Context: Open-source Pre-Trained Models (PTMs) provide extensive resources for various Machine Learning (ML) tasks, yet these resources lack a classification tailored to Software Engineering (SE) needs to support the reliable identification and reuse of models for SE. Objective: To address this gap, we derive a taxonomy encompassing 147 SE tasks and apply an SE-oriented classification to PTMs in a popular open-source ML repository, Hugging Face (HF). Method: Our repository mining study followed a five-phase pipeline: (i) identification SE tasks from the literature; (ii) collection of PTM data from the HF API, including model card descriptions and metadata, and the abstracts of the associated arXiv papers; (iii) text processing to ensure consistency; (iv) a two-phase validation of SE relevance, involving humans and LLM assistance, supported by five pilot studies with human annotators and a generalization test; (v) and data analysis. This process yielded a curated catalogue of 2,205 SE PTMs. Results: We find that most SE PTMs target code generation and coding, emphasizing implementation over early or late development stages. In terms of ML tasks, text generation dominates within SE PTMs. Notably, the number of SE PTMs has increased markedly since 2023 Q2, while evaluation remains limited: only 9.6% report benchmark results, mostly scoring below 50%. Conclusions: Our catalogue reveals documentation and transparency gaps, highlights imbalances across SDLC phases, and provides a foundation for automated SE scenarios, such as the sampling and selection of suitable PTMs.

Recent efficient sequence modeling methods such as Gated DeltaNet, TTT, and RWKV-7 have achieved performance improvements by supervising the recurrent memory management through Delta learning rule. Unlike previous state-space models (e.g., Mamba) and gated linear attentions (e.g., GLA), these models introduce interactions between the recurrent state and the key vector, structurally resembling bilinear systems. In this paper, we first introduce the concept of Bilinear RNNs with a comprehensive analysis on the advantages and limitations of these models. Then, based on closed-loop control theory, we propose a novel Bilinear RNN variant named Comba, which adopts a scalar-plus-low-rank state transition, with both state feedback and output feedback corrections. We also implement a hardware-efficient chunk-wise parallel kernel in Triton and train models with 340M/1.3B parameters on large-scale corpus. Comba demonstrates superior performance and computation efficiency in both language and vision modeling.

Genomic Foundation Models (GFMs), such as Evolutionary Scale Modeling (ESM), have demonstrated significant success in variant effect prediction. However, their adversarial robustness remains largely unexplored. To address this gap, we propose SafeGenes: a framework for Secure analysis of genomic foundation models, leveraging adversarial attacks to evaluate robustness against both engineered near-identical adversarial Genes and embedding-space manipulations. In this study, we assess the adversarial vulnerabilities of GFMs using two approaches: the Fast Gradient Sign Method (FGSM) and a soft prompt attack. FGSM introduces minimal perturbations to input sequences, while the soft prompt attack optimizes continuous embeddings to manipulate model predictions without modifying the input tokens. By combining these techniques, SafeGenes provides a comprehensive assessment of GFM susceptibility to adversarial manipulation. Targeted soft prompt attacks induced severe degradation in MLM-based shallow architectures such as ProteinBERT, while still producing substantial failure modes even in high-capacity foundation models such as ESM1b and ESM1v. These findings expose critical vulnerabilities in current foundation models, opening new research directions toward improving their security and robustness in high-stakes genomic applications such as variant effect prediction.

Current LLMs are trained to refuse potentially harmful input queries regardless of whether users actually had harmful intents, causing a tradeoff between safety and user experience. Through a study of 480 participants evaluating 3,840 query-response pairs, we examine how different refusal strategies affect user perceptions across varying motivations. Our findings reveal that response strategy largely shapes user experience, while actual user motivation has negligible impact. Partial compliance -- providing general information without actionable details -- emerges as the optimal strategy, reducing negative user perceptions by over 50% to flat-out refusals. Complementing this, we analyze response patterns of 9 state-of-the-art LLMs and evaluate how 6 reward models score different refusal strategies, demonstrating that models rarely deploy partial compliance naturally and reward models currently undervalue it. This work demonstrates that effective guardrails require focusing on crafting thoughtful refusals rather than detecting intent, offering a path toward AI safety mechanisms that ensure both safety and sustained user engagement.

The democratization of generative AI introduces new forms of human-AI interaction and raises urgent safety, ethical, and cybersecurity concerns. We develop a socio-technical explanation for how generative AI enables and scales cybercrime. Drawing on affordance theory and technological amplification, we argue that generative AI systems create new action possibilities for cybercriminals and magnify pre-existing malicious intent by lowering expertise barriers and increasing attack efficiency. To illustrate this framework, we conduct interrupted time series analyses of two large datasets: (1) 464,190,074 malicious IP address reports from AbuseIPDB, and (2) 281,115 cryptocurrency scam reports from Chainabuse. Using November 30, 2022, as a high-salience public-access shock, we estimate the counterfactual trajectory of reported cyber abuse absent the release, providing an early-warning impact assessment of a general-purpose AI technology. Across both datasets, we observe statistically significant post-intervention increases in reported malicious activity, including an immediate increase of over 1.12 million weekly malicious IP reports and about 722 weekly cryptocurrency scam reports, with sustained growth in the latter. We discuss implications for AI governance, platform-level regulation, and cyber resilience, emphasizing the need for multi-layer socio-technical strategies that help key stakeholders maximize AI's benefits while mitigating its growing cybercrime risks.

Transformer-based language models (LMs) have achieved widespread empirical success, but their theoretical expressive power remains only partially understood. In this work, we analyze a restricted idealization of fixed-precision transformers with strict future masking, soft attention, and no positional encodings. We establish that this class of models is exactly as expressive as a specific fragment of linear temporal logic that contains only a single temporal operator: the past operator. We further connect this fragment to established classes in formal language theory, automata theory, and algebra, yielding a unified framework for understanding transformer expressivity under this idealization. Finally, we present empirical results that align closely with our theory: transformers trained on languages within their characterized expressive capacity generalize reliably across sequence lengths, while they consistently fail to generalize on languages beyond it.

Direct alignment methods typically train large language models (LLMs) by contrasting the likelihoods of preferred and dispreferred responses. While effective at capturing relative preferences, these methods are widely observed to suppress the absolute likelihoods of example responses. As a result, aligned models can deviate from expected patterns, exhibiting rewar-hacking effect even without an explicit reward model. This fundamental limitation of contrastive alignment, which we term likelihood underdetermination, motivates us to revisit direct preference optimization (DPO) -- the seminal direct alignment method. Interestingly, we show that the DPO loss admits a principled decomposition. The reformulated loss not only extends naturally to a broader range of feedback types, but also unveils the root cause of likelihood underdetermination. Specifically, we identify that standard DPO implicitly oversimplifies a regularizer in the reformulated loss; restoring this full term effectively resolves the underdetermination. Building on these insights, we introduce PRoximalized PReference Optimization (PRO), a unified alignment method that accommodates diverse feedback types while eliminating likelihood underdetermination through an efficient approximation of the full regularizer. Empirical evaluations demonstrate the consistent superiority of PRO over existing methods across pairwise, binary and scalar feedback.

DeepSeek-R1 has demonstrated powerful reasoning capabilities in the text domain through stable reinforcement learning (RL). Recently, in the multimodal domain, works have begun to directly apply RL to generate R1-like free-form reasoning for Visual Question Answering (VQA) tasks. However, multimodal tasks share an intrinsically different nature from textual tasks, which heavily rely on the understanding of the input image to solve the problem. Therefore, such free-form reasoning faces two critical limitations in the VQA task: (1) Extended reasoning chains diffuse visual focus away from task-critical regions, degrading answer accuracy. (2) Unverifiable intermediate steps amplify policy-gradient variance and computational costs overhead. To address these issues, in this paper, we introduce SATORI ($\textbf{S}patially$ $\textbf{A}nchored$ $\textbf{T}ask$ $\textbf{O}ptimization$ with $\textbf{R}e\textbf{I}nforcement$ Learning), which decomposes VQA into three verifiable stages, including global image captioning, region localization, and answer prediction, each supplying explicit reward signals. Furthermore, we also introduce VQA-Verify, a 12k dataset annotated with answer-aligned captions and bounding-boxes to facilitate training. Experiments demonstrate consistent performance improvements across seven VQA benchmarks, achieving up to $15.7\%$ improvement in accuracy in accuracy compared to the R1-like baseline. Our analysis of the attention map confirms enhanced focus on critical regions, which brings improvements in accuracy. Our code is available at https://github.com/justairr/SATORI-R1.

Physics-informed neural networks (PINNs) have emerged as a promising approach for solving complex fluid dynamics problems, yet their application to fluid-structure interaction (FSI) problems with moving boundaries remains largely unexplored. This work addresses the critical challenge of modeling FSI systems with moving interfaces, where traditional unified PINN architectures struggle to capture the distinct physics governing fluid and structural domains simultaneously. We present an innovative Eulerian-Lagrangian PINN architecture that integrates immersed boundary method (IBM) principles to solve FSI problems with moving boundary conditions. Our approach fundamentally departs from conventional unified architectures by introducing domain-specific neural networks: an Eulerian network for fluid dynamics and a Lagrangian network for structural interfaces, coupled through physics-based constraints. Additionally, we incorporate learnable B-spline activation functions with SiLU to capture both localized high-gradient features near interfaces and global flow patterns. Empirical studies on a 2D cavity flow problem involving a moving solid structure show that while baseline unified PINNs achieve reasonable velocity predictions, they suffer from substantial pressure errors (12.9%) in structural regions. Our Eulerian-Lagrangian architecture with learnable activations (EL-L) achieves better performance across all metrics, improving accuracy by 24.1-91.4% and particularly reducing pressure errors from 12.9% to 2.39%. These results demonstrate that domain decomposition aligned with physical principles, combined with locality-aware activation functions, is essential for accurate FSI modeling within the PINN framework.

Large language models (LLMs) excel in tasks like question answering and dialogue, but complex tasks requiring interaction, such as negotiation and persuasion, require additional long-horizon reasoning and planning. Reinforcement learning (RL) fine-tuning can enable such planning in principle, but suffers from drawbacks that hinder scalability. In particular, multi-turn RL training incurs high memory and computational costs, which are exacerbated when training LLMs as policies. Furthermore, the largest LLMs do not expose the APIs necessary to be trained in such manner. As a result, modern methods to improve the reasoning of LLMs rely on sophisticated prompting mechanisms rather than RL fine-tuning. To remedy this, we propose a novel approach that uses goal-conditioned value functions to guide the reasoning of LLM agents, that scales even to large API-based models. These value functions predict how a task will unfold given an action, allowing the LLM agent to evaluate multiple possible outcomes, both positive and negative, to plan effectively. In addition, these value functions are trained over reasoning steps rather than full actions, to be a concise and light-weight module that facilitates decision-making in multi-turn interactions. We validate our method on tasks requiring interaction, including tool use, social deduction, and dialogue, demonstrating superior performance over both RL fine-tuning and prompting methods while maintaining efficiency and scalability.