OpenRaiser/Intern-Atlas huggingface dataset:
Understanding Transformer Architecture through Continuous Dynamics: A Partial Differential Equation Perspective
Venue: arXiv cs.LG 2025
Year: 2025

The Transformer architecture has revolutionized artificial intelligence, yet a principled theoretical understanding of its internal mechanisms remains elusive. This paper introduces a novel analytical framework that reconceptualizes the Transformer's discrete, layered structure as a continuous spatiotemporal dynamical system governed by a master Partial Differential Equation (PDE). Within this paradigm, we map core architectural components to distinct mathematical operators: self-attention as a non-local interaction, the feed-forward network as a local reaction, and, critically, residual connections and layer normalization as indispensable stabilization mechanisms. We do not propose a new model, but rather employ the PDE system as a theoretical probe to analyze the mathematical necessity of these components. By comparing a standard Transformer with a PDE simulator that lacks explicit stabilizers, our experiments provide compelling empirical evidence for our central thesis. We demonstrate that without residual connections, the system suffers from catastrophic representational drift, while the absence of layer normalization leads to unstable, explosive training dynamics. Our findings reveal that these seemingly heuristic "tricks" are, in fact, fundamental mathematical stabilizers required to tame an otherwise powerful but inherently unstable continuous system. This work offers a first-principles explanation for the Transformer's design and establishes a new paradigm for analyzing deep neural networks through the lens of continuous dynamics.
Work-Efficient Parallel Counting via Sampling
Venue: arXiv cs.DS 2025
Year: 2025

A canonical approach to approximating the partition function of a Gibbs distribution via sampling is simulated annealing. This method has led to efficient reductions from counting to sampling, including: $\bullet$ classic non-adaptive (parallel) algorithms with sub-optimal cost (Dyer-Frieze-Kannan '89; Bezáková-Štefankovič-Vazirani-Vigoda '08); $\bullet$ adaptive (sequential) algorithms with near-optimal cost (Štefankovič-Vempala-Vigoda '09; Huber '15; Kolmogorov '18; Harris-Kolmogorov '24). We present an algorithm that achieves both near-optimal total work and efficient parallelism, providing a reduction from counting to sampling with logarithmic depth and near-optimal work. As consequences, we obtain work-efficient parallel counting algorithms for several important models, including the hardcore and Ising models within the uniqueness regime.
Reset-free Reinforcement Learning with World Models
Venue: arXiv cs.AI 2025
Year: 2025

Reinforcement learning (RL) is an appealing paradigm for training intelligent agents, enabling policy acquisition from the agent's own autonomously acquired experience. However, the training process of RL is far from automatic, requiring extensive human effort to reset the agent and environments. To tackle the challenging reset-free setting, we first demonstrate the superiority of model-based (MB) RL methods in such setting, showing that a straightforward adaptation of MBRL can outperform all the prior state-of-the-art methods while requiring less supervision. We then identify limitations inherent to this direct extension and propose a solution called model-based reset-free (MoReFree) agent, which further enhances the performance. MoReFree adapts two key mechanisms, exploration and policy learning, to handle reset-free tasks by prioritizing task-relevant states. It exhibits superior data-efficiency across various reset-free tasks without access to environmental reward or demonstrations while significantly outperforming privileged baselines that require supervision. Our findings suggest model-based methods hold significant promise for reducing human effort in RL. Website: https://yangzhao-666.github.io/morefree
Improved Baselines with Synchronized Encoding for Universal Medical Image Segmentation
Venue: arXiv cs.CV 2025
Year: 2025

Large foundation models, known for their strong zero-shot generalization capabilities, can be applied to a wide range of downstream tasks. However, developing foundation models for medical image segmentation poses a significant challenge due to the domain gap between natural and medical images. While fine-tuning techniques based on the Segment Anything Model (SAM) have been explored, they primarily focus on scaling up data or refining inference strategies without incorporating domain-specific architectural designs, limiting their zero-shot performance. To optimize segmentation performance under standard inference settings and provide a strong baseline for future research, we introduce SyncSAM, which employs a synchronized dual-branch encoder that integrates convolution and Transformer features in a synchronized manner to enhance medical image encoding, and a multi-scale dual-branch decoder to preserve image details. SyncSAM is trained on two of the largest medical image segmentation datasets, SA-Med2D-20M and IMed-361M, resulting in a series of pre-trained models for universal medical image segmentation. Experimental results demonstrate that SyncSAM not only achieves state-of-the-art performance on test sets but also exhibits strong zero-shot capabilities on unseen datasets. Code and checkpoints are available at https://github.com/Hhankyangg/SyncSAM.
Towards a Knowledge Graph for Models and Algorithms in Applied Mathematics
Venue: arXiv cs.AI 2025
Year: 2025

Mathematical models and algorithms are an essential part of mathematical research data, as they are epistemically grounding numerical data. In order to represent models and algorithms as well as their relationship semantically to make this research data FAIR, two previously distinct ontologies were merged and extended, becoming a living knowledge graph. The link between the two ontologies is established by introducing computational tasks, as they occur in modeling, corresponding to algorithmic tasks. Moreover, controlled vocabularies are incorporated and a new class, distinguishing base quantities from specific use case quantities, was introduced. Also, both models and algorithms can now be enriched with metadata. Subject-specific metadata is particularly relevant here, such as the symmetry of a matrix or the linearity of a mathematical model. This is the only way to express specific workflows with concrete models and algorithms, as the feasible solution algorithm can only be determined if the mathematical properties of a model are known. We demonstrate this using two examples from different application areas of applied mathematics. In addition, we have already integrated over 250 research assets from applied mathematics into our knowledge graph.
Physics-Aware Combinatorial Assembly Sequence Planning using Data-free Action Masking
Venue: arXiv cs.RO 2025
Year: 2025

Combinatorial assembly uses standardized unit primitives to build objects that satisfy user specifications. This paper studies assembly sequence planning (ASP) for physical combinatorial assembly. Given the shape of the desired object, the goal is to find a sequence of actions for placing unit primitives to build the target object. In particular, we aim to ensure the planned assembly sequence is physically executable. However, ASP for combinatorial assembly is particularly challenging due to its combinatorial nature. To address the challenge, we employ deep reinforcement learning to learn a construction policy for placing unit primitives sequentially to build the desired object. Specifically, we design an online physics-aware action mask that filters out invalid actions, which effectively guides policy learning and ensures violation-free deployment. In the end, we apply the proposed method to Lego assembly with more than 250 3D structures. The experiment results demonstrate that the proposed method plans physically valid assembly sequences to build all structures, achieving a $100\%$ success rate, whereas the best comparable baseline fails more than $40$ structures. Our implementation is available at \url{https://github.com/intelligent-control-lab/PhysicsAwareCombinatorialASP}.
FedKBP: Federated dose prediction framework for knowledge-based planning in radiation therapy
Venue: arXiv cs.LG 2025
Year: 2025

Dose prediction plays a key role in knowledge-based planning (KBP) by automatically generating patient-specific dose distribution. Recent advances in deep learning-based dose prediction methods necessitates collaboration among data contributors for improved performance. Federated learning (FL) has emerged as a solution, enabling medical centers to jointly train deep-learning models without compromising patient data privacy. We developed the FedKBP framework to evaluate the performances of centralized, federated, and individual (i.e. separated) training of dose prediction model on the 340 plans from OpenKBP dataset. To simulate FL and individual training, we divided the data into 8 training sites. To evaluate the effect of inter-site data variation on model training, we implemented two types of case distributions: 1) Independent and identically distributed (IID), where the training and validating cases were evenly divided among the 8 sites, and 2) non-IID, where some sites have more cases than others. The results show FL consistently outperforms individual training on both model optimization speed and out-of-sample testing scores, highlighting the advantage of FL over individual training. Under IID data division, FL shows comparable performance to centralized training, underscoring FL as a promising alternative to traditional pooled-data training. Under non-IID division, larger sites outperformed smaller sites by up to 19% on testing scores, confirming the need of collaboration among data owners to achieve better prediction accuracy. Meanwhile, non-IID FL showed reduced performance as compared to IID FL, posing the need for more sophisticated FL method beyond mere model averaging to handle data variation among participating sites.
Kubrick: Multimodal Agent Collaborations for Synthetic Video Generation
Venue: arXiv cs.CV 2025
Year: 2025

Text-to-video generation has been dominated by diffusion-based or autoregressive models. These novel models provide plausible versatility, but are criticized for improper physical motion, shading and illumination, camera motion, and temporal consistency. The film industry relies on manually-edited Computer-Generated Imagery (CGI) using 3D modeling software. Human-directed 3D synthetic videos address these shortcomings, but require tight collaboration between movie makers and 3D rendering experts. We introduce an automatic synthetic video generation pipeline based on Vision Large Language Model (VLM) agent collaborations. Given a language description of a video, multiple VLM agents direct various processes of the generation pipeline. They cooperate to create Blender scripts which render a video following the given description. Augmented with Blender-based movie making knowledge, the Director agent decomposes the text-based video description into sub-processes. For each sub-process, the Programmer agent produces Python-based Blender scripts based on function composing and API calling. The Reviewer agent, with knowledge of video reviewing, character motion coordinates, and intermediate screenshots, provides feedback to the Programmer agent. The Programmer agent iteratively improves scripts to yield the best video outcome. Our generated videos show better quality than commercial video generation models in five metrics on video quality and instruction-following performance. Our framework outperforms other approaches in a user study on quality, consistency, and rationality.
Speech Representation Learning Revisited: The Necessity of Separate Learnable Parameters and Robust Data Augmentation
Venue: arXiv cs.CL 2025
Year: 2025

Speech modeling methods learn one embedding for a fixed segment of speech, typically in between 10-25 ms. The information present in speech can be divided into two categories: "what is being said" (content) and "how it is expressed" (other) and these two are orthogonal in nature causing the optimization algorithm to find a sub-optimal solution if forced to optimize together. This leads to sub-optimal performance in one or all downstream tasks as shown by previous studies. Current self-supervised learning (SSL) methods such as HuBERT are very good at modeling the content information present in speech. Data augmentation improves the performance on tasks which require effective modeling of other information but this leads to a divided capacity of the model. In this work, we conduct a preliminary study to understand the importance of modeling other information using separate learnable parameters. We propose a modified version of HuBERT, termed Other HuBERT (O-HuBERT), to test our hypothesis. Our findings are twofold: first, the O-HuBERT method is able to utilize all layers to build complex features to encode other information; second, a robust data augmentation strategy is essential for learning the information required by tasks that depend on other information and to achieve state-of-the-art (SOTA) performance on the SUPERB benchmark with a similarly sized model (100 million parameters) and pre-training data (960 hours).
Design and Implementation of a Takum Arithmetic Hardware Codec
Venue: arXiv cs.AR 2025
Year: 2025

The takum machine number format has been recently proposed as an enhancement over the posit number format, which is considered a promising alternative to the IEEE 754 floating-point standard. Takums retain the useful posit properties, but feature a novel exponent coding scheme that yields more precision for small and large magnitude numbers and a much higher and bounded dynamic range. This paper presents the design and implementation of a hardware codec for both takums (logarithmic number system, LNS) and linear takums (floating-point format). The codec design is emphasised, as it constitutes the primary distinguishing feature compared to logarithmic posits (LNS) and posits (floating-point format), which otherwise share similar internal representations. Furthermore, a novel internal representation for LNS is proposed. The presented takum codec, implemented in VHDL, demonstrates near-optimal scalability and performance on an FPGA. It achieves latency reductions of up to 38% and reduces LUT utilisation up to 50% compared to the best state-of-the-art posit codecs.
PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis
Venue: arXiv cs.LG 2025
Year: 2025

We introduce a comprehensive framework for modeling single cell transcriptomic responses to perturbations, aimed at standardizing benchmarking in this rapidly evolving field. Our approach includes a modular and user-friendly model development and evaluation platform, a collection of diverse perturbational datasets, and a set of metrics designed to fairly compare models and dissect their performance. Through extensive evaluation of both published and baseline models across diverse datasets, we highlight the limitations of widely used models, such as mode collapse. We also demonstrate the importance of rank metrics which complement traditional model fit measures, such as RMSE, for validating model effectiveness. Notably, our results show that while no single model architecture clearly outperforms others, simpler architectures are generally competitive and scale well with larger datasets. Overall, this benchmarking exercise sets new standards for model evaluation, supports robust model development, and furthers the use of these models to simulate genetic and chemical screens for therapeutic discovery.
On the Approximation of Stationary Processes using the ARMA Model
Venue: arXiv cs.LG 2025
Year: 2025

We look at a problem related to Autoregressive Moving Average (ARMA) models, on quantifying the approximation error between a true stationary process $X_t$ and an ARMA model $Y_t$. We take the transfer function representation $x(L)$ of a stationary process $X_t$ and show that the $L^{\infty}$ norm of $x$ acts as a valid norm on $X_t$ that controls the $\ell^2$ norm of its Wold coefficients. We then show that a certain subspace of stationary processes, which includes ARMA models, forms a Banach algebra under the $L^{\infty}$ norm that respects the multiplicative structure of $H^{\infty}$ transfer functions and thus improves on the structural properties of the cepstral norm for ARMA models. The natural definition of invertibility in this algebra is consistent with the original definition of ARMA invertibility, and generalizes better to non-ARMA processes than Wiener's $\ell^1$ condition. Finally, we calculate some explicit approximation bounds in the simpler context of continuous transfer functions, and critique some heuristic ideas on Padé approximations and parsimonious models.
Analyzing the Impact of Electric Vehicles on Local Energy Systems using Digital Twins
Venue: arXiv cs.MA 2025
Year: 2025

The electrification of the transportation and heating sector, the so-called sector coupling, is one of the core elements to achieve independence from fossil fuels. As it highly affects the electricity demand, especially on the local level, the integrated modeling and simulation of all sectors is a promising approach for analyzing design decisions or complex control strategies. This paper analyzes the increase in electricity demand resulting from sector coupling, mainly due to integrating electric vehicles into urban energy systems. Therefore, we utilize a digital twin of an existing local energy system and extend it with a mobility simulation model to evaluate the impact of electric vehicles on the distribution grid level. Our findings indicate a significant rise in annual electricity consumption attributed to electric vehicles, with home charging alone resulting in a 78% increase. However, we demonstrate that integrating photovoltaic and battery energy storage systems can effectively mitigate this rise.
DiffZOO: A Purely Query-Based Black-Box Attack for Red-teaming Text-to-Image Generative Model via Zeroth Order Optimization
Venue: arXiv cs.CR 2025
Year: 2025

Current text-to-image (T2I) synthesis diffusion models raise misuse concerns, particularly in creating prohibited or not-safe-for-work (NSFW) images. To address this, various safety mechanisms and red teaming attack methods are proposed to enhance or expose the T2I model's capability to generate unsuitable content. However, many red teaming attack methods assume knowledge of the text encoders, limiting their practical usage. In this work, we rethink the case of \textit{purely black-box} attacks without prior knowledge of the T2l model. To overcome the unavailability of gradients and the inability to optimize attacks within a discrete prompt space, we propose DiffZOO which applies Zeroth Order Optimization to procure gradient approximations and harnesses both C-PRV and D-PRV to enhance attack prompts within the discrete prompt domain. We evaluated our method across multiple safety mechanisms of the T2I diffusion model and online servers. Experiments on multiple state-of-the-art safety mechanisms show that DiffZOO attains an 8.5% higher average attack success rate than previous works, hence its promise as a practical red teaming tool for T2l models.
Solving Oscillator Ordinary Differential Equations in the Time Domain with High Performance via Soft-constrained Physics-informed Neural Network with Small Data
Venue: arXiv cs.LG 2025
Year: 2025

In many scientific and engineering (e.g., physical, biochemical, medical) practices, data generated through expensive experiments or large-scale simulations, are often sparse and noisy. Physics-informed neural network (PINN) incorporates physical information and knowledge into network topology or computational processes as model priors, with the unique advantage of achieving strong generalization with small data. This study aims to investigate the performance characteristics of the soft-constrained PINN method to solving typical linear and nonlinear ordinary differential equations (ODEs) such as primer, Van der Pol and Duffing oscillators, especially the effectiveness, efficiency, and robustness to noise with minimal data. It is verified that the soft-constrained PINN significantly reduces the need for labeled data. With the aid of appropriate collocation points no need to be labeled, it can predict and also extrapolate with minimal data. First-order and second-order ODEs, no matter linear or nonlinear oscillators, require only one and two training data (containing initial values) respectively, just like classical analytic or Runge-Kutta methods, and with equivalent precision and comparable efficiency (fast training in seconds for scalar ODEs). Furthermore, it can conveniently impose a physical law (e.g., conservation of energy) constraint by adding a regularization term to the total loss function, improving the performance to deal with various complexities such as nonlinearity like Duffing. The DeepXDE-based PINN implementation is light code and can be efficiently trained on both GPU and CPU platforms. The mathematical and computational framework of this alternative and feasible PINN method to ODEs, can be easily extended to PDEs, etc., and is becoming a favorable catalyst for the era of Digital Twins.
Want to train KANS at scale? Now UKAN!
Venue: arXiv cs.LG 2025
Year: 2025

Kolmogorov-Arnold Networks (KANs) have recently emerged as a powerful alternative to traditional multilayer perceptrons. However, their reliance on predefined, bounded grids restricts their ability to approximate functions on unbounded domains. To address this, we present Unbounded Kolmogorov-Arnold Networks (UKANs), a method that removes the need for bounded grids in traditional Kolmogorov-Arnold Networks (KANs). The key innovation of this method is a coefficient-generator (CG) model that produces, on the fly, only the B-spline coefficients required locally on an unbounded symmetric grid. UKANs couple multilayer perceptrons with KANs by feeding the positional encoding of grid groups into the CG model, enabling function approximation on unbounded domains without requiring data normalization. To reduce the computational cost of both UKANs and KANs, we introduce a GPU-accelerated library that lowers B-spline evaluation complexity by a factor proportional to the grid size, enabling large-scale learning by leveraging efficient memory management, in line with recent software advances such as FlashAttention and FlashFFTConv. Performance benchmarking confirms the superior memory and computational efficiency of our accelerated KAN (warpKAN), and UKANs, showing a 3-30x speed-up and up to 1000x memory reduction compared to vanilla KANs. Experiments on regression, classification, and generative tasks demonstrate the effectiveness of UKANs to match or surpass KAN accuracy. Finally, we use both accelerated KAN and UKAN in a molecular property prediction task, establishing the feasibility of large-scale end-to-end training with our optimized implementation.