OpenRaiser/Intern-Atlas huggingface dataset:
RoSA: Enhancing Parameter-Efficient Fine-Tuning via RoPE-aware Selective Adaptation in Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Fine-tuning large language models is essential for task-specific adaptation, yet it remains computationally prohibitive. Parameter-Efficient Fine-Tuning (PEFT) methods have emerged as a solution, but current approaches typically ignore the distinct roles of model components and the heterogeneous importance across layers, thereby limiting adaptation efficiency. Motivated by the observation that Rotary Position Embeddings (RoPE) induce critical activations in the low-frequency dimensions of attention states, we propose RoPE-aware Selective Adaptation (RoSA), a novel PEFT framework that allocates trainable parameters in a more targeted and effective manner. RoSA comprises a RoPE-aware Attention Enhancement (RoAE) module, which selectively enhances the low-frequency components of RoPE-influenced attention states, and a Dynamic Layer Selection (DLS) strategy that adaptively identifies and updates the most critical layers based on LayerNorm gradient norms. By combining dimension-wise enhancement with layer-wise adaptation, RoSA achieves more targeted and efficient fine-tuning. Extensive experiments on fifteen commonsense and arithmetic benchmarks demonstrate that RoSA outperforms existing mainstream PEFT methods under comparable trainable parameters. The code is available to ease reproducibility at https://github.com/Applied-Machine-Learning-Lab/RoSA.
Polarity-Aware Probing for Quantifying Latent Alignment in Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Advances in unsupervised probes such as Contrast-Consistent Search (CCS), which reveal latent beliefs without relying on token outputs, raise the question of whether these methods can reliably assess model alignment. We investigate this by examining the sensitivity of CCS to harmful vs. safe statements and by introducing Polarity-Aware CCS (PA-CCS), a method for evaluating whether a model's internal representations remain consistent under polarity inversion. We propose two alignment-oriented metrics, Polar-Consistency and the Contradiction Index, to quantify the semantic robustness of a model's latent knowledge. To validate PA-CCS, we curate two main datasets and one control dataset containing matched harmful-safe sentence pairs constructed using different methodologies (concurrent and antagonistic statements). We apply PA-CCS to 16 language models. Our results show that PA-CCS identifies both architectural and layer-specific differences in the encoding of latent harmful knowledge. Notably, replacing the negation token with a meaningless marker degrades PA-CCS scores for models with well-aligned internal representations, while models lacking robust internal calibration do not exhibit this degradation. Our findings highlight the potential of unsupervised probing for alignment evaluation and emphasize the need to incorporate structural robustness checks into interpretability benchmarks. Code and datasets are available at: https://github.com/SadSabrina/polarity-probing. WARNING: This paper contains potentially sensitive, harmful, and offensive content.
Tacit Bidder-Side Collusion: Artificial Intelligence in Dynamic Auctions
Venue: arXiv cs.GT 2025
Year: 2025

We study whether large language models acting as autonomous bidders can tacitly collude by coordinating when to accept platform posted payouts in repeated Dutch auctions, without any communication. We present a minimal repeated auction model that yields a simple incentive compatibility condition and a closed form threshold for sustainable collusion for subgame-perfect Nash equilibria. In controlled simulations with multiple language models, we observe systematic supra-competitive prices in small auction settings and a return to competitive behavior as the number of bidders in the market increases, consistent with the theoretical model. We also find LLMs use various mechanisms to facilitate tacit coordination, such as focal point acceptance timing versus patient strategies that track the theoretical incentives. The results provide, to our knowledge, the first evidence of bidder side tacit collusion by LLMs and show that market structure levers can be more effective than capability limits for mitigation.
Evaluating Strategies for Synthesizing Clinical Notes for Medical Multimodal AI
Venue: arXiv cs.AI 2025
Year: 2025

Multimodal (MM) learning is emerging as a promising paradigm in biomedical artificial intelligence (AI) applications, integrating complementary modality, which highlight different aspects of patient health. The scarcity of large heterogeneous biomedical MM data has restrained the development of robust models for medical AI applications. In the dermatology domain, for instance, skin lesion datasets typically include only images linked to minimal metadata describing the condition, thereby limiting the benefits of MM data integration for reliable and generalizable predictions. Recent advances in Large Language Models (LLMs) enable the synthesis of textual description of image findings, potentially allowing the combination of image and text representations. However, LLMs are not specifically trained for use in the medical domain, and their naive inclusion has raised concerns about the risk of hallucinations in clinically relevant contexts. This work investigates strategies for generating synthetic textual clinical notes, in terms of prompt design and medical metadata inclusion, and evaluates their impact on MM architectures toward enhancing performance in classification and cross-modal retrieval tasks. Experiments across several heterogeneous dermatology datasets demonstrate that synthetic clinical notes not only enhance classification performance, particularly under domain shift, but also unlock cross-modal retrieval capabilities, a downstream task that is not explicitly optimized during training.
Towards a Foundation Model for Partial Differential Equations Across Physics Domains
Venue: arXiv cs.LG 2025
Year: 2025

We present PDE-FM, a modular foundation model for physics-informed machine learning that unifies spatial, spectral, and temporal reasoning across heterogeneous partial differential equation (PDE) systems. PDE-FM combines spatial-spectral tokenization, physics-aware conditioning, and a Mamba-based state-space backbone with an operator-theoretic decoder, enabling scalable and data-efficient modeling of complex physical dynamics. In contrast to task-specific neural operators, PDE-FM is pretrained once on diverse PDE datasets and can be transferred to new physical regimes without architectural or data-specific modifications. Evaluated on twelve 2D and 3D datasets from The Well benchmark - spanning hydrodynamic, radiative, elastic, and astrophysical phenomena - PDE-FM achieves state-of-the-art accuracy in six domains, reducing mean VRMSE by 46% relative to prior operator-learning baselines. The model demonstrates robust cross-physics generalization, excelling in turbulent and radiative systems while maintaining strong performance in linear and steady-state regimes. These results suggest that large-scale pretraining across diverse physical processes can yield transferable representations of dynamics, marking a step toward unified, foundation-level surrogates for multi-physics simulation and scientific discovery.
OOCO: Latency-disaggregated Architecture for Online-Offline Co-locate LLM Serving
Venue: arXiv cs.DC 2025
Year: 2025

Large Language Models (LLMs) are increasingly deployed in both latency-sensitive online services and cost-sensitive offline workloads. Co-locating these workloads on shared serving instances can improve resource utilization, but directly applying this approach to Prefill/Decode (P/D) disaggregated systems introduces severe load imbalance, as fluctuating request mixes alter the intrinsic P/D ratio. Existing dynamic adjustment techniques cannot keep up with the bursty traffic patterns of online services. We propose a latency-constraint disaggregated architecture, which separates cluster resources into latency-strict and latency-relaxed pools based on task latency requirements. This design enables flexible placement of offline decode tasks, mitigating P/D imbalance while preserving online performance. To fully exploit this flexibility, we propose (1) a bottleneck-based scheduler guided by a Roofline-based performance model for performance bottleneck based scheduling, and (2) a fast preemption mechanism that strictly enforces Service Level Objectives (SLOs) for online requests. Experiments on real-world traces show that compared to existing offline system approaches, our method improves offline throughput by up to 3x, while maintaining online request SLOs.
Saddle-Free Guidance: Improved On-Manifold Sampling without Labels or Additional Training
Venue: arXiv cs.CV 2025
Year: 2025

Score-based generative models require guidance in order to generate plausible, on-manifold samples. The most popular guidance method, Classifier-Free Guidance (CFG), is only applicable in settings with labeled data and requires training an additional unconditional score-based model. More recently, Auto-Guidance adopts a smaller, less capable version of the original model to guide generation. While each method effectively promotes the fidelity of generated data, each requires labeled data or the training of additional models, making it challenging to guide score-based models when (labeled) training data are not available or training new models is not feasible. We make the surprising discovery that the positive curvature of log density estimates in saddle regions provides strong guidance for score-based models. Motivated by this, we develop saddle-free guidance (SFG) which maintains estimates of maximal positive curvature of the log density to guide individual score-based models. SFG has the same computational cost of classifier-free guidance, does not require additional training, and works with off-the-shelf diffusion and flow matching models. Our experiments indicate that SFG achieves state-of-the-art FID and FD-DINOv2 metrics in single-model unconditional ImageNet-512 generation. When SFG is combined with Auto-Guidance, its unconditional samples achieve general state-of-the-art in FD-DINOv2 score. Our experiments with FLUX.1-dev and Stable Diffusion v3.5 indicate that SFG boosts the diversity of output images compared to CFG while maintaining excellent prompt adherence and image fidelity.
The Evolution of Trust under Institutional Moral Hazard
Venue: arXiv cs.GT 2025
Year: 2025

We study the behavior of for-profit institutions that broadcast reputations to foster trust among market participants. We develop a theoretical model in which buyers and sellers are matched on a platform to engage in transactions involving a moral hazard: sellers can either faithfully deliver goods after receiving payment, or not. Although the buyer does not know a seller's true type, the platform maintains a reputation system that probabilistically assigns binary reputation signals. Buyers make purchase decisions based on reputation signals, which influence the payoffs to sellers who then adapt their type over time. These market dynamics ultimately shape the platform's profit from commissions on sales. Our analysis reveals that platforms inherently have an incentive for rating inflation, driven by the desire to increase commission. This introduces a second layer of moral hazard: the platform's incentive to distort reputations for its own profit. Such distortion is self-limited by the platform's need to maintain enough accuracy that trustworthy sellers remain in the market, without which rational buyers would refrain from purchases altogether. Nonetheless, the optimal strategy for the platform can be to invest in order to reduce signal accuracy. When the platform can freely set commission fees, however, maximum profit may be achieved by costly investment in an accurate reputation system. These findings highlight the intricate tensions between platform incentives and resulting social utility for marketplace participants.
Closed-Loop Transformers: Autoregressive Modeling as Iterative Latent Equilibrium
Venue: arXiv cs.LG 2025
Year: 2025

Contemporary autoregressive transformers operate in open loop: each hidden state is computed in a single forward pass and never revised, causing errors to propagate uncorrected through the sequence. We identify this open-loop bottleneck as a fundamental architectural limitation underlying well-documented failures in long-range reasoning, factual consistency, and multi-step planning. To address this limitation, we introduce the closed-loop prediction principle, which requires that models iteratively refine latent representations until reaching a self-consistent equilibrium before committing to each token. We instantiate this principle as Equilibrium Transformers (EqT), which augment standard transformer layers with an Equilibrium Refinement Module that minimizes a learned energy function via gradient descent in latent space. The energy function enforces bidirectional prediction consistency, episodic memory coherence, and output confidence, all computed without external supervision. Theoretically, we prove that EqT performs approximate MAP inference in a latent energy-based model, establish linear convergence guarantees, and show that refinement improves predictions precisely on hard instances where one-shot inference is suboptimal. The framework unifies deep equilibrium models, diffusion language models, and test-time training as special cases. Preliminary experiments on the binary parity task demonstrate +3.28% average improvement on challenging sequences, with gains reaching +8.07% where standard transformers approach random performance, validating that the benefit of deliberation scales with task difficulty. Just as attention mechanisms resolved the sequential bottleneck of recurrent networks, we propose that closed-loop equilibrium may resolve the commitment bottleneck of open-loop autoregression, representing a foundational step toward language models.
Exploring Fusion Strategies for Multimodal Vision-Language Systems
Venue: arXiv cs.LG 2025
Year: 2025

Modern machine learning models often combine multiple input streams of data to more accurately capture the information that informs their decisions. In multimodal machine learning, choosing the strategy for fusing data together requires careful consideration of the application's accuracy and latency requirements, as fusing the data at earlier or later stages in the model architecture can lead to performance changes in accuracy and latency. To demonstrate this tradeoff, we investigate different fusion strategies using a hybrid BERT and vision network framework that integrates image and text data. We explore two different vision networks: MobileNetV2 and ViT. We propose three models for each vision network, which fuse data at late, intermediate, and early stages in the architecture. We evaluate the proposed models on the CMU MOSI dataset and benchmark their latency on an NVIDIA Jetson Orin AGX. Our experimental results demonstrate that while late fusion yields the highest accuracy, early fusion offers the lowest inference latency. We describe the three proposed model architectures and discuss the accuracy and latency tradeoffs, concluding that data fusion earlier in the model architecture results in faster inference times at the cost of accuracy.
Beyond Atoms: Evaluating Electron Density Representation for 3D Molecular Learning
Venue: arXiv cs.LG 2025
Year: 2025

Machine learning models for 3D molecular property prediction typically rely on atom-based representations, which may overlook subtle physical information. Electron density maps -- the direct output of X-ray crystallography and cryo-electron microscopy -- offer a continuous, physically grounded alternative. We compare three voxel-based input types for 3D convolutional neural networks (CNNs): atom types, raw electron density, and density gradient magnitude, across two molecular tasks -- protein-ligand binding affinity prediction (PDBbind) and quantum property prediction (QM9). We focus on voxel-based CNNs because electron density is inherently volumetric, and voxel grids provide the most natural representation for both experimental and computed densities. On PDBbind, all representations perform similarly with full data, but in low-data regimes, density-based inputs outperform atom types, while a shape-based baseline performs comparably -- suggesting that spatial occupancy dominates this task. On QM9, where labels are derived from Density Functional Theory (DFT) but input densities from a lower-level method (XTB), density-based inputs still outperform atom-based ones at scale, reflecting the rich structural and electronic information encoded in density. Overall, these results highlight the task- and regime-dependent strengths of density-derived inputs, improving data efficiency in affinity prediction and accuracy in quantum property modeling.
PathReasoning: A multimodal reasoning agent for query-based ROI navigation on whole-slide images
Venue: arXiv cs.CV 2025
Year: 2025

Deciphering tumor microenvironment from Whole Slide Images (WSIs) is intriguing as it is key to cancer diagnosis, prognosis and treatment response. While these gigapixel images on one hand offer a comprehensive portrait of cancer, on the other hand, the extremely large size, as much as more than 10 billion pixels, make it challenging and time-consuming to navigate to corresponding regions to support diverse clinical inspection. Inspired by pathologists who conducted navigation on WSIs with a combination of sampling, reasoning and self-reflection, we proposed "PathReasoning", a multi-modal reasoning agent that iteratively navigates across WSIs through multiple rounds of reasoning and refinements. Specifically, starting with randomly sampled candidate regions, PathReasoning reviews current selections with self-reflection, reasoning over the correspondence between visual observations and clinical questions, and concludes by proposing new regions to explore. Across rounds, PathReasoning builds a reasoning chain that gradually directs attention to diagnostically relevant areas. PathReasoning turns each whole slide into a sequence of question-guided views, allowing the model to efficiently find informative ROIs within a fixed number of steps, without the need for dense pixel-level annotations. PathReasoning can substantially outperform strong ROI-selection approaches by 6.7% and 3.1% of AUROC on subtyping and longitudinal analysis tasks. The high-quality ROIs further support accurate report generation on breast cancer, significantly outperforming the standard GPT-4o by 10% in accuracy. PathReasoning prioritizes question-specific regions and constructs interpretable reasoning chains, supporting efficient slide review, consistent diagnostic interpretations, comprehensive reporting, and evidence traceability in digital pathology.
Identifying all snarls and superbubbles in linear-time, via a unified SPQR-tree framework
Venue: arXiv cs.DS 2025
Year: 2025

Snarls and superbubbles are fundamental pangenome decompositions capturing variant sites. These bubble-like structures underpin key tasks in computational pangenomics, including structural-variant genotyping, distance indexing, haplotype sampling, and variant annotation. Snarls can be quadratically-many in the size of the graph, and since their introduction in 2018 with the vg toolkit, there has been no work on identifying all snarls in linear time. Moreover, while it is known how to find superbubbles in linear time, this result is a highly specialized solution only achieved after a long series of papers. We present the first algorithm identifying all snarls in linear time. This is based on a new representation of all snarls, of size linear in the input graph size, and which can be computed in linear time. Our algorithm is based on a unified framework that also provides a new linear-time algorithm for finding superbubbles. An observation behind our results is that all such structures are separated from the rest of the graph by two vertices (except for cases which are trivially computable), i.e. their endpoints are a 2-separator of the underlying undirected graph. Based on this, we employ the well-known SPQR tree decomposition, which encodes all 2-separators, to guide a traversal that finds the bubble-like structures efficiently. We implemented our algorithms in C++ (available at https://github.com/algbio/BubbleFinder) and evaluated them on various pangenomic datasets. Our algorithms outcompete or they are on the same level of existing methods. For snarls, we are up to two times faster than vg, while identifying all snarls. When computing superbubbles, we are up to 50 times faster than BubbleGun. Our SPQR tree framework provides a unifying perspective on bubble-like structures in pangenomics, together with a template for finding other bubble-like structures efficiently.
Exploring Dynamic Properties of Backdoor Training Through Information Bottleneck
Venue: arXiv cs.LG 2025
Year: 2025

Understanding how backdoor data influences neural network training dynamics remains a complex and underexplored challenge. In this paper, we present a rigorous analysis of the impact of backdoor data on the learning process, with a particular focus on the distinct behaviors between the target class and other clean classes. Leveraging the Information Bottleneck (IB) principle connected with clustering of internal representation, We find that backdoor attacks create unique mutual information (MI) signatures, which evolve across training phases and differ based on the attack mechanism. Our analysis uncovers a surprising trade-off: visually conspicuous attacks like BadNets can achieve high stealthiness from an information-theoretic perspective, integrating more seamlessly into the model than many visually imperceptible attacks. Building on these insights, we propose a novel, dynamics-based stealthiness metric that quantifies an attack's integration at the model level. We validate our findings and the proposed metric across multiple datasets and diverse attack types, offering a new dimension for understanding and evaluating backdoor threats. Our code is available in: https://github.com/XinyuLiu71/Information_Bottleneck_Backdoor.git.
Secure Command, Control and Communications Systems (C3) for Army UxVs
Venue: arXiv cs.NI 2025
Year: 2025

Unmanned Vehicles (UxVs) are increasingly used in modern military operations for reconnaissance, surveillance, and strike missions, enhancing situational awareness while reducing risk to personnel. Their affordability and rapid deployment have encouraged the adoption of commercial solutions. However, many rely on insecure protocols such as MAVLink, which lack authentication and encryption mechanisms. This paper designed, implemented, and evaluated a new secure command-and-control architecture that ensures confidentiality, integrity, and authentication (CIA) while supporting real-time control delegation between Ground Control Stations (GCSs). The proposed solution, named New Command and Control System (NC2S), enforces a zero-trust model integrating hierarchical credential-based privileges to regulate access and control among Tactical Commanders (TC), GCSs, and UxVs. It employs mutual Transport Layer Security (mTLS) with Elliptic Curve Digital Signature Algorithm (ECDSA) certificates and Elliptic Curve Diffie-Hellman (ECDH) key exchange, while message integrity is ensured through Hash-based Message Authentication Codes (HMAC). Multiple lightweight protocols were developed for credential management, key renewal, and control handover. The NC2S prototype was experimentally validated over Wi-Fi and Rohde&Schwarz HR-5000H tactical radios. Results showed that HR-5000H links introduce latencies roughly two orders of magnitude higher than broadband technologies (e.g., Wi-Fi or 5G&Beyond technologies) but are still able to maintain stable communication with minimal message loss, making them suitable for the NC2S links among TC terminals and GCSs.