 12 (not fixed). We illustrate the NAV method by application to a recently discovered Algol-type eclipsing variable 2MASS J11080308-6145589 (in the field of previously known variable star RS Car) and compare results to that obtained using the TP fits. For this system, the statistically optimal number of parameters is 44, but the fit is still worse than that of the NAV fit. Application to the system GSC 3692-00624 argues that the NAV fit is better than the TP one even for the case of EW-type stars with much wider eclipses. Model parameters are listed.

  • 3 authors
·
Sep 17, 2015

Can Mamba Learn In Context with Outliers? A Theoretical Generalization Analysis

The Mamba model has gained significant attention for its computational advantages over Transformer-based models, while achieving comparable performance across a wide range of language tasks. Like Transformers, Mamba exhibits in-context learning (ICL) capabilities, i.e., making predictions for new tasks based on a prompt containing input-label pairs and a query, without requiring fine-tuning. Despite its empirical success, the theoretical understanding of Mamba remains limited, largely due to the nonlinearity introduced by its gating mechanism. To the best of our knowledge, this paper presents the first theoretical analysis of the training dynamics of a one-layer Mamba model, which consists of a linear attention component followed by a nonlinear gating layer, and its ICL generalization on unseen binary classification tasks, even when the prompt includes additive outliers. Our analysis shows that Mamba leverages the linear attention layer to select informative context examples and uses the nonlinear gating layer to suppress the influence of outliers. By establishing and comparing to the analysis of linear Transformers under the same setting, we show that although Mamba may require more training iterations to converge, it maintains accurate predictions even when the proportion of outliers exceeds the threshold that a linear Transformer can tolerate. These theoretical findings are supported by empirical experiments.

  • 5 authors
·
Sep 30, 2025

Implementation of the rROF denoising method in the cWB pipeline for gravitational-wave data analysis

The data collected by the current network of gravitational-wave detectors are largely dominated by instrumental noise. Total variation methods based on L1-norm minimization have recently been proposed as a powerful technique for noise removal in gravitational-wave data. In particular, the regularized Rudin-Osher-Fatemi (rROF) model has proven effective to denoise signals embedded in either simulated Gaussian noise or actual detector noise. Importing the rROF model to existing search pipelines seems therefore worth considering. In this paper, we discuss the implementation of two variants of the rROF algorithm as two separate plug-ins of the coherent Wave Burst (cWB) pipeline designed to conduct searches of unmodelled gravitational-wave burst sources. The first approach is based on a single-step rROF method and the second one employs an iterative rROF procedure. Both approaches are calibrated using actual gravitational-wave events from the first three observing runs of the LIGO-Virgo-KAGRA collaboration, namely GW1501914, GW151226, GW170817, and GW190521, encompassing different types of compact binary coalescences. Our analysis shows that the iterative version of the rROF denoising algorithm implemented in the cWB pipeline effectively eliminates noise while preserving the waveform signals intact. Therefore, the combined approach yields higher signal-to-noise values than those computed by the cWB pipeline without the rROF denoising step. The incorporation of the iterative rROF algorithm in the cWB pipeline might hence impact the detectability capabilities of the pipeline along with the inference of source properties.

  • 6 authors
·
Feb 21, 2022

Enhancing Graph Representations with Neighborhood-Contextualized Message-Passing

Graph neural networks (GNNs) have become an indispensable tool for analyzing relational data. In the literature, classical GNNs may be classified into three variants: convolutional, attentional, and message-passing. While the standard message-passing variant is highly expressive, its typical pair-wise messages nevertheless only consider the features of the center node and each neighboring node individually. This design fails to incorporate the rich contextual information contained within the broader local neighborhood, potentially hindering its ability to learn complex relationships within the entire set of neighboring nodes. To address this limitation, this work first formalizes the concept of neighborhood-contextualization, rooted in a key property of the attentional variant. This then serves as the foundation for generalizing the message-passing variant to the proposed neighborhood-contextualized message-passing (NCMP) framework. To demonstrate its utility, a simple, practical, and efficient method to parametrize and operationalize NCMP is presented, leading to the development of the proposed Soft-Isomorphic Neighborhood-Contextualized Graph Convolution Network (SINC-GCN). A preliminary analysis on a synthetic binary node classification problem then underscores both the expressivity and efficiency of the proposed GNN architecture. Overall, the paper lays the foundation for the novel NCMP framework as a practical path toward further enhancing the graph representational power of classical GNNs.

  • 1 authors
·
Nov 14, 2025

Judging LLMs on a Simplex

Automated evaluation of free-form outputs from large language models (LLMs) is challenging because many distinct answers can be equally valid. A common practice is to use LLMs themselves as judges, but the theoretical properties of this approach are not yet well understood. We show that a geometric framework that represents both judges and candidates as points on a probability simplex can provide helpful insight on what is or is not identifiable using LLM judges. Our theoretical analysis uncovers a "phase transition" in ranking identifiability: for binary scoring systems, true rankings are identifiable even with weak judges under mild assumptions, while rankings become non-identifiable for three or more scoring levels even with infinite data, absent additional prior knowledge. This non-identifiability highlights how uncertainty in rankings stems from not only aleatoric uncertainty (i.e., inherent stochasticity in the data) but also epistemic uncertainty regarding which assumptions hold, an aspect that has received limited attention until now. To integrate both types of uncertainty, we use Bayesian inference to encode assumptions as priors and conduct sensitivity analysis of ranking estimates and credible intervals. Empirical evaluations across multiple benchmarks demonstrate that Bayesian inference yields more accurate rankings and substantially improves coverage rates. These results underscore the importance of taking a more holistic approach to uncertainty quantification when using LLMs as judges.

  • 4 authors
·
May 28, 2025

A Closer Look at AUROC and AUPRC under Class Imbalance

In machine learning (ML), a widespread adage is that the area under the precision-recall curve (AUPRC) is a superior metric for model comparison to the area under the receiver operating characteristic (AUROC) for binary classification tasks with class imbalance. This paper challenges this notion through novel mathematical analysis, illustrating that AUROC and AUPRC can be concisely related in probabilistic terms. We demonstrate that AUPRC, contrary to popular belief, is not superior in cases of class imbalance and might even be a harmful metric, given its inclination to unduly favor model improvements in subpopulations with more frequent positive labels. This bias can inadvertently heighten algorithmic disparities. Prompted by these insights, a thorough review of existing ML literature was conducted, utilizing large language models to analyze over 1.5 million papers from arXiv. Our investigation focused on the prevalence and substantiation of the purported AUPRC superiority. The results expose a significant deficit in empirical backing and a trend of misattributions that have fuelled the widespread acceptance of AUPRC's supposed advantages. Our findings represent a dual contribution: a significant technical advancement in understanding metric behaviors and a stark warning about unchecked assumptions in the ML community. All experiments are accessible at https://github.com/mmcdermott/AUC_is_all_you_need.

  • 5 authors
·
Jan 11, 2024

Evolution at two levels of gene expression in yeast

Despite the greater functional importance of protein levels, our knowledge of gene expression evolution is based almost entirely on studies of mRNA levels. In contrast, our understanding of how translational regulation evolves has lagged far behind. Here we have applied ribosome profiling - which measures both global mRNA levels and their translation rates - to two species of Saccharomyces yeast and their interspecific hybrid in order to assess the relative contributions of changes in mRNA abundance and translation to regulatory evolution. We report that both cis and trans-acting regulatory divergence in translation are abundant, affecting at least 35% of genes. The majority of translational divergence acts to buffer changes in mRNA abundance, suggesting a widespread role for stabilizing selection acting across regulatory levels. Nevertheless, we observe evidence of lineage-specific selection acting on a number of yeast functional modules, including instances of reinforcing selection acting at both levels of regulation. Finally, we also uncover multiple instances of stop-codon readthrough that are conserved between species. Our analysis reveals the under-appreciated complexity of post-transcriptional regulatory divergence and indicates that partitioning the search for the locus of selection into the binary categories of 'coding' vs. 'regulatory' may overlook a significant source of selection, acting at multiple regulatory levels along the path from genotype to phenotype.

  • 2 authors
·
Nov 27, 2013

BNPO: Beta Normalization Policy Optimization

Recent studies, including DeepSeek-R1 and Kimi-k1.5, have demonstrated that reinforcement learning with rule-based, binary-valued reward functions can significantly enhance the reasoning capabilities of large language models. These models primarily utilize REINFORCE-based policy optimization techniques, such as REINFORCE with baseline and group relative policy optimization (GRPO). However, a key limitation remains: current policy optimization methods either neglect reward normalization or employ static normalization strategies, which fail to adapt to the dynamic nature of policy updates during training. This may result in unstable gradient estimates and hinder training stability. To address this issue, we propose Beta Normalization Policy Optimization (BNPO), a novel policy optimization method that adaptively normalizes rewards using a Beta distribution with dynamically updated parameters. BNPO aligns the normalization with the changing policy distribution, enabling more precise and lower-variance gradient estimation, which in turn promotes stable training dynamics. We provide theoretical analysis demonstrating BNPO's variance-reducing properties and show that it generalizes both REINFORCE and GRPO under binary-valued reward settings. Furthermore, we introduce an advantage decomposition mechanism to extend BNPO's applicability to more complex reward systems. Experimental results confirm that BNPO achieves state-of-the-art performance among policy optimization methods on reasoning tasks. The code is available at https://github.com/changyi7231/BNPO.

  • 3 authors
·
Jun 3, 2025

The NANOGrav Nine-year Data Set: Limits on the Isotropic Stochastic Gravitational Wave Background

We compute upper limits on the nanohertz-frequency isotropic stochastic gravitational wave background (GWB) using the 9-year data release from the North American Nanohertz Observatory for Gravitational Waves (NANOGrav) collaboration. We set upper limits for a GWB from supermassive black hole binaries under power law, broken power law, and free spectral coefficient GW spectrum models. We place a 95\% upper limit on the strain amplitude (at a frequency of yr^{-1}) in the power law model of A_{rm gw} < 1.5times 10^{-15}. For a broken power law model, we place priors on the strain amplitude derived from simulations of Sesana (2013) and McWilliams et al. (2014). We find that the data favor a broken power law to a pure power law with odds ratios of 22 and 2.2 to one for the McWilliams and Sesana prior models, respectively. The McWilliams model is essentially ruled out by the data, and the Sesana model is in tension with the data under the assumption of a pure power law. Using the broken power-law analysis we construct posterior distributions on environmental factors that drive the binary to the GW-driven regime including the stellar mass density for stellar-scattering, mass accretion rate for circumbinary disk interaction, and orbital eccentricity for eccentric binaries, marking the first time that the shape of the GWB spectrum has been used to make astrophysical inferences. We then place the most stringent limits so far on the energy density of relic GWs, Omega_gw(f),h^2 < 4.2 times 10^{-10}, yielding a limit on the Hubble parameter during inflation of H_*=1.6times10^{-2}~m_{Pl}, where m_{Pl} is the Planck mass. Our limit on the cosmic string GWB, Omega_gw(f), h^2 < 2.2 times 10^{-10}, translates to a conservative limit of Gmu<3.3times 10^{-8} - a factor of 4 better than the joint Planck and high-l CMB data from other experiments.

  • 48 authors
·
Aug 12, 2015

Tracing the Physical Lineage of GRB 211211A: Population Constraints on NS-WD Merger Gamma-Ray Bursts

The peculiar long gamma-ray burst (GRB) event, GRB 211211A, is known for it is association with a kilonova feature. Whereas most long GRBs are thought to originate in the core collapse of massive stars, the presence of kilonova suggests GRB 211211A was instead produced by a merger of a compact object binary. Building on the interpretation put forward by Yang2022Natur.612..232Y--who argue that GRB 211211A was powered by a massive white-dwarf + neutron-star (WD-NS) merger--we adopt this WD-NS scenario as our observationally supported starting point. If the burst truly originates from that channel, its rarity must mirror the formation and merger rate of WD-NS binaries--a rate still largely unexplored in conventional massive-binary population studies. In this letter, we present a qualitative analysis based on binary evolution physics in order to understand the fraction of GRB 211211A in short GRBs (NS-WD/NS-NS fraction). Since the progenitors of massive WD-NS binaries occupy the initial mass function-preferred regime, where the zero-age main-sequence mass range of the assumed WD mass range (1.2-1.4,M_odot) is comparable to that of NSs, the NS-WD/NS-NS fraction emerging from our standard evolutionary path is expected to be sim14--37\%, far higher than the observed fraction (sim5\%). This discrepancy might imply a large, still-unidentified population of GRB 211211A-like events or an unusual origin of the NS-such as being hypernova-born or accretion-induced-collapse-born. Placing these results in a broader compact-binary context, implications for black-hole systems are also discussed.

  • 4 authors
·
Aug 14, 2025

A Construction of Evolving $k$-threshold Secret Sharing Scheme over A Polynomial Ring

The threshold secret sharing scheme allows the dealer to distribute the share to every participant such that the secret is correctly recovered from a certain amount of shares. The traditional (k, n)-threshold secret sharing scheme requests that the number of participants n is known in advance. In contrast, the evolving secret sharing scheme allows that n can be uncertain and even ever-growing. In this paper, we consider the evolving secret sharing scenario. Using the prefix codes and the properties of the polynomial ring, we propose a brand-new construction of evolving k-threshold secret sharing scheme for an ell-bit secret over a polynomial ring, with correctness and perfect security. The proposed schemes establish the connection between prefix codes and the evolving schemes for kgeq2, and are also first evolving k-threshold secret sharing schemes by generalizing Shamir's scheme onto a polynomial ring. Specifically, the proposal also provides an unified mathematical decryption for prior evolving 2-threshold secret sharing schemes. Besides, the analysis of the proposed schemes show that the size of the t-th share is (k-1)(ell_t-1)+ell bits, where ell_t denotes the length of a binary prefix code of encoding integer t. In particular, when delta code is chosen as the prefix code, the share size achieves (k-1)lfloorlg trfloor+2(k-1)lfloorlg ({lfloorlg trfloor+1}) rfloor+ell, which improves the prior best result (k-1)lg t+6k^4elllg tcdotlg {lg t}+ 7k^4elllg k, where lg denotes the binary logarithm. When k=2, the proposed scheme also achieves the minimal share size for single-bit secret, which is the same as the best known scheme.

  • 4 authors
·
Feb 2, 2024

ProSper -- A Python Library for Probabilistic Sparse Coding with Non-Standard Priors and Superpositions

ProSper is a python library containing probabilistic algorithms to learn dictionaries. Given a set of data points, the implemented algorithms seek to learn the elementary components that have generated the data. The library widens the scope of dictionary learning approaches beyond implementations of standard approaches such as ICA, NMF or standard L1 sparse coding. The implemented algorithms are especially well-suited in cases when data consist of components that combine non-linearly and/or for data requiring flexible prior distributions. Furthermore, the implemented algorithms go beyond standard approaches by inferring prior and noise parameters of the data, and they provide rich a-posteriori approximations for inference. The library is designed to be extendable and it currently includes: Binary Sparse Coding (BSC), Ternary Sparse Coding (TSC), Discrete Sparse Coding (DSC), Maximal Causes Analysis (MCA), Maximum Magnitude Causes Analysis (MMCA), and Gaussian Sparse Coding (GSC, a recent spike-and-slab sparse coding approach). The algorithms are scalable due to a combination of variational approximations and parallelization. Implementations of all algorithms allow for parallel execution on multiple CPUs and multiple machines for medium to large-scale applications. Typical large-scale runs of the algorithms can use hundreds of CPUs to learn hundreds of dictionary elements from data with tens of millions of floating-point numbers such that models with several hundred thousand parameters can be optimized. The library is designed to have minimal dependencies and to be easy to use. It targets users of dictionary learning algorithms and Machine Learning researchers.

  • 7 authors
·
Aug 1, 2019

Time-RA: Towards Time Series Reasoning for Anomaly with LLM Feedback

Time series anomaly detection is critical across various domains, yet current approaches often limit analysis to mere binary anomaly classification without detailed categorization or further explanatory reasoning. To address these limitations, we propose a novel task, Time-series Reasoning for Anomaly (Time-RA) that transforms classical time series anomaly detection from a discriminative into a generative, reasoning-intensive task leveraging Large Language Models (LLMs). Also, we introduce the first real-world multimodal benchmark dataset, RATs40K, explicitly annotated for anomaly reasoning, comprising approximately 40,000 samples across 10 real-world domains. Each sample includes numeric time series data, contextual text information, and visual representations, each annotated with fine-grained categories (14 types for univariate anomalies and 6 for multivariate anomalies) and structured explanatory reasoning. We develop a sophisticated annotation framework utilizing ensemble-generated labels refined through GPT-4-driven feedback, ensuring accuracy and interpretability. Extensive benchmarking of LLMs and multimodal LLMs demonstrates the capabilities and limitations of current models, highlighting the critical role of supervised fine-tuning. Our dataset and task pave the way for significant advancements in interpretable time series anomaly detection and reasoning. The code (https://github.com/yyysjz1997/Time-RA) and dataset (https://huggingface.co/datasets/Time-RA/RATs40K) have been fully open-sourced to support and accelerate future research in this area.

  • 9 authors
·
Jul 20, 2025

Beyond No: Quantifying AI Over-Refusal and Emotional Attachment Boundaries

We present an open-source benchmark and evaluation framework for assessing emotional boundary handling in Large Language Models (LLMs). Using a dataset of 1156 prompts across six languages, we evaluated three leading LLMs (GPT-4o, Claude-3.5 Sonnet, and Mistral-large) on their ability to maintain appropriate emotional boundaries through pattern-matched response analysis. Our framework quantifies responses across seven key patterns: direct refusal, apology, explanation, deflection, acknowledgment, boundary setting, and emotional awareness. Results demonstrate significant variation in boundary-handling approaches, with Claude-3.5 achieving the highest overall score (8.69/10) and producing longer, more nuanced responses (86.51 words on average). We identified a substantial performance gap between English (average score 25.62) and non-English interactions (< 0.22), with English responses showing markedly higher refusal rates (43.20% vs. < 1% for non-English). Pattern analysis revealed model-specific strategies, such as Mistral's preference for deflection (4.2%) and consistently low empathy scores across all models (< 0.06). Limitations include potential oversimplification through pattern matching, lack of contextual understanding in response analysis, and binary classification of complex emotional responses. Future work should explore more nuanced scoring methods, expand language coverage, and investigate cultural variations in emotional boundary expectations. Our benchmark and methodology provide a foundation for systematic evaluation of LLM emotional intelligence and boundary-setting capabilities.

  • 2 authors
·
Feb 20, 2025 3

Automatically Extracting Numerical Results from Randomized Controlled Trials with Large Language Models

Meta-analyses statistically aggregate the findings of different randomized controlled trials (RCTs) to assess treatment effectiveness. Because this yields robust estimates of treatment effectiveness, results from meta-analyses are considered the strongest form of evidence. However, rigorous evidence syntheses are time-consuming and labor-intensive, requiring manual extraction of data from individual trials to be synthesized. Ideally, language technologies would permit fully automatic meta-analysis, on demand. This requires accurately extracting numerical results from individual trials, which has been beyond the capabilities of natural language processing (NLP) models to date. In this work, we evaluate whether modern large language models (LLMs) can reliably perform this task. We annotate (and release) a modest but granular evaluation dataset of clinical trial reports with numerical findings attached to interventions, comparators, and outcomes. Using this dataset, we evaluate the performance of seven LLMs applied zero-shot for the task of conditionally extracting numerical findings from trial reports. We find that massive LLMs that can accommodate lengthy inputs are tantalizingly close to realizing fully automatic meta-analysis, especially for dichotomous (binary) outcomes (e.g., mortality). However, LLMs -- including ones trained on biomedical texts -- perform poorly when the outcome measures are complex and tallying the results requires inference. This work charts a path toward fully automatic meta-analysis of RCTs via LLMs, while also highlighting the limitations of existing models for this aim.

  • 4 authors
·
May 2, 2024