The de-identification of private information in medical data is a crucial process to mitigate the risk of confidentiality breaches, particularly when patient personal details are not adequately removed before the release of medical records. Although rule-based and learning-based methods have been proposed, they often struggle with limited generalizability and require substantial amounts of annotated data for effective performance. Recent advancements in large language models (LLMs) have shown significant promise in addressing these issues due to their superior language comprehension capabilities. However, LLMs present challenges, including potential privacy risks when using commercial LLM APIs and high computational costs for deploying open-source LLMs locally. In this work, we introduce LPPA, an LLM-empowered Privacy-Protected PHI Annotation framework for clinical notes, targeting the English language. By fine-tuning LLMs locally with synthetic notes, LPPA ensures strong privacy protection and high PHI annotation accuracy. Extensive experiments demonstrate LPPA's effectiveness in accurately de-identifying private information, offering a scalable and efficient solution for enhancing patient privacy protection.
We present the Virology Capabilities Test (VCT), a large language model (LLM) benchmark that measures the capability to troubleshoot complex virology laboratory protocols. Constructed from the inputs of dozens of PhD-level expert virologists, VCT consists of $322$ multimodal questions covering fundamental, tacit, and visual knowledge that is essential for practical work in virology laboratories. VCT is difficult: expert virologists with access to the internet score an average of $22.1\%$ on questions specifically in their sub-areas of expertise. However, the most performant LLM, OpenAI's o3, reaches $43.8\%$ accuracy, outperforming $94\%$ of expert virologists even within their sub-areas of specialization. The ability to provide expert-level virology troubleshooting is inherently dual-use: it is useful for beneficial research, but it can also be misused. Therefore, the fact that publicly available models outperform virologists on VCT raises pressing governance considerations. We propose that the capability of LLMs to provide expert-level troubleshooting of dual-use virology work should be integrated into existing frameworks for handling dual-use technologies in the life sciences.
Genome modeling conventionally treats gene sequence as a language, reflecting its structured motifs and long-range dependencies analogous to linguistic units and organization principles such as words and syntax. Recent studies utilize advanced neural networks, ranging from convolutional and recurrent models to Transformer-based models, to capture contextual information of gene sequence, with the primary goal of obtaining effective gene sequence representations and thus enhance the models' understanding of various running gene samples. However, these approaches often directly apply language modeling techniques to gene sequences and do not fully consider the intrinsic information organization in them, where they do not consider how units at different granularities contribute to representation. In this paper, we propose DNAZEN, an enhanced genomic representation framework designed to learn from various granularities in gene sequences, including small polymers and G-grams that are combinations of several contiguous polymers. Specifically, we extract the G-grams from large-scale genomic corpora through an unsupervised approach to construct the G-gram vocabulary, which is used to provide G-grams in the learning process of DNA sequences through dynamically matching from running gene samples. A Transformer-based G-gram encoder is also proposed and the matched G-grams are fed into it to compute their representations and integrated into the encoder for basic unit (E4BU), which is responsible for encoding small units and maintaining the learning and inference process. To further enhance the learning process, we propose whole G-gram masking to train DNAZEN, where the model largely favors the selection of each entire G-gram to mask rather than an ordinary masking mechanism performed on basic units. Experiments on benchmark datasets demonstrate the effectiveness of DNAZEN on various downstream tasks.
Today's security tools predominantly rely on predefined rules crafted by experts, making them poorly adapted to the emergence of software supply chain attacks. To tackle this limitation, we propose a novel tool, RuleLLM, which leverages large language models (LLMs) to automate rule generation for OSS ecosystems. RuleLLM extracts metadata and code snippets from malware as its input, producing YARA and Semgrep rules that can be directly deployed in software development. Specifically, the rule generation task involves three subtasks: crafting rules, refining rules, and aligning rules. To validate RuleLLM's effectiveness, we implemented a prototype system and conducted experiments on the dataset of 1,633 malicious packages. The results are promising that RuleLLM generated 763 rules (452 YARA and 311 Semgrep) with a precision of 85.2\% and a recall of 91.8\%, outperforming state-of-the-art (SOTA) tools and scored-based approaches. We further analyzed generated rules and proposed a rule taxonomy: 11 categories and 38 subcategories.
Code editing is a foundational task in software development, where its effectiveness depends on whether it introduces desired code property changes without changing the original code's intended functionality. Existing approaches often formulate code editing as an implicit end-to-end task, omitting the fact that code-editing procedures inherently consist of discrete and explicit steps. Thus, they suffer from suboptimal performance and lack of robustness and generalization. We introduce EditLord, a code editing framework that makes the code transformation steps explicit. Our key insight is to employ a language model (LM) as an inductive learner to extract code editing rules from the training code pairs as concise meta-rule sets. Such rule sets will be manifested for each training sample to augment them for finetuning or assist in prompting- and iterative-based code editing. EditLordoutperforms the state-of-the-art by an average of 22.7% in editing performance and 58.1% in robustness while achieving 20.2% higher functional correctness across critical software engineering and security applications, LM models, and editing modes.
We present Bielik 11B v2, a state-of-the-art language model optimized for Polish text processing. Built on the Mistral 7B v0.2 architecture and scaled to 11B parameters using depth up-scaling, this model demonstrates exceptional performance across Polish language benchmarks while maintaining strong cross-lingual capabilities. We introduce two key technical innovations: Weighted Instruction Cross-Entropy Loss, which optimizes learning across diverse instruction types by assigning quality-based weights to training examples, and Adaptive Learning Rate, which dynamically adjusts based on context length. Comprehensive evaluation across multiple benchmarks demonstrates that Bielik 11B v2 outperforms many larger models, including those with 2-6 times more parameters, and significantly surpasses other specialized Polish language models on tasks ranging from linguistic understanding to complex reasoning. The model's parameter efficiency and extensive quantization options enable deployment across various hardware configurations, advancing Polish language AI capabilities and establishing new benchmarks for resource-efficient language modeling in less-represented languages.
Target-specific peptides, such as conotoxins, exhibit exceptional binding affinity and selectivity toward ion channels and receptors. However, their therapeutic potential remains underutilized due to the limited diversity of natural variants and the labor-intensive nature of traditional optimization strategies. Here, we present CreoPep, a deep learning-based conditional generative framework that integrates masked language modeling with a progressive masking scheme to design high-affinity peptide mutants while uncovering novel structural motifs. CreoPep employs an integrative augmentation pipeline, combining FoldX-based energy screening with temperature-controlled multinomial sampling, to generate structurally and functionally diverse peptides that retain key pharmacological properties. We validate this approach by designing conotoxin inhibitors targeting the $\alpha$7 nicotinic acetylcholine receptor, achieving submicromolar potency in electrophysiological assays. Structural analysis reveals that CreoPep-generated variants engage in both conserved and novel binding modes, including disulfide-deficient forms, thus expanding beyond conventional design paradigms. Overall, CreoPep offers a robust and generalizable platform that bridges computational peptide design with experimental validation, accelerating the discovery of next-generation peptide therapeutics.
Guiding biological systems toward desired states, such as morphogenetic outcomes, remains a fundamental challenge with far-reaching implications for medicine and synthetic biology. While large language models (LLMs) have enabled natural language as an interface for interpretable control in AI systems, their use as mediators for steering biological or cellular dynamics remains largely unexplored. In this work, we present a functional pipeline that translates natural language prompts into spatial vector fields capable of directing simulated cellular collectives. Our approach combines a large language model with an evolvable neural controller (Prompt-to-Intervention, or P2I), optimized via evolutionary strategies to generate behaviors such as clustering or scattering in a simulated 2D environment. We demonstrate that even with constrained vocabulary and simplified cell models, evolved P2I networks can successfully align cellular dynamics with user-defined goals expressed in plain language. This work offers a complete loop from language input to simulated bioelectric-like intervention to behavioral output, providing a foundation for future systems capable of natural language-driven cellular control.
As language models (LMs) are increasingly deployed as autonomous agents, their robust adherence to human-assigned objectives becomes crucial for safe operation. When these agents operate independently for extended periods without human oversight, even initially well-specified goals may gradually shift. Detecting and measuring goal drift - an agent's tendency to deviate from its original objective over time - presents significant challenges, as goals can shift gradually, causing only subtle behavioral changes. This paper proposes a novel approach to analyzing goal drift in LM agents. In our experiments, agents are first explicitly given a goal through their system prompt, then exposed to competing objectives through environmental pressures. We demonstrate that while the best-performing agent (a scaffolded version of Claude 3.5 Sonnet) maintains nearly perfect goal adherence for more than 100,000 tokens in our most difficult evaluation setting, all evaluated models exhibit some degree of goal drift. We also find that goal drift correlates with models' increasing susceptibility to pattern-matching behaviors as the context length grows.
Chemical reaction and retrosynthesis prediction are fundamental tasks in drug discovery. Recently, large language models (LLMs) have shown potential in many domains. However, directly applying LLMs to these tasks faces two major challenges: (i) lacking a large-scale chemical synthesis-related instruction dataset; (ii) ignoring the close correlation between reaction and retrosynthesis prediction for the existing fine-tuning strategies. To address these challenges, we propose ChemDual, a novel LLM framework for accurate chemical synthesis. Specifically, considering the high cost of data acquisition for reaction and retrosynthesis, ChemDual regards the reaction-and-retrosynthesis of molecules as a related recombination-and-fragmentation process and constructs a large-scale of 4.4 million instruction dataset. Furthermore, ChemDual introduces an enhanced LLaMA, equipped with a multi-scale tokenizer and dual-task learning strategy, to jointly optimize the process of recombination and fragmentation as well as the tasks between reaction and retrosynthesis prediction. Extensive experiments on Mol-Instruction and USPTO-50K datasets demonstrate that ChemDual achieves state-of-the-art performance in both predictions of reaction and retrosynthesis, outperforming the existing conventional single-task approaches and the general open-source LLMs. Through molecular docking analysis, ChemDual generates compounds with diverse and strong protein binding affinity, further highlighting its strong potential in drug design.
We introduce Bielik v3, a series of parameter-efficient generative text models (1.5B and 4.5B) optimized for Polish language processing. These models demonstrate that smaller, well-optimized architectures can achieve performance comparable to much larger counterparts while requiring substantially fewer computational resources. Our approach incorporates several key innovations: a custom Polish tokenizer (APT4) that significantly improves token efficiency, Weighted Instruction Cross-Entropy Loss to balance learning across instruction types, and Adaptive Learning Rate that dynamically adjusts based on training progress. Trained on a meticulously curated corpus of 292 billion tokens spanning 303 million documents, these models excel across multiple benchmarks, including the Open PL LLM Leaderboard, Complex Polish Text Understanding Benchmark, Polish EQ-Bench, and Polish Medical Leaderboard. The 4.5B parameter model achieves results competitive with models 2-3 times its size, while the 1.5B model delivers strong performance despite its extremely compact profile. These advances establish new benchmarks for parameter-efficient language modeling in less-represented languages, making high-quality Polish language AI more accessible for resource-constrained applications.
Large Language Models (LLMs) based on autoregressive, decoder-only Transformers generate text one token at a time, where a token represents a discrete unit of text. As each newly produced token is appended to the partial output sequence, the length grows and so does the memory and compute load, due to the expanding key-value caches, which store intermediate representations of all previously generated tokens in the multi-head attention (MHA) layer. As this iterative process steadily increases memory and compute demands, layer-based partitioning in resource-constrained edge environments often results in memory overload or high inference latency. To address this and reduce inference latency, we propose a resource-aware Transformer architecture partitioning algorithm, where the partitioning decision is updated at regular intervals during token generation. The approach is myopic in that it is based on instantaneous information about device resource availability and network link bandwidths. When first executed, the algorithm places blocks on devices, and in later executions, it migrates these blocks among devices so that the sum of migration delay and inference delay remains low. Our approach partitions the decoder at the attention head level, co-locating each attention head with its key-value cache and allowing dynamic migrations whenever resources become tight. By allocating different attention heads to different devices, we exploit parallel execution of attention heads and thus achieve substantial reductions in inference delays. Our experiments show that in small-scale settings (3-5 devices), the proposed method achieves within 15 to 20 percent of an exact optimal solver's latency, while in larger-scale tests it achieves notable improvements in inference speed and memory usage compared to state-of-the-art layer-based partitioning approaches.
The increasing complexity and scale of the Internet of Things (IoT) have made security a critical concern. This paper presents a novel Large Language Model (LLM)-based framework for comprehensive threat detection and prevention in IoT environments. The system integrates lightweight LLMs fine-tuned on IoT-specific datasets (IoT-23, TON_IoT) for real-time anomaly detection and automated, context-aware mitigation strategies optimized for resource-constrained devices. A modular Docker-based deployment enables scalable and reproducible evaluation across diverse network conditions. Experimental results in simulated IoT environments demonstrate significant improvements in detection accuracy, response latency, and resource efficiency over traditional security methods. The proposed framework highlights the potential of LLM-driven, autonomous security solutions for future IoT ecosystems.
Large language models (LLMs) excel at generating code from natural language instructions, yet they often lack an understanding of security vulnerabilities. This limitation makes it difficult for LLMs to avoid security risks in generated code, particularly in high-security programming tasks such as smart contract development for blockchain. Researchers have attempted to enhance the vulnerability awareness of these models by training them to differentiate between vulnerable and fixed code snippets. However, this approach relies heavily on manually labeled vulnerability data, which is only available for popular languages like Python and C++. For low-resource languages like Solidity, used in smart contracts, large-scale annotated datasets are scarce and difficult to obtain. To address this challenge, we introduce CodeBC, a code generation model specifically designed for generating secure smart contracts in blockchain. CodeBC employs a three-stage fine-tuning approach based on CodeLlama, distinguishing itself from previous methods by not relying on pairwise vulnerability location annotations. Instead, it leverages vulnerability and security tags to teach the model the differences between vulnerable and secure code. During the inference phase, the model leverages security tags to generate secure and robust code. Experimental results demonstrate that CodeBC outperforms baseline models in terms of BLEU, CodeBLEU, and compilation pass rates, while significantly reducing vulnerability rates. These findings validate the effectiveness and cost-efficiency of our three-stage fine-tuning strategy, making CodeBC a promising solution for generating secure smart contract code.
Best-of-$n$ (BoN) sampling is a practical approach for aligning language model outputs with human preferences without expensive fine-tuning. BoN sampling is performed by generating $n$ responses to a prompt and then selecting the sample that maximizes a reward function. BoN yields high reward values in practice at a distortion cost, as measured by the KL-divergence between the sampled and original distribution. This distortion is coarsely controlled by varying the number of samples: larger $n$ yields a higher reward at a higher distortion cost. We introduce Soft Best-of-$n$ sampling, a generalization of BoN that allows for smooth interpolation between the original distribution and reward-maximizing distribution through a temperature parameter $\lambda$. We establish theoretical guarantees showing that Soft Best-of-$n$ sampling converges sharply to the optimal tilted distribution at a rate of $O(1/n)$ in KL and the expected (relative) reward. For sequences of discrete outputs, we analyze an additive reward model that reveals the fundamental limitations of blockwise sampling.
This study explores the application of chaos engineering to enhance the robustness of Large Language Model-Based Multi-Agent Systems (LLM-MAS) in production-like environments under real-world conditions. LLM-MAS can potentially improve a wide range of tasks, from answering questions and generating content to automating customer support and improving decision-making processes. However, LLM-MAS in production or preproduction environments can be vulnerable to emergent errors or disruptions, such as hallucinations, agent failures, and agent communication failures. This study proposes a chaos engineering framework to proactively identify such vulnerabilities in LLM-MAS, assess and build resilience against them, and ensure reliable performance in critical applications.
Given a text, can we determine whether it was generated by a large language model (LLM) or by a human? A widely studied approach to this problem is watermarking. We propose an undetectable and elementary watermarking scheme in the closed setting. Also, in the harder open setting, where the adversary has access to most of the model, we propose an unremovable watermarking scheme.
Uncontrollable autonomous replication of language model agents poses a critical safety risk. To better understand this risk, we introduce RepliBench, a suite of evaluations designed to measure autonomous replication capabilities. RepliBench is derived from a decomposition of these capabilities covering four core domains: obtaining resources, exfiltrating model weights, replicating onto compute, and persisting on this compute for long periods. We create 20 novel task families consisting of 86 individual tasks. We benchmark 5 frontier models, and find they do not currently pose a credible threat of self-replication, but succeed on many components and are improving rapidly. Models can deploy instances from cloud compute providers, write self-propagating programs, and exfiltrate model weights under simple security setups, but struggle to pass KYC checks or set up robust and persistent agent deployments. Overall the best model we evaluated (Claude 3.7 Sonnet) has a >50% pass@10 score on 15/20 task families, and a >50% pass@10 score for 9/20 families on the hardest variants. These findings suggest autonomous replication capability could soon emerge with improvements in these remaining areas or with human assistance.
Free play is a fundamental aspect of early childhood education, supporting children's cognitive, social, emotional, and motor development. However, assessing children's development during free play poses significant challenges due to the unstructured and spontaneous nature of the activity. Traditional assessment methods often rely on direct observations by teachers, parents, or researchers, which may fail to capture comprehensive insights from free play and provide timely feedback to educators. This study proposes an innovative approach combining Large Language Models (LLMs) with learning analytics to analyze children's self-narratives of their play experiences. The LLM identifies developmental abilities, while performance scores across different play settings are calculated using learning analytics techniques. We collected 2,224 play narratives from 29 children in a kindergarten, covering four distinct play areas over one semester. According to the evaluation results from eight professionals, the LLM-based approach achieved high accuracy in identifying cognitive, motor, and social abilities, with accuracy exceeding 90% in most domains. Moreover, significant differences in developmental outcomes were observed across play settings, highlighting each area's unique contributions to specific abilities. These findings confirm that the proposed approach is effective in identifying children's development across various free play settings. This study demonstrates the potential of integrating LLMs and learning analytics to provide child-centered insights into developmental trajectories, offering educators valuable data to support personalized learning and enhance early childhood education practices.
Financial sectors are rapidly adopting language model technologies, yet evaluating specialized RAG systems in this domain remains challenging. This paper introduces SMARTFinRAG, addressing three critical gaps in financial RAG assessment: (1) a fully modular architecture where components can be dynamically interchanged during runtime; (2) a document-centric evaluation paradigm generating domain-specific QA pairs from newly ingested financial documents; and (3) an intuitive interface bridging research-implementation divides. Our evaluation quantifies both retrieval efficacy and response quality, revealing significant performance variations across configurations. The platform's open-source architecture supports transparent, reproducible research while addressing practical deployment challenges faced by financial institutions implementing RAG systems.