OpenRaiser/Intern-Atlas huggingface dataset:
Minimizers in Semi-Dynamic Strings
Venue: arXiv cs.DS 2025
Year: 2025

Minimizers sampling is one of the most widely-used mechanisms for sampling strings. Let $S=S[0]\ldots S[n-1]$ be a string over an alphabet $Σ$. In addition, let $w\geq 2$ and $k\geq 1$ be two integers and $ρ=(Σ^k,\leq)$ be a total order on $Σ^k$. The minimizer of window $X=S[i\mathinner{.\,.} i+w+k-2]$ is the smallest position in $[i,i+w-1]$ where the smallest length-$k$ substring of $S[i\mathinner{.\,.} i+w+k-2]$ based on $ρ$ starts. The set of minimizers for all $i\in[0,n-w-k+1]$ is the set $\mathcal{M}_{w,k,ρ}(S)$ of the minimizers of $S$. The set $\mathcal{M}_{w,k,ρ}(S)$ can be computed in $\mathcal{O}(n)$ time. The folklore algorithm for this computation computes the minimizer of every window in $\mathcal{O}(1)$ amortized time using $\mathcal{O}(w)$ working space. It is thus natural to pose the following two questions: Question 1: Can we efficiently support other dynamic updates on the window? Question 2: Can we improve on the $\mathcal{O}(w)$ working space? We answer both questions in the affirmative: 1. We term a string $X$ semi-dynamic when one is allowed to insert or delete a letter at any of its ends. We show a data structure that maintains a semi-dynamic string $X$ and supports minimizer queries in $X$ in $\mathcal{O}(1)$ time with amortized $\mathcal{O}(1)$ time per update operation. 2. We show that this data structure can be modified to occupy strongly sublinear space without increasing the asymptotic complexity of its operations. To the best of our knowledge, this yields the first algorithm for computing $\mathcal{M}_{w,k,ρ}(S)$ in $\mathcal{O}(n)$ time using $\mathcal{O}(\sqrt{w})$ working space. We complement our theoretical results with a concrete application and an experimental evaluation.
The Challenges and Benefits of Bringing Religious Values Into Design
Venue: arXiv cs.HC 2025
Year: 2025

HCI is increasingly taking inspiration from religious traditions as a basis for ethical technology designs. Such ethically-inspired designs can be especially important for social communications technologies, which are associated with numerous societal concerns. If religious values are to be incorporated into real-world designs, there may be challenges when designers work with values unfamiliar to them. Therefore, we investigate the difference in interpretations of values when they are translated to technology designs. To do so we studied design patterns that embody Catholic Social Teaching (CST). We interviewed 24 technologists and 7 CST scholars to assess how their understanding of how those values would manifest in social media designs. We found that for the most part the technologists responded similarly to the CST scholars. However, CST scholars had a better understanding of the principle of subsidiarity, and they believed moderation upheld human dignity more than the technologists did. We discuss the implications of our findings on the designs of social technologies and design processes at large.
Child vs. machine language learning: Can the logical structure of human language unleash LLMs?
Venue: arXiv cs.CL 2025
Year: 2025

We argue that human language learning proceeds in a manner that is different in nature from current approaches to training LLMs, predicting a difference in learning biases. We then present evidence from German plural formation by LLMs that confirm our hypothesis that even very powerful implementations produce results that miss aspects of the logic inherent to language that humans have no problem with. We conclude that attention to the different structures of human language and artificial neural networks is likely to be an avenue to improve LLM performance.
Continuous Integration Practices in Machine Learning Projects: The Practitioners` Perspective
Venue: arXiv cs.SE 2025
Year: 2025

Continuous Integration (CI) is a cornerstone of modern software development. However, while widely adopted in traditional software projects, applying CI practices to Machine Learning (ML) projects presents distinctive characteristics. For example, our previous work revealed that ML projects often experience longer build durations and lower test coverage rates compared to their non-ML counterparts. Building on these quantitative findings, this study surveys 155 practitioners from 47 ML projects to investigate the underlying reasons for these distinctive characteristics through a qualitative perspective. Practitioners highlighted eight key differences, including test complexity, infrastructure requirements, and build duration and stability. Common challenges mentioned by practitioners include higher project complexity, model training demands, extensive data handling, increased computational resource needs, and dependency management, all contributing to extended build durations. Furthermore, ML systems' non-deterministic nature, data dependencies, and computational constraints were identified as significant barriers to effective testing. The key takeaway from this study is that while foundational CI principles remain valuable, ML projects require tailored approaches to address their unique challenges. To bridge this gap, we propose a set of ML-specific CI practices, including tracking model performance metrics and prioritizing test execution within CI pipelines. Additionally, our findings highlight the importance of fostering interdisciplinary collaboration to strengthen the testing culture in ML projects. By bridging quantitative findings with practitioners' insights, this study provides a deeper understanding of the interplay between CI practices and the unique demands of ML projects, laying the groundwork for more efficient and robust CI strategies in this domain.
Low-Rank and Sparse Model Merging for Multi-Lingual Speech Recognition and Translation
Venue: arXiv cs.SD 2025
Year: 2025

Language diversity presents a significant challenge in speech-to-text (S2T) tasks, such as automatic speech recognition and translation. Traditional multi-lingual multi-task training approaches aim to address this by jointly optimising multiple speech recognition and translation tasks across various languages. While models like Whisper, built on these strategies, demonstrate strong performance, they still face issues of high computational cost, language interference, suboptimal training configurations, and limited extensibility. To overcome these challenges, we introduce LoRS-Merging (low-rank and sparse model merging), a novel technique designed to efficiently integrate models trained on different languages or tasks while preserving performance and reducing computational overhead. LoRS-Merging combines low-rank and sparse pruning to retain essential structures while eliminating redundant parameters, mitigating language interference, and enhancing extensibility. Experimental results across 10 languages demonstrate that LoRS-Merging significantly outperforms multi-lingual multi-task training, sequential training, and other merging methods, achieving over 20% improvement in normalised performance. Our findings suggest that model merging, particularly LoRS-Merging, is a scalable and effective complement to traditional multi-lingual training strategies for S2T applications.
Which Questions Improve Learning the Most? Utility Estimation of Questions with LM-based Simulations
Venue: arXiv cs.CL 2025
Year: 2025

Asking good questions is critical for comprehension and learning, yet evaluating and generating such questions remains a challenging problem. Prior work on inquisitive questions focuses on learner-generated, curiosity-driven queries and evaluates them using indirect metrics, such as salience or information gain, that do not directly capture a question's impact on actual learning outcomes. We introduce QUEST (Question Utility Estimation with Simulated Tests), a framework that uses language models to simulate learners and directly quantify the utility of a question - its contribution to exam performance. QUEST simulates a learner who asks questions and receives answers while studying a textbook chapter, then uses them to take an end-of-chapter exam. Through this simulation, the utility of each question is estimated by its direct effect on exam performance, rather than inferred indirectly based on the underlying content. To support this evaluation, we curate TEXTBOOK-EXAM, a benchmark that aligns textbook sections with end-of-section exam questions across five academic disciplines. Using QUEST, we filter for high-utility questions and fine-tune question generators via rejection sampling. Experiments show that questions generated by QUEST-trained models improve simulated test scores by over 20% compared to strong baselines that are fine-tuned using indirect metrics or leverage prompting methods. Furthermore, utility is only weakly correlated with salience and similarity to exam questions, suggesting that it captures unique signal that benefits downstream performance. QUEST offers a new outcome-driven paradigm for question evaluation and generation - one that moves beyond question-answer content toward measurable improvements in learning outcomes.
The Empirical Impact of Reducing Symmetries on the Performance of Deep Ensembles and MoE
Venue: arXiv cs.LG 2025
Year: 2025

Recent studies have shown that reducing symmetries in neural networks enhances linear mode connectivity between networks without requiring parameter space alignment, leading to improved performance in linearly interpolated neural networks. However, in practical applications, neural network interpolation is rarely used; instead, ensembles of networks are more common. In this paper, we empirically investigate the impact of reducing symmetries on the performance of deep ensembles and Mixture of Experts (MoE) across five datasets. Additionally, to explore deeper linear mode connectivity, we introduce the Mixture of Interpolated Experts (MoIE). Our results show that deep ensembles built on asymmetric neural networks achieve significantly better performance as ensemble size increases compared to their symmetric counterparts. In contrast, our experiments do not provide conclusive evidence on whether reducing symmetries affects both MoE and MoIE architectures.
Emoti-Attack: Zero-Perturbation Adversarial Attacks on NLP Systems via Emoji Sequences
Venue: arXiv cs.AI 2025
Year: 2025

Deep neural networks (DNNs) have achieved remarkable success in the field of natural language processing (NLP), leading to widely recognized applications such as ChatGPT. However, the vulnerability of these models to adversarial attacks remains a significant concern. Unlike continuous domains like images, text exists in a discrete space, making even minor alterations at the sentence, word, or character level easily perceptible to humans. This inherent discreteness also complicates the use of conventional optimization techniques, as text is non-differentiable. Previous research on adversarial attacks in text has focused on character-level, word-level, sentence-level, and multi-level approaches, all of which suffer from inefficiency or perceptibility issues due to the need for multiple queries or significant semantic shifts. In this work, we introduce a novel adversarial attack method, Emoji-Attack, which leverages the manipulation of emojis to create subtle, yet effective, perturbations. Unlike character- and word-level strategies, Emoji-Attack targets emojis as a distinct layer of attack, resulting in less noticeable changes with minimal disruption to the text. This approach has been largely unexplored in previous research, which typically focuses on emoji insertion as an extension of character-level attacks. Our experiments demonstrate that Emoji-Attack achieves strong attack performance on both large and small models, making it a promising technique for enhancing adversarial robustness in NLP systems.
[RETRACTED]Evolving Form and Function: Dual-Objective Optimization in Neural Symbolic Regression Networks
Venue: arXiv cs.NE 2025
Year: 2025

[RETRACTED]Data increasingly abounds, but distilling their underlying relationships down to something interpretable remains challenging. One approach is genetic programming, which `symbolically regresses' a data set down into an equation. However, symbolic regression (SR) faces the issue of requiring training from scratch for each new dataset. To generalize across all datasets, deep learning techniques have been applied to SR. These networks, however, are only able to be trained using a symbolic objective: NN-generated and target equations are symbolically compared. But this does not consider the predictive power of these equations, which could be measured by a behavioral objective that compares the generated equation's predictions to actual data. Here we introduce a method that combines gradient descent and evolutionary computation to yield neural networks that minimize the symbolic and behavioral errors of the equations they generate from data. As a result, these evolved networks are shown to generate more symbolically and behaviorally accurate equations than those generated by networks trained by state-of-the-art gradient based neural symbolic regression methods. We hope this method suggests that evolutionary algorithms, combined with gradient descent, can improve SR results by yielding equations with more accurate form and function.
From System 1 to System 2: A Survey of Reasoning Large Language Models
Venue: arXiv cs.AI 2025
Year: 2025

Achieving human-level intelligence requires refining the transition from the fast, intuitive System 1 to the slower, more deliberate System 2 reasoning. While System 1 excels in quick, heuristic decisions, System 2 relies on logical reasoning for more accurate judgments and reduced biases. Foundational Large Language Models (LLMs) excel at fast decision-making but lack the depth for complex reasoning, as they have not yet fully embraced the step-by-step analysis characteristic of true System 2 thinking. Recently, reasoning LLMs like OpenAI's o1/o3 and DeepSeek's R1 have demonstrated expert-level performance in fields such as mathematics and coding, closely mimicking the deliberate reasoning of System 2 and showcasing human-like cognitive abilities. This survey begins with a brief overview of the progress in foundational LLMs and the early development of System 2 technologies, exploring how their combination has paved the way for reasoning LLMs. Next, we discuss how to construct reasoning LLMs, analyzing their features, the core methods enabling advanced reasoning, and the evolution of various reasoning LLMs. Additionally, we provide an overview of reasoning benchmarks, offering an in-depth comparison of the performance of representative reasoning LLMs. Finally, we explore promising directions for advancing reasoning LLMs and maintain a real-time \href{https://github.com/zzli2022/Awesome-Slow-Reason-System}{GitHub Repository} to track the latest developments. We hope this survey will serve as a valuable resource to inspire innovation and drive progress in this rapidly evolving field.
Studying How Configurations Impact Code Generation in LLMs: the Case of ChatGPT
Venue: arXiv cs.SE 2025
Year: 2025

Leveraging LLMs for code generation is becoming increasingly common, as tools like ChatGPT can suggest method implementations with minimal input, such as a method signature and brief description. Empirical studies further highlight the effectiveness of LLMs in handling such tasks, demonstrating notable performance in code generation scenarios. However, LLMs are inherently non-deterministic, with their output influenced by parameters such as temperature, which regulates the model's level of creativity, and top-p, which controls the choice of the tokens that shall appear in the output. Despite their significance, the role of these parameters is often overlooked. This paper systematically studies the impact of these parameters, as well as the number of prompt repetitions required to account for non-determinism, in the context of 548 Java methods. We observe significantly different performances across different configurations of ChatGPT, with temperature having a marginal impact compared to the more prominent influence of the top-p parameter. Additionally, we show how creativity can enhance code generation tasks. Finally, we provide concrete recommendations for addressing the non-determinism of the model.
SpikeRL: A Scalable and Energy-efficient Framework for Deep Spiking Reinforcement Learning
Venue: arXiv cs.LG 2025
Year: 2025

In this era of AI revolution, massive investments in large-scale data-driven AI systems demand high-performance computing, consuming tremendous energy and resources. This trend raises new challenges in optimizing sustainability without sacrificing scalability or performance. Among the energy-efficient alternatives of the traditional Von Neumann architecture, neuromorphic computing and its Spiking Neural Networks (SNNs) are a promising choice due to their inherent energy efficiency. However, in some real-world application scenarios such as complex continuous control tasks, SNNs often lack the performance optimizations that traditional artificial neural networks have. Researchers have addressed this by combining SNNs with Deep Reinforcement Learning (DeepRL), yet scalability remains unexplored. In this paper, we extend our previous work on SpikeRL, which is a scalable and energy efficient framework for DeepRL-based SNNs for continuous control. In our initial implementation of SpikeRL framework, we depended on the population encoding from the Population-coded Spiking Actor Network (PopSAN) method for our SNN model and implemented distributed training with Message Passing Interface (MPI) through mpi4py. Also, further optimizing our model training by using mixed-precision for parameter updates. In our new SpikeRL framework, we have implemented our own DeepRL-SNN component with population encoding, and distributed training with PyTorch Distributed package with NCCL backend while still optimizing with mixed precision training. Our new SpikeRL implementation is 4.26X faster and 2.25X more energy efficient than state-of-the-art DeepRL-SNN methods. Our proposed SpikeRL framework demonstrates a truly scalable and sustainable solution for complex continuous control tasks in real-world applications.
RAG-Enhanced Collaborative LLM Agents for Drug Discovery
Venue: arXiv cs.LG 2025
Year: 2025

Recent advances in large language models (LLMs) have shown great potential to accelerate drug discovery. However, the specialized nature of biochemical data often necessitates costly domain-specific fine-tuning, posing major challenges. First, it hinders the application of more flexible general-purpose LLMs for cutting-edge drug discovery tasks. More importantly, it limits the rapid integration of the vast amounts of scientific data continuously generated through experiments and research. Compounding these challenges is the fact that real-world scientific questions are typically complex and open-ended, requiring reasoning beyond pattern matching or static knowledge retrieval.To address these challenges, we propose CLADD, a retrieval-augmented generation (RAG)-empowered agentic system tailored to drug discovery tasks. Through the collaboration of multiple LLM agents, CLADD dynamically retrieves information from biomedical knowledge bases, contextualizes query molecules, and integrates relevant evidence to generate responses - all without the need for domain-specific fine-tuning. Crucially, we tackle key obstacles in applying RAG workflows to biochemical data, including data heterogeneity, ambiguity, and multi-source integration. We demonstrate the flexibility and effectiveness of this framework across a variety of drug discovery tasks, showing that it outperforms general-purpose and domain-specific LLMs as well as traditional deep learning approaches. Our code is publicly available at https://github.com/Genentech/CLADD.
C2-DPO: Constrained Controlled Direct Preference Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Direct preference optimization (\texttt{DPO}) has emerged as a promising approach for solving the alignment problem in AI. In this paper, we make two counter-intuitive observations about \texttt{DPO}. First, we show that \texttt{DPO} loss could be derived by starting from an alternative optimization problem that only defines the KL guardrail on in-sample responses, unlike the original RLHF problem where guardrails are defined on the entire distribution. Second, we prove a surprising property of this alternative optimization problem, namely that under its optimal policy, both preferred and rejected responses tend to decrease in probability, a phenomenon typically displayed by DPO in practice. To control this behavior, we propose a set of constraints designed to limit the displacement of probability mass between the preferred and rejected responses in the reference and target policies. The resulting algorithm, which we call Constrained Controlled DPO (\texttt{C2-DPO}), has a meaningful RLHF interpretation. By hedging against the displacement, \texttt{C2-DPO} provides practical improvements over vanilla \texttt{DPO} when aligning several language models using standard preference datasets.
The Lottery LLM Hypothesis, Rethinking What Abilities Should LLM Compression Preserve?
Venue: arXiv cs.LG 2025
Year: 2025

Motivated by reducing the computational and storage costs of LLMs, model compression and KV cache compression have attracted much attention from researchers. However, current methods predominantly emphasize maintaining the performance of compressed LLMs, as measured by perplexity or simple accuracy on tasks of common sense knowledge QA and basic arithmetic reasoning. In this blog, we present a brief review of recent advancements in LLMs related to retrieval-augmented generation, multi-step reasoning, external tools, and computational expressivity, all of which substantially enhance LLM performance. Then, we propose a lottery LLM hypothesis suggesting that for a given LLM and task, there exists a smaller lottery LLM capable of producing the same performance as the original LLM with the assistance of multi-step reasoning and external tools. Based on the review of current progress in LLMs, we discuss and summarize the essential capabilities that the lottery LLM and KV cache compression must possess, which are currently overlooked in existing methods.
Rethinking the Vulnerability of Concept Erasure and a New Method
Venue: arXiv cs.LG 2025
Year: 2025

The proliferation of text-to-image diffusion models has raised significant privacy and security concerns, particularly regarding the generation of copyrighted or harmful images. In response, concept erasure (defense) methods have been developed to "unlearn" specific concepts through post-hoc finetuning. However, recent concept restoration (attack) methods have demonstrated that these supposedly erased concepts can be recovered using adversarially crafted prompts, revealing a critical vulnerability in current defense mechanisms. In this work, we first investigate the fundamental sources of adversarial vulnerability and reveal that vulnerabilities are pervasive in the prompt embedding space of concept-erased models, a characteristic inherited from the original pre-unlearned model. Furthermore, we introduce **RECORD**, a novel coordinate-descent-based restoration algorithm that consistently outperforms existing restoration methods by up to 17.8 times. We conduct extensive experiments to assess its compute-performance tradeoff and propose acceleration strategies.