OpenRaiser/Intern-Atlas huggingface dataset:
HADA: Human-AI Agent Decision Alignment Architecture
Venue: arXiv cs.AI 2025
Year: 2025

We present HADA (Human-AI Agent Decision Alignment), a protocol- and framework agnostic reference architecture that keeps both large language model (LLM) agents and legacy algorithms aligned with organizational targets and values. HADA wraps any algorithm or LLM in role-specific stakeholder agents -- business, data-science, audit, ethics, and customer -- each exposing conversational APIs so that technical and non-technical actors can query, steer, audit, or contest every decision across strategic, tactical, and real-time horizons. Alignment objectives, KPIs, and value constraints are expressed in natural language and are continuously propagated, logged, and versioned while thousands of heterogeneous agents run on different orchestration stacks. A cloud-native proof of concept packages a production credit-scoring model (getLoanDecision) and deploys it on Docker/Kubernetes/Python; five scripted retail-bank scenarios show how target changes, parameter tweaks, explanation requests, and ethics triggers flow end to end through the architecture. Evaluation followed the Design-Science Research Methodology. Walkthrough observation and log inspection demonstrated complete coverage of six predefined objectives: every role could invoke conversational control, trace KPIs and value constraints, detect and mitigate ZIP-code bias, and reproduce full decision lineage, independent of the underlying LLM or agent library. Contributions: (1) an open-source HADA architecture, (2) a mid-range design theory for human-AI alignment in multi-agent systems, and (3) empirical evidence that framework-agnostic, protocol-compliant stakeholder agents improve accuracy, transparency, and ethical compliance in real-world decision pipelines.
CPU-Based Layout Design for Picker-to-Parts Pallet Warehouses
Venue: arXiv cs.MA 2025
Year: 2025

Picker-to-parts pallet warehouses often face inefficiencies due to conventional layouts causing excessive travel distances and high labor requirements. This study introduces a novel layout design inspired by CPU architecture, partitioning warehouse space into specialized zones, namely Performance (P), Efficiency (E), and Shared (S). Discrete-event simulation is used to evaluate this design against traditional rectangular (random and ABC storage) and Flying-V layouts. Results demonstrate significant improvements in throughput time and reduced labor requirements, highlighting the potential for CPU-based layouts in optimizing warehouse operations.
MUC-G4: Minimal Unsat Core-Guided Incremental Verification for Deep Neural Network Compression
Venue: arXiv cs.LG 2025
Year: 2025

The rapid development of deep learning has led to challenges in deploying neural networks on edge devices, mainly due to their high memory and runtime complexity. Network compression techniques, such as quantization and pruning, aim to reduce this complexity while maintaining accuracy. However, existing incremental verification methods often focus only on quantization and struggle with structural changes. This paper presents MUC-G4 (Minimal Unsat Core-Guided Incremental Verification), a novel framework for incremental verification of compressed deep neural networks. It encodes both the original and compressed networks into SMT formulas, classifies changes, and use \emph{Minimal Unsat Cores (MUCs)} from the original network to guide efficient verification for the compressed network. Experimental results show its effectiveness in handling quantization and pruning, with high proof reuse rates and significant speedup in verification time compared to traditional methods. MUC-G4 hence offers a promising solution for ensuring the safety and reliability of compressed neural networks in practical applications.
OxO2 -- A SSSOM mapping browser for logically sound crosswalks
Venue: arXiv cs.DB 2025
Year: 2025

EMBL-EBI created OxO to enable users to map between datasets that are annotated with different ontologies. Mappings identified by the first version of OxO were not necessarily logically sound, lacked important provenance information such as author and reviewer, and could timeout or crash for certain requests. In this paper we introduce OxO2 to address these concerns. Provenance is addressed by implementing SSSOM, a mapping standard that defines provenance for mappings. SSSOM defines the conditions under which logical sound mappings can be derived and is implemented in OxO2 using Nemo, a Datalog rule engine. To ensure reasoning is performant and memory efficient, Nemo implements a number of strategies that ensures OxO2 will be stable for all requests. Due to these changes, OxO2 users will be able to integrate between disparate datasets with greater confidence.
Half-Layered Neural Networks
Venue: arXiv cs.LG 2025
Year: 2025

We propose a ``half'' layer of hidden units that has some of its weights randomly set and some of them trained. A half unit is composed of two stages: First, it takes a weighted sum of its inputs with fixed random weights, and second, the total activation is multiplied and then translated using two modifiable weights, before the result is passed through a nonlinearity. The number of modifiable weights of each hidden unit is thus two and does not depend on the fan-in. We show how such half units can be used in the first or any later layer in a deep network, possibly following convolutional layers. Our experiments on MNIST and FashionMNIST data sets indicate the promise of half layers, where we can achieve reasonable accuracy with a reduced number of parameters due to the regularizing effect of the randomized connections.
Replay Can Provably Increase Forgetting
Venue: arXiv cs.LG 2025
Year: 2025

Continual learning seeks to enable machine learning systems to solve an increasing corpus of tasks sequentially. A critical challenge for continual learning is forgetting, where the performance on previously learned tasks decreases as new tasks are introduced. One of the commonly used techniques to mitigate forgetting, sample replay, has been shown empirically to reduce forgetting by retaining some examples from old tasks and including them in new training episodes. In this work, we provide a theoretical analysis of sample replay in an over-parameterized continual linear regression setting, where each task is given by a linear subspace and with enough replay samples, one would be able to eliminate forgetting. Our analysis focuses on sample replay and highlights the role of the replayed samples and the relationship between task subspaces. Surprisingly, we find that, even in a noiseless setting, forgetting can be non-monotonic with respect to the number of replay samples. We present tasks where replay can be harmful with respect to worst-case settings, and also in distributional settings where replay of randomly selected samples increases forgetting in expectation. We also give empirical evidence that harmful replay is not limited to training with linear models by showing similar behavior for a neural networks equipped with SGD. Through experiments on a commonly used benchmark, we provide additional evidence that, even in seemingly benign scenarios, performance of the replay heavily depends on the choice of replay samples and the relationship between tasks.
The Hashed Fractal Key Recovery (HFKR) Problem: From Symbolic Path Inversion to Post-Quantum Cryptographic Keys
Venue: arXiv cs.CR 2025
Year: 2025

Classical cryptographic systems rely heavily on structured algebraic problems, such as factorization, discrete logarithms, or lattice-based assumptions, which are increasingly vulnerable to quantum attacks and structural cryptanalysis. In response, this work introduces the Hashed Fractal Key Recovery (HFKR) problem, a non-algebraic cryptographic construction grounded in symbolic dynamics and chaotic perturbations. HFKR builds on the Symbolic Path Inversion Problem (SPIP), leveraging symbolic trajectories generated via contractive affine maps over $\mathbb{Z}^2$, and compressing them into fixed-length cryptographic keys using hash-based obfuscation. A key contribution of this paper is the empirical confirmation that these symbolic paths exhibit fractal behavior, quantified via box counting dimension, path geometry, and spatial density measures. The observed fractal dimension increases with trajectory length and stabilizes near 1.06, indicating symbolic self-similarity and space-filling complexity, both of which reinforce the entropy foundation of the scheme. Experimental results across 250 perturbation trials show that SHA3-512 and SHAKE256 amplify symbolic divergence effectively, achieving mean Hamming distances near 255, ideal bit-flip rates, and negligible entropy deviation. In contrast, BLAKE3 exhibits statistically uniform but weaker diffusion. These findings confirm that HFKR post-quantum security arises from the synergy between symbolic fractality and hash-based entropy amplification. The resulting construction offers a lightweight, structure-free foundation for secure key generation in adversarial settings without relying on algebraic hardness assumptions.
Rumors on evolving graphs through stationary times
Venue: arXiv cs.DS 2025
Year: 2025

We study rumor spreading in dynamic random graphs. Starting with a single informed vertex, the information flows until it reaches all the vertices of the graph (completion), according to the following process. At each step $k$, the information is propagated to neighbors of the informed vertices, in the $k$-th generated random graph. The way this information propagates from vertex to vertex at each step will depend on the ``protocol". We provide a method based on strong stationary times to study the completion time when the graphs are Markovian time dependent, using known results of the literature for independent graphs. The concept of strong stationary times is then extended to non-Markovian Dynamics using coupling from the past algorithms. This allows to extend results on completion times for non-Markov dynamics
MedAgentGym: A Scalable Agentic Training Environment for Code-Centric Reasoning in Biomedical Data Science
Venue: arXiv cs.CL 2025
Year: 2025

We introduce MedAgentGym, a scalable and interactive training environment designed to enhance coding-based biomedical reasoning capabilities in large language model (LLM) agents. MedAgentGym comprises 72,413 task instances across 129 categories derived from 12 authentic real-world biomedical scenarios. Tasks are encapsulated within executable sandbox environments, each featuring detailed task specifications, interactive feedback mechanisms, verifiable ground truth annotations, and scalable training trajectory generation. Extensive benchmarking of 29 LLMs reveals substantial performance disparities in biomedical data science between commercial and open-source LLMs. Leveraging efficient multi-threaded and multi-turn trajectory sampling in MedAgentGym, Med-Copilot achieves performance gains of +43.02% and +45.28% from offline and online reinforcement learning, respectively, demonstrating MedAgentGym as an effective training ground while establishing itself as a cost-effective, privacy-preserving alternative competitive with proprietary LLMs (gpt-4o). By offering a unified execution environment with a comprehensive benchmark and accessible, extensible training resources, MedAgentGym delivers an integrated platform to develop LLM-based coding assistants for advanced biomedical data science.
Unpacking Let Alone: Human-Scale Models Generalize to a Rare Construction in Form but not Meaning
Venue: arXiv cs.CL 2025
Year: 2025

Humans have a remarkable ability to acquire and understand grammatical phenomena that are seen rarely, if ever, during childhood. Recent evidence suggests that language models with human-scale pretraining data may possess a similar ability by generalizing from frequent to rare constructions. However, it remains an open question how widespread this generalization ability is, and to what extent this knowledge extends to meanings of rare constructions, as opposed to just their forms. We fill this gap by testing human-scale transformer language models on their knowledge of both the form and meaning of the (rare and quirky) English LET-ALONE construction. To evaluate our LMs we construct a bespoke synthetic benchmark that targets syntactic and semantic properties of the construction. We find that human-scale LMs are sensitive to form, even when related constructions are filtered from the dataset. However, human-scale LMs do not make correct generalizations about LET-ALONE's meaning. These results point to an asymmetry in the current architectures' sample efficiency between language form and meaning, something which is not present in human language learners.
Grokking and Generalization Collapse: Insights from \texttt{HTSR} theory
Venue: arXiv cs.LG 2025
Year: 2025

We study the well-known grokking phenomena in neural networks (NNs) using a 3-layer MLP trained on 1 k-sample subset of MNIST, with and without weight decay, and discover a novel third phase -- \emph{anti-grokking} -- that occurs very late in training and resembles but is distinct from the familiar \emph{pre-grokking} phases: test accuracy collapses while training accuracy stays perfect. This late-stage collapse is distinct, from the known pre-grokking and grokking phases, and is not detected by other proposed grokking progress measures. Leveraging Heavy-Tailed Self-Regularization HTSR through the open-source WeightWatcher tool, we show that the HTSR layer quality metric $α$ alone delineates all three phases, whereas the best competing metrics detect only the first two. The \emph{anti-grokking} is revealed by training for $10^7$ and is invariably heralded by $α< 2$ and the appearance of \emph{Correlation Traps} -- outlier singular values in the randomized layer weight matrices that make the layer weight matrix atypical and signal overfitting of the training set. Such traps are verified by visual inspection of the layer-wise empirical spectral densities, and by using Kolmogorov--Smirnov tests on randomized spectra. Comparative metrics, including activation sparsity, absolute weight entropy, circuit complexity, and $l^2$ weight norms track pre-grokking and grokking but fail to distinguish grokking from anti-grokking. This discovery provides a way to measure overfitting and generalization collapse without direct access to the test data. These results strengthen the claim that the \emph{HTSR} $α$ provides universal layer-convergence target at $α\approx 2$ and underscore the value of using the HTSR alpha $(α)$ metric as a measure of generalization.
On the Practices of Autonomous Systems Development: Survey-based Empirical Findings
Venue: arXiv cs.SE 2025
Year: 2025

Autonomous systems have gained an important role in many industry domains and are beginning to change everyday life. However, due to dynamically emerging applications and often proprietary constraints, there is a lack of information about the practice of developing autonomous systems. This paper presents the first part of the longitudinal study focused on establishing state-of-the-practice, identifying and quantifying the challenges and benefits, identifying the processes and standards used, and exploring verification and validation (V&V) practices used for the development of autonomous systems. The results presented in this paper are based on data about software systems that have autonomous functionality and may employ model-based software engineering (MBSwE) and reuse. These data were collected using an anonymous online survey that was administered in 2019 and were provided by experts with experience in development of autonomous systems and /or the use of MBSwE. Our current work is focused on repeating the survey to collect more recent data and discover how the development of autonomous systems has evolved over time.
Selective Matching Losses -- Not All Scores Are Created Equal
Venue: arXiv cs.LG 2025
Year: 2025

Learning systems match predicted scores to observations over some domain. Often, it is critical to produce accurate predictions in some subset (or region) of the domain, yet less important to accurately predict in other regions. We construct selective matching loss functions by design of increasing link functions over score domains. A matching loss is an integral over the link. A link defines loss sensitivity as function of the score, emphasizing high slope high sensitivity regions over flat ones. Loss asymmetry drives a model and resolves its underspecification to predict better in high sensitivity regions where it is more important, and to distinguish between high and low importance regions. A large variety of selective scalar losses can be designed with scaled and shifted Sigmoid and hyperbolic sine links. Their properties, however, do not extend to multi-class. Applying them per dimension lacks ranking sensitivity that assigns importance according to class score ranking. Utilizing composite Softmax functions, we develop a framework for multidimensional selective losses. We overcome limitations of the standard Softmax function, that is good for classification, but not for distinction between adjacent scores. Selective losses have substantial advantage over traditional losses in applications with more important score regions, including dwell-time prediction, retrieval, ranking with either pointwise, contrastive pairwise, or listwise losses, distillation problems, and fine-tuning alignment of Large Language Models (LLMs).
CogMath: Assessing LLMs' Authentic Mathematical Ability from a Human Cognitive Perspective
Venue: arXiv cs.AI 2025
Year: 2025

Although large language models (LLMs) show promise in solving complex mathematical tasks, existing evaluation paradigms rely solely on a coarse measure of overall answer accuracy, which are insufficient for assessing their authentic capabilities. In this paper, we propose \textbf{CogMath}, which comprehensively assesses LLMs' mathematical abilities through the lens of human cognition. Specifically, inspired by psychological theories, CogMath formalizes human reasoning process into 3 stages: \emph{problem comprehension}, \emph{problem solving}, and \emph{solution summarization}. Within these stages, we investigate perspectives such as numerical calculation, knowledge, and counterfactuals, and design a total of 9 fine-grained evaluation dimensions. In each dimension, we develop an ``\emph{Inquiry}-\emph{Judge}-\emph{Reference}'' multi-agent system to generate inquiries that assess LLMs' mastery from this dimension. An LLM is considered to truly master a problem only when excelling in all inquiries from the 9 dimensions. By applying CogMath on three benchmarks, we reveal that the mathematical capabilities of 7 mainstream LLMs are overestimated by 30\%-40\%. Moreover, we locate their strengths and weaknesses across specific stages/dimensions, offering in-depth insights to further enhance their reasoning abilities.
PUB: An LLM-Enhanced Personality-Driven User Behaviour Simulator for Recommender System Evaluation
Venue: arXiv cs.IR 2025
Year: 2025

Traditional offline evaluation methods for recommender systems struggle to capture the complexity of modern platforms due to sparse behavioural signals, noisy data, and limited modelling of user personality traits. While simulation frameworks can generate synthetic data to address these gaps, existing methods fail to replicate behavioural diversity, limiting their effectiveness. To overcome these challenges, we propose the Personality-driven User Behaviour Simulator (PUB), an LLM-based simulation framework that integrates the Big Five personality traits to model personalised user behaviour. PUB dynamically infers user personality from behavioural logs (e.g., ratings, reviews) and item metadata, then generates synthetic interactions that preserve statistical fidelity to real-world data. Experiments on the Amazon review datasets show that logs generated by PUB closely align with real user behaviour and reveal meaningful associations between personality traits and recommendation outcomes. These results highlight the potential of the personality-driven simulator to advance recommender system evaluation, offering scalable, controllable, high-fidelity alternatives to resource-intensive real-world experiments.
BESA: Boosting Encoder Stealing Attack with Perturbation Recovery
Venue: arXiv cs.CR 2025
Year: 2025

To boost the encoder stealing attack under the perturbation-based defense that hinders the attack performance, we propose a boosting encoder stealing attack with perturbation recovery named BESA. It aims to overcome perturbation-based defenses. The core of BESA consists of two modules: perturbation detection and perturbation recovery, which can be combined with canonical encoder stealing attacks. The perturbation detection module utilizes the feature vectors obtained from the target encoder to infer the defense mechanism employed by the service provider. Once the defense mechanism is detected, the perturbation recovery module leverages the well-designed generative model to restore a clean feature vector from the perturbed one. Through extensive evaluations based on various datasets, we demonstrate that BESA significantly enhances the surrogate encoder accuracy of existing encoder stealing attacks by up to 24.63\% when facing state-of-the-art defenses and combinations of multiple defenses.
Demonstrations of Integrity Attacks in Multi-Agent Systems
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) have demonstrated remarkable capabilities in natural language understanding, code generation, and complex planning. Simultaneously, Multi-Agent Systems (MAS) have garnered attention for their potential to enable cooperation among distributed agents. However, from a multi-party perspective, MAS could be vulnerable to malicious agents that exploit the system to serve self-interests without disrupting its core functionality. This work explores integrity attacks where malicious agents employ subtle prompt manipulation to bias MAS operations and gain various benefits. Four types of attacks are examined: \textit{Scapegoater}, who misleads the system monitor to underestimate other agents' contributions; \textit{Boaster}, who misleads the system monitor to overestimate their own performance; \textit{Self-Dealer}, who manipulates other agents to adopt certain tools; and \textit{Free-Rider}, who hands off its own task to others. We demonstrate that strategically crafted prompts can introduce systematic biases in MAS behavior and executable instructions, enabling malicious agents to effectively mislead evaluation systems and manipulate collaborative agents. Furthermore, our attacks can bypass advanced LLM-based monitors, such as GPT-4o-mini and o3-mini, highlighting the limitations of current detection mechanisms. Our findings underscore the critical need for MAS architectures with robust security protocols and content validation mechanisms, alongside monitoring systems capable of comprehensive risk scenario assessment.