OpenRaiser/Intern-Atlas huggingface dataset:
DANCE: Deep Learning-Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images
Venue: arXiv cs.LG 2025
Year: 2025

Cancer is a complex disease characterized by uncontrolled cell growth. T cell receptors (TCRs), crucial proteins in the immune system, play a key role in recognizing antigens, including those associated with cancer. Recent advancements in sequencing technologies have facilitated comprehensive profiling of TCR repertoires, uncovering TCRs with potent anti-cancer activity and enabling TCR-based immunotherapies. However, analyzing these intricate biomolecules necessitates efficient representations that capture their structural and functional information. T-cell protein sequences pose unique challenges due to their relatively smaller lengths compared to other biomolecules. An image-based representation approach becomes a preferred choice for efficient embeddings, allowing for the preservation of essential details and enabling comprehensive analysis of T-cell protein sequences. In this paper, we propose to generate images from the protein sequences using the idea of Chaos Game Representation (CGR) using the Kaleidoscopic images approach. This Deep Learning Assisted Analysis of Protein Sequences Using Chaos Enhanced Kaleidoscopic Images (called DANCE) provides a unique way to visualize protein sequences by recursively applying chaos game rules around a central seed point. we perform the classification of the T cell receptors (TCRs) protein sequences in terms of their respective target cancer cells, as TCRs are known for their immune response against cancer disease. The TCR sequences are converted into images using the DANCE method. We employ deep-learning vision models to perform the classification to obtain insights into the relationship between the visual patterns observed in the generated kaleidoscopic images and the underlying protein properties. By combining CGR-based image generation with deep learning classification, this study opens novel possibilities in the protein analysis domain.
Fast Simulation of Cellular Automata by Self-Composition
Venue: arXiv cs.CC 2025
Year: 2025

Computing the configuration of any one-dimensional cellular automaton at generation $n$ can be accelerated by constructing and running a composite rule with a radius proportional to $\log n$. The new automaton is the original one, but with its local rule function composed with itself. Consequently, the asymptotic time complexity to compute the configuration of generation $n$ is reduced from $O(n^2)$-time to $O(n^2 / \log n)$, but with $O(n^2/(\log n)^3)$-space, demonstrating a time-memory tradeoff. Experimental results are given in the case of Rule 30.
Reranking Laws for Language Generation: A Communication-Theoretic Perspective
Venue: arXiv cs.CL 2025
Year: 2025

To ensure large language models (LLMs) are used safely, one must reduce their propensity to hallucinate or to generate unacceptable answers. A simple and often used strategy is to first let the LLM generate multiple hypotheses and then employ a reranker to choose the best one. In this paper, we draw a parallel between this strategy and the use of redundancy to decrease the error rate in noisy communication channels. We conceptualize the generator as a sender transmitting multiple descriptions of a message through parallel noisy channels. The receiver decodes the message by ranking the (potentially corrupted) descriptions and selecting the one found to be most reliable. We provide conditions under which this protocol is asymptotically error-free (i.e., yields an acceptable answer almost surely) even in scenarios where the reranker is imperfect (governed by Mallows or Zipf-Mandelbrot models) and the channel distributions are statistically dependent. We use our framework to obtain reranking laws which we validate empirically on two real-world tasks using LLMs: text-to-code generation with DeepSeek-Coder 7B and machine translation of medical data with TowerInstruct 13B.
Riemannian Federated Learning via Averaging Gradient Streams
Venue: arXiv cs.LG 2025
Year: 2025

Federated learning (FL) as a distributed learning paradigm has a significant advantage in addressing large-scale machine learning tasks. In the Euclidean setting, FL algorithms have been extensively studied with both theoretical and empirical success. However, there exist few works that investigate federated learning algorithms in the Riemannian setting. In particular, critical challenges such as partial participation and data heterogeneity among agents are not explored in the Riemannian federated setting. This paper presents and analyzes a Riemannian FL algorithm, called RFedAGS, based on a new efficient server aggregation -- averaging gradient streams, which can simultaneously handle partial participation and data heterogeneity. We theoretically show that the proposed RFedAGS has global convergence and sublinear convergence rate under decaying step sizes cases; and converges sublinearly/linearly to a neighborhood of a stationary point/solution under fixed step sizes cases. These analyses are based on a vital and non-trivial assumption induced by partial participation, which is shown to hold with high probability. Extensive experiments conducted on synthetic and real-world data demonstrate the good performance of RFedAGS.
MiniDrive: More Efficient Vision-Language Models with Multi-Level 2D Features as Text Tokens for Autonomous Driving
Venue: arXiv cs.CV 2025
Year: 2025

Vision-language models (VLMs) serve as general-purpose end-to-end models in autonomous driving, performing subtasks such as prediction, planning, and perception through question-and-answer interactions. However, most existing methods rely on computationally expensive visual encoders and large language models (LLMs), making them difficult to deploy in real-world scenarios and real-time applications. Meanwhile, most existing VLMs lack the ability to process multiple images, making it difficult to adapt to multi-camera perception in autonomous driving. To address these issues, we propose a novel framework called MiniDrive, which incorporates our proposed Feature Engineering Mixture of Experts (FE-MoE) module and Dynamic Instruction Adapter (DI-Adapter). The FE-MoE effectively maps 2D features into visual token embeddings before being input into the language model. The DI-Adapter enables the visual token embeddings to dynamically change with the instruction text embeddings, resolving the issue of static visual token embeddings for the same image in previous approaches. Compared to previous works, MiniDrive achieves state-of-the-art performance in terms of parameter size, floating point operations, and response efficiency, with the smallest version containing only 83M parameters.
Think Together and Work Better: Combining Humans' and LLMs' Think-Aloud Outcomes for Effective Text Evaluation
Venue: arXiv cs.CL 2025
Year: 2025

This study introduces \textbf{InteractEval}, a framework that integrates human expertise and Large Language Models (LLMs) using the Think-Aloud (TA) method to generate attributes for checklist-based text evaluation. By combining human flexibility and reasoning with LLM consistency, InteractEval outperforms traditional non-LLM-based and LLM-based baselines across four distinct dimensions, consisting of Coherence, Fluency, Consistency, and Relevance. The experiment also investigates the effectiveness of the TA method, showing that it promotes divergent thinking in both humans and LLMs, leading to the generation of a wider range of relevant attributes and enhance text evaluation performance. Comparative analysis reveals that humans excel at identifying attributes related to internal quality (Coherence and Fluency), but LLMs perform better at those attributes related to external alignment (Consistency and Relevance). Consequently, leveraging both humans and LLMs together produces the best evaluation outcomes. In other words, this study emphasizes the necessity of effectively combining humans and LLMs in an automated checklist-based text evaluation framework. The code is available at \textbf{\url{https://github.com/BBeeChu/InteractEval.git}}.
Convergence of continuous-time stochastic gradient descent with applications to deep neural networks
Venue: arXiv cs.LG 2025
Year: 2025

We study a continuous-time approximation of the stochastic gradient descent process for minimizing the population expected loss in learning problems. The main results establish general sufficient conditions for the convergence, extending the results of Chatterjee (2022) established for (nonstochastic) gradient descent. We show how the main result can be applied to the case of overparametrized neural network training.
A Novel Mathematical Framework for Objective Characterization of Ideas
Venue: arXiv cs.AI 2025
Year: 2025

The demand for innovation in product design necessitates a prolific ideation phase. Conversational AI (CAI) systems that use Large Language Models (LLMs) such as GPT (Generative Pre-trained Transformer) have been shown to be fruitful in augmenting human creativity, providing numerous novel and diverse ideas. Despite the success in ideation quantity, the qualitative assessment of these ideas remains challenging and traditionally reliant on expert human evaluation. This method suffers from limitations such as human judgment errors, bias, and oversight. Addressing this gap, our study introduces a comprehensive mathematical framework for automated analysis to objectively evaluate the plethora of ideas generated by CAI systems and/or humans. This framework is particularly advantageous for novice designers who lack experience in selecting promising ideas. By converting the ideas into higher dimensional vectors and quantitatively measuring the diversity between them using tools such as UMAP, DBSCAN and PCA, the proposed method provides a reliable and objective way of selecting the most promising ideas, thereby enhancing the efficiency of the ideation phase.
MOSAIC: Multiple Observers Spotting AI Content
Venue: arXiv cs.CL 2025
Year: 2025

The dissemination of Large Language Models (LLMs), trained at scale, and endowed with powerful text-generating abilities, has made it easier for all to produce harmful, toxic, faked or forged content. In response, various proposals have been made to automatically discriminate artificially generated from human-written texts, typically framing the problem as a binary classification problem. Early approaches evaluate an input document with a well-chosen detector LLM, assuming that low-perplexity scores reliably signal machine-made content. More recent systems instead consider two LLMs and compare their probability distributions over the document to further discriminate when perplexity alone cannot. However, using a fixed pair of models can induce brittleness in performance. We extend these approaches to the ensembling of several LLMs and derive a new, theoretically grounded approach to combine their respective strengths. Our experiments, conducted with various generator LLMs, indicate that this approach effectively leverages the strengths of each model, resulting in robust detection performance across multiple domains. Our code and data are available at https://github.com/BaggerOfWords/MOSAIC .
A Deep Dive Into How Open-Source Project Maintainers Review and Resolve Bug Bounty Reports
Venue: arXiv cs.SE 2025
Year: 2025

Researchers have investigated the bug bounty ecosystem from the lens of platforms, programs, and bug hunters. Understanding the perspectives of bug bounty report reviewers, especially those who historically lack a security background and little to no funding for bug hunters, is currently understudied. In this paper, we primarily investigate the perspective of open-source software (OSS) maintainers who have used \texttt{huntr}, a bug bounty platform that pays bounties to bug hunters who find security bugs in GitHub projects and have had valid vulnerabilities patched as a result. We address this area by conducting three studies: identifying characteristics through a listing survey ($n_1=51$), their ranked importance with Likert-scale survey data ($n_2=90$), and conducting semi-structured interviews to dive deeper into real-world experiences ($n_3=17$). As a result, we categorize 40 identified characteristics into benefits, challenges, helpful features, and wanted features. We find that private disclosure and project visibility are the most important benefits, while hunters focused on money or CVEs and pressure to review are the most challenging to overcome. Surprisingly, lack of communication with bug hunters is the least challenging, and CVE creation support is the second-least helpful feature for OSS maintainers when reviewing bug bounty reports. We present recommendations to make the bug bounty review process more accommodating to open-source maintainers and identify areas for future work.
Maximum And- vs. Even-SAT
Venue: arXiv cs.DS 2025
Year: 2025

A multiset of literals, called a clause, is \emph{strongly satisfied} by an assignment if \emph{no} literal evaluates to false. Finding an assignment that maximises the number of strongly satisfied clauses is NP-hard. We present a simple algorithm that finds, given a multiset of clauses that admits an assignment that strongly satisfies $ρ$ of the clauses, an assignment in which at least $ρ$ of the clauses are \emph{weakly satisfied}, in the sense that an \emph{even} number of literals evaluate to false. In particular, this implies an efficient algorithm for finding an undirected cut of value $ρ$ in a graph $G$ given that a directed cut of value $ρ$ in $G$ is promised to exist. A similar argument also gives an efficient algorithm for finding an acyclic subgraph of $G$ with $ρ$ edges under the same promise.
Objection Overruled! Lay People can Distinguish Large Language Models from Lawyers, but still Favour Advice from an LLM
Venue: arXiv cs.HC 2025
Year: 2025

Large Language Models (LLMs) are seemingly infiltrating every domain, and the legal context is no exception. In this paper, we present the results of three experiments (total N = 288) that investigated lay people's willingness to act upon, and their ability to discriminate between, LLM- and lawyer-generated legal advice. In Experiment 1, participants judged their willingness to act on legal advice when the source of the advice was either known or unknown. When the advice source was unknown, participants indicated that they were significantly more willing to act on the LLM-generated advice. The result of the source unknown condition was replicated in Experiment 2. Intriguingly, despite participants indicating higher willingness to act on LLM-generated advice in Experiments 1 and 2, participants discriminated between the LLM- and lawyer-generated texts significantly above chance-level in Experiment 3. Lastly, we discuss potential explanations and risks of our findings, limitations and future work.
BLens: Contrastive Captioning of Binary Functions using Ensemble Embedding
Venue: arXiv cs.LG 2025
Year: 2025

Function names can greatly aid human reverse engineers, which has spurred the development of machine learning-based approaches to predicting function names in stripped binaries. Much current work in this area now uses transformers, applying a metaphor of machine translation from code to function names. Still, function naming models face challenges in generalizing to projects unrelated to the training set. In this paper, we take a completely new approach by transferring advances in automated image captioning to the domain of binary reverse engineering, such that different parts of a binary function can be associated with parts of its name. We propose BLens, which combines multiple binary function embeddings into a new ensemble representation, aligns it with the name representation latent space via a contrastive learning approach, and generates function names with a transformer architecture tailored for function names. Our experiments demonstrate that BLens significantly outperforms the state of the art. In the usual setting of splitting per binary, we achieve an $F_1$ score of 0.79 compared to 0.70. In the cross-project setting, which emphasizes generalizability, we achieve an $F_1$ score of 0.46 compared to 0.29. Finally, in an experimental setting reducing shared components across projects, we achieve an $F_1$ score of $0.32$ compared to $0.19$.
MambaMIC: An Efficient Baseline for Microscopic Image Classification with State Space Models
Venue: arXiv cs.CV 2025
Year: 2025

In recent years, CNN and Transformer-based methods have made significant progress in Microscopic Image Classification (MIC). However, existing approaches still face the dilemma between global modeling and efficient computation. While the Selective State Space Model (SSM) can simulate long-range dependencies with linear complexity, it still encounters challenges in MIC, such as local pixel forgetting, channel redundancy, and lack of local perception. To address these issues, we propose a simple yet efficient vision backbone for MIC tasks, named MambaMIC. Specifically, we introduce a Local-Global dual-branch aggregation module: the MambaMIC Block, designed to effectively capture and fuse local connectivity and global dependencies. In the local branch, we use local convolutions to capture pixel similarity, mitigating local pixel forgetting and enhancing perception. In the global branch, SSM extracts global dependencies, while Locally Aware Enhanced Filter reduces channel redundancy and local pixel forgetting. Additionally, we design a Feature Modulation Interaction Aggregation Module for deep feature interaction and key feature re-localization. Extensive benchmarking shows that MambaMIC achieves state-of-the-art performance across five datasets. code is available at https://zs1314.github.io/MambaMIC
Universal Trajectory Optimization Framework for Differential Drive Robot Class
Venue: arXiv cs.RO 2025
Year: 2025

Differential drive robots are widely used in various scenarios thanks to their straightforward principle, from household service robots to disaster response field robots. There are several types of driving mechanisms for real-world applications, including two-wheeled, four-wheeled skid-steering, tracked robots, and so on. The differences in the driving mechanisms usually require specific kinematic modeling when precise control is desired. Furthermore, the nonholonomic dynamics and possible lateral slip lead to different degrees of difficulty in getting feasible and high-quality trajectories. Therefore, a comprehensive trajectory optimization framework to compute trajectories efficiently for various kinds of differential drive robots is highly desirable. In this paper, we propose a universal trajectory optimization framework that can be applied to differential drive robots, enabling the generation of high-quality trajectories within a restricted computational timeframe. We introduce a novel trajectory representation based on polynomial parameterization of motion states or their integrals, such as angular and linear velocities, which inherently matches the robots' motion to the control principle. The trajectory optimization problem is formulated to minimize complexity while prioritizing safety and operational efficiency. We then build a full-stack autonomous planning and control system to demonstrate its feasibility and robustness. We conduct extensive simulations and real-world testing in crowded environments with three kinds of differential drive robots to validate the effectiveness of our approach.
Enhancing Few-Shot Image Classification through Learnable Multi-Scale Embedding and Attention Mechanisms
Venue: arXiv cs.CV 2025
Year: 2025

In the context of few-shot classification, the goal is to train a classifier using a limited number of samples while maintaining satisfactory performance. However, traditional metric-based methods exhibit certain limitations in achieving this objective. These methods typically rely on a single distance value between the query feature and support feature, thereby overlooking the contribution of shallow features. To overcome this challenge, we propose a novel approach in this paper. Our approach involves utilizing a multi-output embedding network that maps samples into distinct feature spaces. The proposed method extracts feature vectors at different stages, enabling the model to capture both global and abstract features. By utilizing these diverse feature spaces, our model enhances its performance. Moreover, employing a self-attention mechanism improves the refinement of features at each stage, leading to even more robust representations and improved overall performance. Furthermore, assigning learnable weights to each stage significantly improved performance and results. We conducted comprehensive evaluations on the MiniImageNet and FC100 datasets, specifically in the 5-way 1-shot and 5-way 5-shot scenarios. Additionally, we performed cross-domain tasks across eight benchmark datasets, achieving high accuracy in the testing domains. These evaluations demonstrate the efficacy of our proposed method in comparison to state-of-the-art approaches. https://github.com/FatemehAskari/MSENet
Edge-Wise Graph-Instructed Neural Networks
Venue: arXiv cs.LG 2025
Year: 2025

The problem of multi-task regression over graph nodes has been recently approached through Graph-Instructed Neural Network (GINN), which is a promising architecture belonging to the subset of message-passing graph neural networks. In this work, we discuss the limitations of the Graph-Instructed (GI) layer, and we formalize a novel edge-wise GI (EWGI) layer. We discuss the advantages of the EWGI layer and we provide numerical evidence that EWGINNs perform better than GINNs over some graph-structured input data, like the ones inferred from the Barabasi-Albert graph, and improve the training regularization on graphs with chaotic connectivity, like the ones inferred from the Erdos-Renyi graph.
Style-based Clustering of Visual Artworks and the Play of Neural Style-Representations
Venue: arXiv cs.CV 2025
Year: 2025

Clustering artworks based on style can have many potential real-world applications like art recommendations, style-based search and retrieval, and the study of artistic style evolution of an artist or in an artwork corpus. We introduce and deliberate over the notion of 'Style-based clustering of visual artworks'. We argue that clustering artworks based on style is largely an unaddressed problem. We explore and devise different neural feature representations - from the style-classification, style-transfer to large language vision models - that can be then used for style-based clustering. Our objective is to assess the relative effectiveness of these devised style-based clustering approaches through qualitative and quantitative analysis by applying them to multiple artwork corpora and curated synthetically styled datasets. Besides providing a broad framework for style-based clustering and evaluation, our analysis provides some key novel insights on feature representations, architectures and implications for style-based clustering.