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arXiv:2509.05481v1 Announce Type: new Abstract: Biomolecular Neural Networks (BNNs), artificial neural networks with biologically synthesizable architectures, achieve universal function approximation capabilities beyond simple biological circuits. However, training BNNs remains challenging due to the lack of target data. To address this, we propose leveraging Signal Temporal Logic (STL) specifications to define training objectives for BNNs. We build on the quantitative semantics of STL, enabling gradient-based optimization of the BNN weights, and introduce a learning algorithm that enables BNNs to perform regression and control tasks in biological systems. Specifically, we investigate two regression problems in which we train BNNs to act as reporters of dysregulated states, and a feedback control problem in which we train the BNN in closed-loop with a chronic disease model, learning to reduce inflammation while avoiding adverse responses to external infections. Our numerical experiments demonstrate that STL-based learning can solve the investigated regression and control tasks efficiently.

arXiv:2509.05449v1 Announce Type: new Abstract: Membership inference attacks (MIAs) reveal whether specific data was used to train machine learning models, serving as important tools for privacy auditing and compliance assessment. Recent studies have reported that MIAs perform only marginally better than random guessing against large language models, suggesting that modern pre-training approaches with massive datasets may be free from privacy leakage risks. Our work offers a complementary perspective to these findings by exploring how examining LLMs' internal representations, rather than just their outputs, may provide additional insights into potential membership inference signals. Our framework, emph{memTrace}, follows what we call enquote{neural breadcrumbs} extracting informative signals from transformer hidden states and attention patterns as they process candidate sequences. By analyzing layer-wise representation dynamics, attention distribution characteristics, and cross-layer transition patterns, we detect potential memorization fingerprints that traditional loss-based approaches may not capture. This approach yields strong membership detection across several model families achieving average AUC scores of 0.85 on popular MIA benchmarks. Our findings suggest that internal model behaviors can reveal aspects of training data exposure even when output-based signals appear protected, highlighting the need for further research into membership privacy and the development of more robust privacy-preserving training techniques for large language models.

arXiv:2509.05429v1 Announce Type: new Abstract: Graph Neural Networks (GNNs) have emerged as powerful models for learning from graph-structured data. However, their widespread adoption has raised serious privacy concerns. While prior research has primarily focused on edge-level privacy, a critical yet underexplored threat lies in topology privacy - the confidentiality of the graph's overall structure. In this work, we present a comprehensive study on topology privacy risks in GNNs, revealing their vulnerability to graph-level inference attacks. To this end, we propose a suite of Topology Inference Attacks (TIAs) that can reconstruct the structure of a target training graph using only black-box access to a GNN model. Our findings show that GNNs are highly susceptible to these attacks, and that existing edge-level differential privacy mechanisms are insufficient as they either fail to mitigate the risk or severely compromise model accuracy. To address this challenge, we introduce Private Graph Reconstruction (PGR), a novel defense framework designed to protect topology privacy while maintaining model accuracy. PGR is formulated as a bi-level optimization problem, where a synthetic training graph is iteratively generated using meta-gradients, and the GNN model is concurrently updated based on the evolving graph. Extensive experiments demonstrate that PGR significantly reduces topology leakage with minimal impact on model accuracy. Our code is anonymously available at https://github.com/JeffffffFu/PGR.

arXiv:2505.08299v2 Announce Type: replace Abstract: State-space models (SSMs), particularly the Mamba architecture, have emerged as powerful alternatives to Transformers for sequence modeling, offering linear-time complexity and competitive performance across diverse tasks. However, their large parameter counts pose significant challenges for deployment in resource-constrained environments. We propose a novel unstructured pruning framework tailored for Mamba models that achieves up to 70% parameter reduction while retaining over 95% of the original performance. Our approach integrates three key innovations: (1) a gradient-aware magnitude pruning technique that combines weight magnitude and gradient information to identify less critical parameters, (2) an iterative pruning schedule that gradually increases sparsity to maintain model stability, and (3) a global pruning strategy that optimizes parameter allocation across the entire model. Through extensive experiments on WikiText-103, Long Range Arena, and ETT time-series benchmarks, we demonstrate significant efficiency gains with minimal performance degradation. Our analysis of pruning effects on Mamba's components reveals critical insights into the architecture's redundancy and robustness, enabling practical deployment in resource-constrained settings while broadening Mamba's applicability.

arXiv:2509.05489v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards has significantly advanced reasoning in large language models (LLMs), but such signals remain coarse, offering only binary correctness feedback. This limitation often results in inefficiencies, including overly verbose reasoning and high computational cost, while existing solutions often compromise accuracy. To address this, we introduce self-aligned reward (SAR), a self-guided signal that complements verifiable rewards to encourage both reasoning accuracy and efficiency. SAR is defined as the relative perplexity difference between an answer conditioned on the query and the standalone answer, thereby favoring responses that are concise and query-specific. Quantitative analysis reveals that SAR reliably distinguishes answer quality: concise, correct answers score higher than redundant ones, and partially correct answers score higher than entirely incorrect ones. Evaluation on 4 models across 7 benchmarks shows that integrating SAR with prevalent RL algorithms like PPO and GRPO improves accuracy by 4%, while reducing inference cost by 30%. Further analysis demonstrates that SAR achieves a Pareto-optimal trade-off between correctness and efficiency compared to reward signals based on length or self-confidence. We also show that SAR shortens responses while preserving advanced reasoning behaviors, demonstrating its ability to suppress unnecessary elaboration without losing critical reasoning. These results highlight the promise of self-aligned reward as a fine-grained complement to verifiable rewards, paving the way for more efficient and effective LLM training.

arXiv:2507.07032v2 Announce Type: replace Abstract: Protein structure prediction often hinges on multiple sequence alignments (MSAs), which underperform on low-homology and orphan proteins. We introduce PLAME, a lightweight MSA design framework that leverages evolutionary embeddings from pretrained protein language models to generate MSAs that better support downstream folding. PLAME couples these embeddings with a conservation-diversity loss that balances agreement on conserved positions with coverage of plausible sequence variation. Beyond generation, we develop (i) an MSA selection strategy to filter high-quality candidates and (ii) a sequence-quality metric that is complementary to depth-based measures and predictive of folding gains. On AlphaFold2 low-homology/orphan benchmarks, PLAME delivers state-of-the-art improvements in structure accuracy (e.g., lDDT/TM-score), with consistent gains when paired with AlphaFold3. Ablations isolate the benefits of the selection strategy, and case studies elucidate how MSA characteristics shape AlphaFold confidence and error modes. Finally, we show PLAME functions as a lightweight adapter, enabling ESMFold to approach AlphaFold2-level accuracy while retaining ESMFold-like inference speed. PLAME thus provides a practical path to high-quality folding for proteins lacking strong evolutionary neighbors.

arXiv:2509.05542v1 Announce Type: new Abstract: Training multimodal process reward models (PRMs) is challenged by distribution shifts and noisy data. We introduce DreamPRM-1.5, an instance-reweighted framework that adaptively adjusts the importance of each training example via bi-level optimization. We design two complementary strategies: Instance Table, effective for smaller datasets, and Instance Net, scalable to larger ones. Integrated into test-time scaling, DreamPRM-1.5 achieves 84.6 accuracy on the MMMU benchmark, surpassing GPT-5.

arXiv:2402.12391v3 Announce Type: replace-cross Abstract: Machine learning has emerged as a powerful tool for scientific discovery, enabling researchers to extract meaningful insights from complex datasets. For instance, it has facilitated the identification of disease-predictive genes from gene expression data, significantly advancing healthcare. However, the traditional process for analyzing such datasets demands substantial human effort and expertise for the data selection, processing, and analysis. To address this challenge, we introduce a novel framework, a Team of AI-made Scientists (TAIS), designed to streamline the scientific discovery pipeline. TAIS comprises simulated roles, including a project manager, data engineer, and domain expert, each represented by a Large Language Model (LLM). These roles collaborate to replicate the tasks typically performed by data scientists, with a specific focus on identifying disease-predictive genes. Furthermore, we have curated a benchmark dataset to assess TAIS's effectiveness in gene identification, demonstrating our system's potential to significantly enhance the efficiency and scope of scientific exploration. Our findings represent a solid step towards automating scientific discovery through large language models.

arXiv:2509.05545v1 Announce Type: new Abstract: Solving long-horizon goal-conditioned tasks remains a significant challenge in reinforcement learning (RL). Hierarchical reinforcement learning (HRL) addresses this by decomposing tasks into more manageable sub-tasks, but the automatic discovery of the hierarchy and the joint training of multi-level policies often suffer from instability and can lack theoretical guarantees. In this paper, we introduce Reinforcement Learning with Anticipation (RLA), a principled and potentially scalable framework designed to address these limitations. The RLA agent learns two synergistic models: a low-level, goal-conditioned policy that learns to reach specified subgoals, and a high-level anticipation model that functions as a planner, proposing intermediate subgoals on the optimal path to a final goal. The key feature of RLA is the training of the anticipation model, which is guided by a principle of value geometric consistency, regularized to prevent degenerate solutions. We present proofs that RLA approaches the globally optimal policy under various conditions, establishing a principled and convergent method for hierarchical planning and execution in long-horizon goal-conditioned tasks.

arXiv:2502.03365v2 Announce Type: replace-cross Abstract: Software vulnerabilities are commonly detected via static analysis, penetration testing, and fuzzing. They can also be found by running unit tests - so-called vulnerability-witnessing tests - that stimulate the security-sensitive behavior with crafted inputs. Developing such tests is difficult and time-consuming; thus, automated data-driven approaches could help developers intercept vulnerabilities earlier. However, training and validating such approaches require a lot of data, which is currently scarce. This paper introduces VUTECO, a deep learning-based approach for collecting instances of vulnerability-witnessing tests from Java repositories. VUTECO carries out two tasks: (1) the "Finding" task to determine whether a test case is security-related, and (2) the "Matching" task to relate a test case to the exact vulnerability it is witnessing. VUTECO successfully addresses the Finding task, achieving perfect precision and 0.83 F0.5 score on validated test cases in VUL4J and returning 102 out of 145 (70%) correct security-related test cases from 244 open-source Java projects. Despite showing sufficiently good performance for the Matching task - i.e., 0.86 precision and 0.68 F0.5 score - VUTECO failed to retrieve any valid match in the wild. Nevertheless, we observed that in almost all of the matches, the test case was still security-related despite being matched to the wrong vulnerability. In the end, VUTECO can help find vulnerability-witnessing tests, though the matching with the right vulnerability is yet to be solved; the findings obtained lay the stepping stone for future research on the matter.