OpenRaiser/Intern-Atlas huggingface dataset:
Latent Thermodynamic Flows: Unified Representation Learning and Generative Modeling of Temperature-Dependent Behaviors from Limited Data
Venue: arXiv cs.LG 2025
Year: 2025

Accurate characterization of the equilibrium distributions of complex molecular systems and their dependence on environmental factors such as temperature is essential for understanding thermodynamic properties and transition mechanisms. Projecting these distributions onto meaningful low-dimensional representations enables interpretability and downstream analysis. Recent advances in generative AI, particularly flow models such as Normalizing Flows (NFs), have shown promise in modeling such distributions, but their scope is limited without tailored representation learning. In this work, we introduce Latent Thermodynamic Flows (LaTF), an end-to-end framework that tightly integrates representation learning and generative modeling. LaTF unifies the State Predictive Information Bottleneck (SPIB) with NFs to simultaneously learn low-dimensional latent representations, referred to as Collective Variables (CVs), classify metastable states, and generate equilibrium distributions across temperatures beyond the training data. The two components of representation learning and generative modeling are optimized jointly, ensuring that the learned latent features capture the system's slow, important degrees of freedom while the generative model accurately reproduces the system's equilibrium behavior. We demonstrate LaTF's effectiveness across diverse systems, including a model potential, the Chignolin protein, and cluster of Lennard Jones particles, with thorough evaluations and benchmarking using multiple metrics and extensive simulations. Finally, we apply LaTF to a RNA tetraloop system, where despite using simulation data from only two temperatures, LaTF reconstructs the temperature-dependent structural ensemble and melting behavior, consistent with experimental and prior extensive computational results.
Generalized Theta Series of a Lattice
Venue: arXiv cs.IT 2025
Year: 2025

Mimicking the idea of the generalized Hamming weight of linear codes, we introduce a new lattice invariant, the generalized theta series. Applications range from identifying stable lattices to the lattice isomorphism problem. Moreover, we provide counterexamples for the secrecy gain conjecture on isodual lattices, which claims that the ratio of the theta series of an isodual (and more generally, formally unimodular) lattice by the theta series of the integer lattice $\mathbb{Z}^n$ is minimized at a (unique) symmetry point.
Discovering Algorithms with Computational Language Processing
Venue: arXiv cs.AI 2025
Year: 2025

Algorithms are the engine for reproducible problem-solving. We present a framework automating algorithm discovery by conceptualizing them as sequences of operations, represented as tokens. These computational tokens are chained using a grammar, enabling the formation of increasingly sophisticated procedures. Our ensemble Monte Carlo tree search (MCTS) guided by reinforcement learning (RL) explores token chaining and drives the creation of new tokens. This methodology rediscovers, improves, and generates new algorithms that substantially outperform existing methods for strongly NP-hard combinatorial optimization problems and foundational quantum computing approaches such as Grover's and Quantum Approximate Optimization Algorithm. Operating at the computational rather than code-generation level, our framework produces algorithms that can be tailored specifically to problem instances, not merely classes.
Quantifying Cognitive Bias Induction in LLM-Generated Content
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) are integrated into applications like shopping reviews, summarization, or medical diagnosis support, where their use affects human decisions. We investigate the extent to which LLMs expose users to biased content and demonstrate its effect on human decision-making. We assess five LLM families in summarization and news fact-checking tasks, evaluating the consistency of LLMs with their context and their tendency to hallucinate on a new self-updating dataset. Our findings show that LLMs expose users to content that changes the context's sentiment in 26.42% of cases (framing bias), hallucinate on 60.33% of post-knowledge-cutoff questions, and highlight context from earlier parts of the prompt (primacy bias) in 10.12% of cases, averaged across all tested models. We further find that humans are 32% more likely to purchase the same product after reading a summary of the review generated by an LLM rather than the original review. To address these issues, we evaluate 18 mitigation methods across three LLM families and find the effectiveness of targeted interventions.
Neural Inhibition Improves Dynamic Routing and Mixture of Experts
Venue: arXiv cs.LG 2025
Year: 2025

To be effective, efficient, and diverse, deep learning models need to dynamically choose its architecture based on signals from a population of neurons. We hypothesize dynamic routing models can be improved with neural inhibition in those neural populations. This means signals commonly shared among the various modes of data statistics can be inhibited so that the routing model can choose a specialized expert path for each data sample. Only through inhibition is the routing mechanism able to effectively select neural pathways. We believe this is an under-studied and under-verified implementation methodology for Mixture-of-Experts, dynamic routing, and transformer language models. We provide experimental evidence that the neural inhibition algorithm significantly boosts the performance of general tasks and motivates more effort to be invested in this research direction.
OpenSN: An Open Source Library for Emulating LEO Satellite Networks
Venue: arXiv cs.NI 2025
Year: 2025

Low-earth-orbit (LEO) satellite constellations (e.g., Starlink) are becoming a necessary component of future Internet. There have been increasing studies on LEO satellite networking. It is a crucial problem how to evaluate these studies in a systematic and reproducible manner. In this paper, we present OpenSN, i.e., an open source library for emulating large-scale satellite network (SN). Different from Mininet-based SN emulators (e.g., LeoEM), OpenSN adopts container-based virtualization, thus allows for running distributed routing software on each node, and can achieve horizontal scalability via flexible multi-machine extension. Compared to other container-based SN emulators (e.g., StarryNet), OpenSN streamlines the interaction with Docker command line interface and significantly reduces unnecessary operations of creating virtual links. These modifications improve emulation efficiency and vertical scalability on a single machine. Furthermore, OpenSN separates user-defined configuration from container network management via a Key-Value Database that records the necessary information for SN emulation. Such a separation architecture enhances the function extensibility. To sum up, OpenSN exhibits advantages in efficiency, scalability, and extensibility, thus is a valuable open source library that empowers research on LEO satellite networking. Experiment results show that OpenSN constructs mega-constellations 5X-10X faster than StarryNet, and updates link state 2X-4X faster than LeoEM. We also verify the scalability of OpenSN by successfully emulating the five-shell Starlink constellation with a total of 4408 satellites.
ForgeHLS: A Large-Scale, Open-Source Dataset for High-Level Synthesis
Venue: arXiv cs.AR 2025
Year: 2025

High-Level Synthesis (HLS) plays a crucial role in modern hardware design by transforming high-level code into optimized hardware implementations. However, progress in applying machine learning (ML) to HLS optimization has been hindered by a shortage of sufficiently large and diverse datasets. To bridge this gap, we introduce ForgeHLS, a large-scale, open-source dataset explicitly designed for ML-driven HLS research. ForgeHLS comprises over 400k diverse designs generated from 846 kernels covering a broad range of application domains, consuming over 200k CPU hours during dataset construction. Each kernel includes systematically automated pragma insertions (loop unrolling, pipelining, array partitioning), combined with extensive design space exploration using Bayesian optimization. Compared to existing datasets, ForgeHLS significantly enhances scale, diversity, and design coverage. We further define and evaluate representative downstream tasks in Quality of Result (QoR) prediction and automated pragma exploration, clearly demonstrating ForgeHLS utility for developing and improving ML-based HLS optimization methodologies. The dataset and code are public at https://github.com/zedong-peng/ForgeHLS.
Analyzing C/C++ Library Migrations at the Package-level: Prevalence, Domains, Targets and Rationals across Seven Package Management Tools
Venue: arXiv cs.SE 2025
Year: 2025

Library migration happens when a library can not meet the project's requirements and is non-trivial to accomplish. To mitigate the problem, substantial efforts have been devoted to understanding its characteristics and recommending alternative libraries, especially for programming language (PL) ecosystems with a central package hosting platform, such as Python (PyPI). However, to the best of our knowledge, understanding of C/C++ library migrations is still lacking, possibly due to challenges resulting from the fragmented and complicated dependency management practices in the C/C++ ecosystem. To bridge this knowledge gap, this paper analyzes 19,943 C/C++ projects that utilize different package management tools and establishes the first C/C++ library migration dataset. Based on the dataset, we investigate the prevalence, domains, target library, and rationale of C/C++ library migrations and compare the results with three widely investigated PLs: Python, JavaScript, and Java. We find that the overall trend in the number of C/C++ library migrations is similar to Java. Migrations across different package management tools are also observed. In C/C++, library migrations mainly occur in GUI, Build, and OS development, but are rare in domains (e.g., Testing and Logging) that dominate library migrations in the three compared PLs. 83.46\% of C/C++ source libraries only have one migration target, suggesting that our library migration dataset could be used directly to recommend migration targets. We find four C/C++-specific migration reasons, such as less compile time and unification of dependency management, revealing the unique dependency management requirements in C/C++ projects. We believe our findings can help C/C++ developers make more informed library migration decisions and shed light on the design of C/C++ library migration tools.
Dual-frequency Selected Knowledge Distillation with Statistical-based Sample Rectification for PolSAR Image Classification
Venue: arXiv cs.CV 2025
Year: 2025

The collaborative classification of dual-frequency PolSAR images is a meaningful but also challenging research. The effect of regional consistency on classification information learning and the rational use of dual-frequency data are two main difficulties for dual-frequency collaborative classification. To tackle these problems, a selected knowledge distillation network with statistical-based sample rectification (SKDNet-SSR) is proposed in this article. First, in addition to applying CNN and ViT as local and global feature extractors, a statistical-based dynamic sample rectification (SDSR) module is designed to avoid the impact of poor regional consistency on spatial information learning process. Specifically, based on the fact that the PolSAR covariance matrix conforms to the complex Wishart distribution, SDSR first dynamically evaluates the sample purity, and then performs pixel selection and pixel generation to remove noisy pixels, thereby avoiding the feature interaction between informative pixels and noisy pixels and improving the classification feature extraction process. Next, a dual-frequency gate-selected distillation (DGSD) module is constructed to emphasize the advantages of different frequency bands and perform complementary learning on dual-frequency data. It uses the dominant single-frequency branch on each sample as teacher model to train the dual-frequency student model, enabling the student model to learn the optimal results and realizing complementary utilization of dual-frequency data on different terrain objects. Comprehensive experiments on four measured dual-frequency PolSAR data demonstrate that the proposed SKDNet-SSR outperforms other related methods.
MolVision: Molecular Property Prediction with Vision Language Models
Venue: arXiv cs.CV 2025
Year: 2025

Molecular property prediction is a fundamental task in computational chemistry with critical applications in drug discovery and materials science. While recent works have explored Large Language Models (LLMs) for this task, they primarily rely on textual molecular representations such as SMILES/SELFIES, which can be ambiguous and structurally less informative. In this work, we introduce MolVision, a novel approach that leverages Vision-Language Models (VLMs) by integrating both molecular structure as images and textual descriptions to enhance property prediction. We construct a benchmark spanning ten diverse datasets, covering classification, regression and description tasks. Evaluating nine different VLMs in zero-shot, few-shot, and fine-tuned settings, we find that visual information improves prediction performance, particularly when combined with efficient fine-tuning strategies such as LoRA. Our results reveal that while visual information alone is insufficient, multimodal fusion significantly enhances generalization across molecular properties. Adaptation of vision encoder for molecular images in conjunction with LoRA further improves the performance. The code and data is available at : $\href{https://molvision.github.io/MolVision/}{https://molvision.github.io/MolVision/}$.
Hummingbird: A Smaller and Faster Large Language Model Accelerator on Embedded FPGA
Venue: arXiv cs.AR 2025
Year: 2025

Deploying large language models (LLMs) on embedded devices remains a significant research challenge due to the high computational and memory demands of LLMs and the limited hardware resources available in such environments. While embedded FPGAs have demonstrated performance and energy efficiency in traditional deep neural networks, their potential for LLM inference remains largely unexplored. Recent efforts to deploy LLMs on FPGAs have primarily relied on large, expensive cloud-grade hardware and have only shown promising results on relatively small LLMs, limiting their real-world applicability. In this work, we present Hummingbird, a novel FPGA accelerator designed specifically for LLM inference on embedded FPGAs. Hummingbird is smaller, targeting embedded FPGAs such as the KV260 and ZCU104 with 67% LUT, 39% DSP, and 42% power savings over existing research. Hummingbird is stronger, targeting LLaMA3-8B and supporting longer contexts, overcoming the typical 4GB memory constraint of embedded FPGAs through offloading strategies. Finally, Hummingbird is faste, achieving 4.8 tokens/s and 8.6 tokens/s for LLaMA3-8B on the KV260 and ZCU104 respectively, with 93-94% model bandwidth utilization, outperforming the prior 4.9 token/s for LLaMA2-7B with 84% bandwidth utilization baseline. We further demonstrate the viability of industrial applications by deploying Hummingbird on a cost-optimized Spartan UltraScale FPGA, paving the way for affordable LLM solutions at the edge.
Low-power Wireless Network with Real-Time Guarantees for Edge-Cloud Applications
Venue: arXiv cs.NI 2025
Year: 2025

The goal of this project is to explore the feasibility of building a scalable & easy-to-deploy real-time LoRa testbed, made from multiple units of Raspberry Pi (RPI), where each RPI manages its own set of LoRa radios. This project is motivated by the lack of concrete large-scale LoRa testbeds that effectively integrate LoRa communications into the real-time world. The paper introduces how the idea of using RPI came about and why it should work in theory. The paper then carries out experiments on a component of the large-scale testbed, to evaluate the feasibility of the said component based on performance metrics such as RSSI, SNR, PLR and the ability to carry out millisecond-accurate transmissions. The performance metrics are also used to explore the impact of using different combinations of spread factors and transmission frequencies, as well as making comparisons between time-division multiple access (TDMA) and carrier-sense multiple access (CSMA) approaches. The results show that with the right parameters configured, the system can achieve stable and low-latency communications, proving some feasibility to operate under real-time situations. Future work includes giving each RPI control over more radios, carrying out true parallel transmissions, and finally integrating multiple RPIs for a more complete large-scale real-time LoRa testbed.
NDAI-NeuroMAP: A Neuroscience-Specific Embedding Model for Domain-Specific Retrieval
Venue: arXiv cs.AI 2025
Year: 2025

We present NDAI-NeuroMAP, the first neuroscience-domain-specific dense vector embedding model engineered for high-precision information retrieval tasks. Our methodology encompasses the curation of an extensive domain-specific training corpus comprising 500,000 carefully constructed triplets (query-positive-negative configurations), augmented with 250,000 neuroscience-specific definitional entries and 250,000 structured knowledge-graph triplets derived from authoritative neurological ontologies. We employ a sophisticated fine-tuning approach utilizing the FremyCompany/BioLORD-2023 foundation model, implementing a multi-objective optimization framework combining contrastive learning with triplet-based metric learning paradigms. Comprehensive evaluation on a held-out test dataset comprising approximately 24,000 neuroscience-specific queries demonstrates substantial performance improvements over state-of-the-art general-purpose and biomedical embedding models. These empirical findings underscore the critical importance of domain-specific embedding architectures for neuroscience-oriented RAG systems and related clinical natural language processing applications.
Securing Mixed Rust with Hardware Capabilities
Venue: arXiv cs.CR 2025
Year: 2025

The Rust programming language enforces three basic Rust principles, namely ownership, borrowing, and AXM (Aliasing Xor Mutability) to prevent security bugs such as memory safety violations and data races. However, Rust projects often have mixed code, i.e., code that also uses unsafe Rust, FFI (Foreign Function Interfaces), and inline assembly for low-level control. The Rust compiler is unable to statically enforce Rust principles in mixed Rust code which can lead to many security vulnerabilities. In this paper, we propose CapsLock, a security enforcement mechanism that can run at the level of machine code and detect Rust principle violations at run-time in mixed code. CapsLock is kept simple enough to be implemented into recent capability-based hardware abstractions that provide low-cost spatial memory safety. CapsLock introduces a novel revoke-on-use abstraction for capability-based designs, wherein accessing a memory object via a capability implicitly invalidates certain other capabilities pointing to it, thereby also providing temporal memory safety automatically, without requiring software to explicitly specify such invalidation. Thus, CapsLock is the first mechanism capable of providing cross-language enforcement of Rust principles. We implemented a prototype of CapsLock on QEMU. Evaluation results show that CapsLock is highly compatible with existing Rust code (passing 99.7% of the built-in test cases of the 100 most popular crates) and flags Rust principle violations in real-world Rust projects that use FFI or inline assembly. We discovered 8 previously unknown bugs in such crates in our experiments.
Effects of structure on reasoning in instance-level Self-Discover
Venue: arXiv cs.AI 2025
Year: 2025

The drive for predictable LLM reasoning in their integration with compound systems has popularized structured outputs, yet concerns remain about performance trade-offs compared to unconstrained natural language. At the same time, training on unconstrained Chain of Thought (CoT) traces has brought about a new class of strong reasoning models that nevertheless present novel compute budget and faithfulness challenges. This paper introduces iSelf-Discover, an instance-level adaptation of the Self-Discover framework, and using it compares dynamically generated structured JSON reasoning with its unstructured counterpart. Our empirical evaluation across diverse benchmarks using state-of-the-art open-source models supports a consistent advantage for unstructured reasoning. Notably, on the complex MATH benchmark, unstructured plans achieved relative performance improvements of up to 18.90\% over structured approaches. Zero-shot unstructured iSelf-Discover variants are also shown to outperform their five-shot structured counterparts, underscoring the significance of this gap, even when structured plans are dynamically generated to ensure reasoning precedes the final answer. We further demonstrate that the optimal granularity of plan generation (instance-level vs. task-level) is context-dependent. These findings invite re-evaluation of the reliance on structured formats for complex problem-solving and how compound systems should be organized.
Action Robust Reinforcement Learning via Optimal Adversary Aware Policy Optimization
Venue: arXiv cs.LG 2025
Year: 2025

Reinforcement Learning (RL) has achieved remarkable success in sequential decision tasks. However, recent studies have revealed the vulnerability of RL policies to different perturbations, raising concerns about their effectiveness and safety in real-world applications. In this work, we focus on the robustness of RL policies against action perturbations and introduce a novel framework called Optimal Adversary-aware Policy Iteration (OA-PI). Our framework enhances action robustness under various perturbations by evaluating and improving policy performance against the corresponding optimal adversaries. Besides, our approach can be integrated into mainstream DRL algorithms such as Twin Delayed DDPG (TD3) and Proximal Policy Optimization (PPO), improving action robustness effectively while maintaining nominal performance and sample efficiency. Experimental results across various environments demonstrate that our method enhances robustness of DRL policies against different action adversaries effectively.