OpenRaiser/Intern-Atlas huggingface dataset:
Kitsune: Enabling Dataflow Execution on GPUs
Venue: arXiv cs.AR 2025
Year: 2025

State of art DL models are growing in size and complexity, with many modern models also increasing in heterogeneity of behavior. GPUs are still the dominant platform for DL applications, relying on a bulk-synchronous execution model which has many drawbacks and is ill-suited for the graph structure of DL applications. Many industry and academic works attempt to overcome these by employing vertical fusion but this approach still fails to realize three untapped opportunities: (1) the fact that many resources on the GPU are idle while only one operator executes due to temporal multiplexing of the SM; (2) lower energy from more intelligent on-chip data-movement which lends to higher performance in a power-provisioned environment. (3) inability to exploit hidden or reduction dimensions as a source of parallelism to ease pressure on batch size. This paper explores relatively uncharted territory, answering the following key question: Can modest adjustments to the current GPU architecture enable efficient dataflow execution, thereby circumventing the constraints of vertical fusion without necessitating a clean-slate architecture design. We develop Kitsune -- a set of primitives that enable dataflow execution on GPUs and an end-to-end compiler based on PyTorch Dynamo. Across 5 challenge applications, Kitsune can provide 1.3$\times$-2.3$\times$ and 1.1$\times$-2.4$\times$ performance improvement as well as 41%-98% and 16%-42% off-chip traffic reduction for inference and training, respectively.
Equidistant-Sample or Wait-and-Sample to Minimize Age Under Sampling Constraint?
Venue: arXiv cs.IT 2025
Year: 2025

We study a status update system with a source, a sampler, a transmitter, and a monitor. The source governs a stochastic process that the monitor wants to observe in a timely manner. To achieve this, the sampler samples fresh update packets which the transmitter transmits via an error prone communication channel to the monitor. The transmitter can transmit without any constraint, i.e., it can transmit whenever an update packet is available to the transmitter. However, the sampler is imposed with a sampling rate constraint. The goal of the sampler is to devise an optimal policy that satisfies the resource constraint while minimizing the age of the monitor. We formulate this problem as a constrained Markov decision process (CMDP). We find several structures of an optimal policy. We leverage the optimal structures to find a low complexity optimal policy in an explicit manner, without resorting to complex iterative schemes or techniques that require bounding the age.
Enhancing DNA Foundation Models to Address Masking Inefficiencies
Venue: arXiv cs.LG 2025
Year: 2025

Masked language modelling (MLM) as a pretraining objective has been widely adopted in genomic sequence modelling. While pretrained models can successfully serve as encoders for various downstream tasks, the distribution shift between pretraining and inference detrimentally impacts performance, as the pretraining task is to map [MASK] tokens to predictions, yet the [MASK] is absent during downstream applications. This means the encoder does not prioritize its encodings of non-[MASK] tokens, and expends parameters and compute on work only relevant to the MLM task, despite this being irrelevant at deployment time. In this work, we propose a modified encoder-decoder architecture based on the masked autoencoder framework, designed to address this inefficiency within a BERT-based transformer. We empirically show that the resulting mismatch is particularly detrimental in genomic pipelines where models are often used for feature extraction without fine-tuning. We evaluate our approach on the BIOSCAN-5M dataset, comprising over 2 million unique DNA barcodes. We achieve substantial performance gains in both closed-world and open-world classification tasks when compared against causal models and bidirectional architectures pretrained with MLM tasks.
Random Number Generation from Pulsars
Venue: arXiv cs.CR 2025
Year: 2025

Pulsars exhibit signals with precise inter-arrival times that are on the order of milliseconds to seconds, depending on the individual pulsar. There are subtle variations in the timing of pulsar signals. We show that these variations can serve as a natural entropy source for the creation of Random Number Generators (RNGs). We also explore the effects of using randomness extractors to increase the entropy of random bits extracted from Pulsar timing data. To evaluate the quality of the Pulsar RNG, we model its entropy as a $k$-source and use well-known cryptographic results to show its closeness to a theoretically ideal uniformly random source. To remain consistent with prior work, we also show that the Pulsar RNG passes well-known statistical tests such as the NIST test suite.
FRIDA to the Rescue! Analyzing Synthetic Data Effectiveness in Object-Based Common Sense Reasoning for Disaster Response
Venue: arXiv cs.CL 2025
Year: 2025

During Human Robot Interactions in disaster relief scenarios, Large Language Models (LLMs) have the potential for substantial physical reasoning to assist in mission objectives. However, these reasoning capabilities are often found only in larger models, which are not currently reasonable to deploy on robotic systems due to size constraints. To meet our problem space requirements, we introduce a dataset and pipeline to create Field Reasoning and Instruction Decoding Agent (FRIDA) models. In our pipeline, domain experts and linguists combine their knowledge to make high-quality, few-shot prompts used to generate synthetic data for fine-tuning. We hand-curate datasets for this few-shot prompting and for evaluation to improve LLM reasoning on both general and disaster-specific objects. We concurrently run an ablation study to understand which kinds of synthetic data most affect performance. We fine-tune several small instruction-tuned models and find that ablated FRIDA models only trained on objects' physical state and function data outperformed both the FRIDA models trained on all synthetic data and the base models in our evaluation. We demonstrate that the FRIDA pipeline is capable of instilling physical common sense with minimal data.
Empirical Research on Utilizing LLM-based Agents for Automated Bug Fixing via LangGraph
Venue: arXiv cs.SE 2025
Year: 2025

This paper presents a novel framework for automated code generation and debugging, designed to improve accuracy, efficiency, and scalability in software development. The proposed system integrates three core components LangGraph, GLM4 Flash, and ChromaDB within a four step iterative workflow to deliver robust performance and seamless functionality. LangGraph serves as a graph-based library for orchestrating tasks, providing precise control and execution while maintaining a unified state object for dynamic updates and consistency. It supports multi-agent, hierarchical, and sequential processes, making it highly adaptable to complex software engineering workflows. GLM4 Flash, a large language model, leverages its advanced capabilities in natural language understanding, contextual reasoning, and multilingual support to generate accurate code snippets based on user prompts. ChromaDB acts as a vector database for semantic search and contextual memory storage, enabling the identification of patterns and the generation of context-aware bug fixes based on historical data. The system operates through a structured four-step process: (1) Code Generation, which translates natural language descriptions into executable code; (2) Code Execution, which validates the code by identifying runtime errors and inconsistencies; (3) Code Repair, which iteratively refines buggy code using ChromaDB's memory capabilities and LangGraph's state tracking; and (4) Code Update, which ensures the code meets functional and performance requirements through iterative modifications.
Disproving Program Equivalence with LLMs
Venue: arXiv cs.SE 2025
Year: 2025

To evaluate large language models (LLMs) for code, research has used manually created unit test-based benchmarks. However, these tests are often inadequate, missing corner cases and other implementation-specific oddities. This work introduces ProbeGen, a whitebox method that takes two or more executable pieces of code and searches for counterexamples to their equivalence. Comparing code semantics requires a deep understanding of code. We demonstrate that LLMs with execution feedback perform well at this task. In a common code synthesis benchmark, ProbeGen disproves 18% of samples considered equivalent to the ground truth by the benchmark-provided unit tests. Additionally, using ProbeGen, we can semantically cluster LLM samples for semantic self-consistency, improving pass@1 by 10% by unifying syntactically distinct but semantically similar samples.
QExplorer: Large Language Model Based Query Extraction for Toxic Content Exploration
Venue: arXiv cs.IR 2025
Year: 2025

Automatically extracting effective queries is challenging in information retrieval, especially in toxic content exploration, as such content is likely to be disguised. With the recent achievements in generative Large Language Model (LLM), we are able to leverage the capabilities of LLMs to extract effective queries for similar content exploration directly. This study proposes QExplorer, an approach of large language model based Query Extraction for toxic content Exploration. The QExplorer approach involves a 2-stage training process: instruction Supervised FineTuning (SFT) and preference alignment using Direct Preference Optimization (DPO), as well as the datasets construction with feedback of search system. To verify the effectiveness of QExplorer, a series of offline and online experiments are conducted on our real-world system. The offline empirical results demonstrate that the performance of our automatic query extraction outperforms that of several LLMs and humans. The online deployment shows a significant increase in the detection of toxic items.
Modeling Churn in Recommender Systems with Aggregated Preferences
Venue: arXiv cs.IR 2025
Year: 2025

While recommender systems (RSs) traditionally rely on extensive individual user data, regulatory and technological shifts necessitate reliance on aggregated user information. This shift significantly impacts the recommendation process, requiring RSs to engage in intensive exploration to identify user preferences. However, this approach risks user churn due to potentially unsatisfactory recommendations. In this paper, we propose a model that addresses the dual challenges of leveraging aggregated user information and mitigating churn risk. Our model assumes that the RS operates with a probabilistic prior over user types and aggregated satisfaction levels for various content types. We demonstrate that optimal policies naturally transition from exploration to exploitation in finite time, develop a branch-and-bound algorithm for computing these policies, and empirically validate its effectiveness.
Rule-based autocorrection of Piping and Instrumentation Diagrams (P&IDs) on graphs
Venue: arXiv cs.CE 2025
Year: 2025

A piping and instrumentation diagram (P&ID) is a central reference document in chemical process engineering. Currently, chemical engineers manually review P&IDs through visual inspection to find and rectify errors. However, engineering projects can involve hundreds to thousands of P&ID pages, creating a significant revision workload. This study proposes a rule-based method to support engineers with error detection and correction in P&IDs. The method is based on a graph representation of P&IDs, enabling automated error detection and correction, i.e., autocorrection, through rule graphs. We use our pyDEXPI Python package to generate P&ID graphs from DEXPI-standard P&IDs. In this study, we developed 33 rules based on chemical engineering knowledge and heuristics, with five selected rules demonstrated as examples. A case study on an illustrative P&ID validates the reliability and effectiveness of the rule-based autocorrection method in revising P&IDs.
TurboFuzzLLM: Turbocharging Mutation-based Fuzzing for Effectively Jailbreaking Large Language Models in Practice
Venue: arXiv cs.CR 2025
Year: 2025

Jailbreaking large-language models (LLMs) involves testing their robustness against adversarial prompts and evaluating their ability to withstand prompt attacks that could elicit unauthorized or malicious responses. In this paper, we present TurboFuzzLLM, a mutation-based fuzzing technique for efficiently finding a collection of effective jailbreaking templates that, when combined with harmful questions, can lead a target LLM to produce harmful responses through black-box access via user prompts. We describe the limitations of directly applying existing template-based attacking techniques in practice, and present functional and efficiency-focused upgrades we added to mutation-based fuzzing to generate effective jailbreaking templates automatically. TurboFuzzLLM achieves $\geq$ 95\% attack success rates (ASR) on public datasets for leading LLMs (including GPT-4o \& GPT-4 Turbo), shows impressive generalizability to unseen harmful questions, and helps in improving model defenses to prompt attacks. TurboFuzzLLM is available open source at https://github.com/amazon-science/TurboFuzzLLM.
FCoT-VL:Advancing Text-oriented Large Vision-Language Models with Efficient Visual Token Compression
Venue: arXiv cs.CV 2025
Year: 2025

The rapid success of Vision Large Language Models (VLLMs) often depends on the high-resolution images with abundant visual tokens, which hinders training and deployment efficiency. Current training-free visual token compression methods exhibit serious performance degradation in tasks involving high-resolution, text-oriented image understanding and reasoning. In this paper, we propose an efficient visual token compression framework for text-oriented VLLMs in high-resolution scenarios. In particular, we employ a light-weight self-distillation pre-training stage to compress the visual tokens, requiring a limited numbers of image-text pairs and minimal learnable parameters. Afterwards, to mitigate potential performance degradation of token-compressed models, we construct a high-quality post-train stage. To validate the effectiveness of our method, we apply it to an advanced VLLMs, InternVL2. Experimental results show that our approach significantly reduces computational overhead while outperforming the baselines across a range of text-oriented benchmarks. We will release the models and code soon.
CipherFace: A Fully Homomorphic Encryption-Driven Framework for Secure Cloud-Based Facial Recognition
Venue: arXiv cs.CR 2025
Year: 2025

Facial recognition systems rely on embeddings to represent facial images and determine identity by verifying if the distance between embeddings is below a pre-tuned threshold. While embeddings are not reversible to original images, they still contain sensitive information, making their security critical. Traditional encryption methods like AES are limited in securely utilizing cloud computational power for distance calculations. Homomorphic Encryption, allowing calculations on encrypted data, offers a robust alternative. This paper introduces CipherFace, a homomorphic encryption-driven framework for secure cloud-based facial recognition, which we have open-sourced at http://github.com/serengil/cipherface. By leveraging FHE, CipherFace ensures the privacy of embeddings while utilizing the cloud for efficient distance computation. Furthermore, we propose a novel encrypted distance computation method for both Euclidean and Cosine distances, addressing key challenges in performing secure similarity calculations on encrypted data. We also conducted experiments with different facial recognition models, various embedding sizes, and cryptosystem configurations, demonstrating the scalability and effectiveness of CipherFace in real-world applications.
Swallowing the Poison Pills: Insights from Vulnerability Disparity Among LLMs
Venue: arXiv cs.CR 2025
Year: 2025

Modern large language models (LLMs) exhibit critical vulnerabilities to poison pill attacks: localized data poisoning that alters specific factual knowledge while preserving overall model utility. We systematically demonstrate these attacks exploit inherent architectural properties of LLMs, achieving 54.6% increased retrieval inaccuracy on long-tail knowledge versus dominant topics and up to 25.5% increase retrieval inaccuracy on compressed models versus original architectures. Through controlled mutations (e.g., temporal/spatial/entity alterations) and, our method induces localized memorization deterioration with negligible impact on models' performance on regular standard benchmarks (e.g., <2% performance drop on MMLU/GPQA), leading to potential detection evasion. Our findings suggest: (1) Disproportionate vulnerability in long-tail knowledge may result from reduced parameter redundancy; (2) Model compression may increase attack surfaces, with pruned/distilled models requiring 30% fewer poison samples for equivalent damage; (3) Associative memory enables both spread of collateral damage to related concepts and amplification of damage from simultaneous attack, particularly for dominant topics. These findings raise concerns over current scaling paradigms since attack costs are lowering while defense complexity is rising. Our work establishes poison pills as both a security threat and diagnostic tool, revealing critical security-efficiency trade-offs in language model compression that challenges prevailing safety assumptions.
Class-Conditional Neural Polarizer: A Lightweight and Effective Backdoor Defense by Purifying Poisoned Features
Venue: arXiv cs.CR 2025
Year: 2025

Recent studies have highlighted the vulnerability of deep neural networks to backdoor attacks, where models are manipulated to rely on embedded triggers within poisoned samples, despite the presence of both benign and trigger information. While several defense methods have been proposed, they often struggle to balance backdoor mitigation with maintaining benign performance.In this work, inspired by the concept of optical polarizer-which allows light waves of specific polarizations to pass while filtering others-we propose a lightweight backdoor defense approach, NPD. This method integrates a neural polarizer (NP) as an intermediate layer within the compromised model, implemented as a lightweight linear transformation optimized via bi-level optimization. The learnable NP filters trigger information from poisoned samples while preserving benign content. Despite its effectiveness, we identify through empirical studies that NPD's performance degrades when the target labels (required for purification) are inaccurately estimated. To address this limitation while harnessing the potential of targeted adversarial mitigation, we propose class-conditional neural polarizer-based defense (CNPD). The key innovation is a fusion module that integrates the backdoored model's predicted label with the features to be purified. This architecture inherently mimics targeted adversarial defense mechanisms without requiring label estimation used in NPD. We propose three implementations of CNPD: the first is r-CNPD, which trains a replicated NP layer for each class and, during inference, selects the appropriate NP layer for defense based on the predicted class from the backdoored model. To efficiently handle a large number of classes, two variants are designed: e-CNPD, which embeds class information as additional features, and a-CNPD, which directs network attention using class information.
ARACNE: An LLM-Based Autonomous Shell Pentesting Agent
Venue: arXiv cs.CR 2025
Year: 2025

We introduce ARACNE, a fully autonomous LLM-based pentesting agent tailored for SSH services that can execute commands on real Linux shell systems. Introduces a new agent architecture with multi-LLM model support. Experiments show that ARACNE can reach a 60\% success rate against the autonomous defender ShelLM and a 57.58\% success rate against the Over The Wire Bandit CTF challenges, improving over the state-of-the-art. When winning, the average number of actions taken by the agent to accomplish the goals was less than 5. The results show that the use of multi-LLM is a promising approach to increase accuracy in the actions.
Enhancing Hepatopathy Clinical Trial Efficiency: A Secure, Large Language Model-Powered Pre-Screening Pipeline
Venue: arXiv cs.AI 2025
Year: 2025

Background: Recruitment for cohorts involving complex liver diseases, such as hepatocellular carcinoma and liver cirrhosis, often requires interpreting semantically complex criteria. Traditional manual screening methods are time-consuming and prone to errors. While AI-powered pre-screening offers potential solutions, challenges remain regarding accuracy, efficiency, and data privacy. Methods: We developed a novel patient pre-screening pipeline that leverages clinical expertise to guide the precise, safe, and efficient application of large language models. The pipeline breaks down complex criteria into a series of composite questions and then employs two strategies to perform semantic question-answering through electronic health records - (1) Pathway A, Anthropomorphized Experts' Chain of Thought strategy, and (2) Pathway B, Preset Stances within an Agent Collaboration strategy, particularly in managing complex clinical reasoning scenarios. The pipeline is evaluated on three key metrics-precision, time consumption, and counterfactual inference - at both the question and criterion levels. Results: Our pipeline achieved high precision (0.921, in criteria level) and efficiency (0.44s per task). Pathway B excelled in complex reasoning, while Pathway A was effective in precise data extraction with faster processing times. Both pathways achieved comparable precision. The pipeline showed promising results in hepatocellular carcinoma (0.878) and cirrhosis trials (0.843). Conclusions: This data-secure and time-efficient pipeline shows high precision in hepatopathy trials, providing promising solutions for streamlining clinical trial workflows. Its efficiency and adaptability make it suitable for improving patient recruitment. And its capability to function in resource-constrained environments further enhances its utility in clinical settings.
ZCCL: Significantly Improving Collective Communication With Error-Bounded Lossy Compression
Venue: arXiv cs.DC 2025
Year: 2025

With the ever-increasing computing power of supercomputers and the growing scale of scientific applications, the efficiency of MPI collective communication turns out to be a critical bottleneck in large-scale distributed and parallel processing. The large message size in MPI collectives is particularly concerning because it can significantly degrade overall parallel performance. To address this issue, prior research simply applies off-the-shelf fixed-rate lossy compressors in the MPI collectives, leading to suboptimal performance, limited generalizability, and unbounded errors. In this paper, we propose a novel solution, called ZCCL, which leverages error-bounded lossy compression to significantly reduce the message size, resulting in a substantial reduction in communication costs. The key contributions are three-fold. (1) We develop two general, optimized lossy-compression-based frameworks for both types of MPI collectives (collective data movement as well as collective computation), based on their particular characteristics. Our framework not only reduces communication costs but also preserves data accuracy. (2) We customize fZ-light, an ultra-fast error-bounded lossy compressor, to meet the specific needs of collective communication. (3) We integrate ZCCL into multiple collectives, such as Allgather, Allreduce, Scatter, and Broadcast, and perform a comprehensive evaluation based on real-world scientific application datasets. Experiments show that our solution outperforms the original MPI collectives as well as multiple baselines by 1.9--8.9X.