OpenRaiser/Intern-Atlas huggingface dataset:
Prot2Chat: Protein LLM with Early-Fusion of Text, Sequence and Structure
Venue: arXiv cs.LG 2025
Year: 2025

Motivation: Proteins are of great significance in living organisms. However, understanding their functions encounters numerous challenges, such as insufficient integration of multimodal information, a large number of training parameters, limited flexibility of classification-based methods, and the lack of systematic evaluation metrics for protein Q&A systems. To tackle these issues, we propose the Prot2Chat framework. Results: We modified ProteinMPNN to encode protein sequence and structural information in a unified way. We used a large language model (LLM) to encode questions into vectors and developed a protein-text adapter to compress protein information into virtual tokens based on these vectors, achieving the early fusion of text and protein information. Finally, the same LLM reads the virtual tokens and the questions to generate answers. To optimize training efficiency, we froze the encoder and employed Low-Rank Adaptation (LoRA) techniques for the LLM. Experiments on two datasets show that both automated metrics and expert evaluations demonstrate the superior performance of our model, and zero-shot prediction results highlight its generalization ability. The models and codes are available at https://github.com/ wangzc1233/Prot2Chat. Contact: zqcao@suda.edu.cn or wangzc025@163.com Key words: Protein Q&A, Early-Fusion, LLM
Beyond Vision: How Large Language Models Interpret Facial Expressions from Valence-Arousal Values
Venue: arXiv cs.CV 2025
Year: 2025

Large Language Models primarily operate through text-based inputs and outputs, yet human emotion is communicated through both verbal and non-verbal cues, including facial expressions. While Vision-Language Models analyze facial expressions from images, they are resource-intensive and may depend more on linguistic priors than visual understanding. To address this, this study investigates whether LLMs can infer affective meaning from dimensions of facial expressions-Valence and Arousal values, structured numerical representations, rather than using raw visual input. VA values were extracted using Facechannel from images of facial expressions and provided to LLMs in two tasks: (1) categorizing facial expressions into basic (on the IIMI dataset) and complex emotions (on the Emotic dataset) and (2) generating semantic descriptions of facial expressions (on the Emotic dataset). Results from the categorization task indicate that LLMs struggle to classify VA values into discrete emotion categories, particularly for emotions beyond basic polarities (e.g., happiness, sadness). However, in the semantic description task, LLMs produced textual descriptions that align closely with human-generated interpretations, demonstrating a stronger capacity for free text affective inference of facial expressions.
CluStRE: Streaming Graph Clustering with Multi-Stage Refinement
Venue: arXiv cs.LG 2025
Year: 2025

We present CluStRE, a novel streaming graph clustering algorithm that balances computational efficiency with high-quality clustering using multi-stage refinement. Unlike traditional in-memory clustering approaches, CluStRE processes graphs in a streaming setting, significantly reducing memory overhead while leveraging re-streaming and evolutionary heuristics to improve solution quality. Our method dynamically constructs a quotient graph, enabling modularity-based optimization while efficiently handling large-scale graphs. We introduce multiple configurations of CluStRE to provide trade-offs between speed, memory consumption, and clustering quality. Experimental evaluations demonstrate that CluStRE improves solution quality by 89.8%, operates 2.6 times faster, and uses less than two-thirds of the memory required by the state-of-the-art streaming clustering algorithm on average. Moreover, our strongest mode enhances solution quality by up to 150% on average. With this, CluStRE achieves comparable solution quality to in-memory algorithms, i.e. over 96% of the quality of clustering approaches, including Louvain, effectively bridging the gap between streaming and traditional clustering methods.
Secure Visual Data Processing via Federated Learning
Venue: arXiv cs.CV 2025
Year: 2025

As the demand for privacy in visual data management grows, safeguarding sensitive information has become a critical challenge. This paper addresses the need for privacy-preserving solutions in large-scale visual data processing by leveraging federated learning. Although there have been developments in this field, previous research has mainly focused on integrating object detection with either anonymization or federated learning. However, these pairs often fail to address complex privacy concerns. On the one hand, object detection with anonymization alone can be vulnerable to reverse techniques. On the other hand, federated learning may not provide sufficient privacy guarantees. Therefore, we propose a new approach that combines object detection, federated learning and anonymization. Combining these three components aims to offer a robust privacy protection strategy by addressing different vulnerabilities in visual data. Our solution is evaluated against traditional centralized models, showing that while there is a slight trade-off in accuracy, the privacy benefits are substantial, making it well-suited for privacy sensitive applications.
Occam's model: Selecting simpler representations for better transferability estimation
Venue: arXiv cs.LG 2025
Year: 2025

Fine-tuning models that have been pre-trained on large datasets has become a cornerstone of modern machine learning workflows. With the widespread availability of online model repositories, such as Hugging Face, it is now easier than ever to fine-tune pre-trained models for specific tasks. This raises a critical question: which pre-trained model is most suitable for a given task? This problem is called transferability estimation. In this work, we introduce two novel and effective metrics for estimating the transferability of pre-trained models. Our approach is grounded in viewing transferability as a measure of how easily a pre-trained model's representations can be trained to separate target classes, providing a unique perspective on transferability estimation. We rigorously evaluate the proposed metrics against state-of-the-art alternatives across diverse problem settings, demonstrating their robustness and practical utility. Additionally, we present theoretical insights that explain our metrics' efficacy and adaptability to various scenarios. We experimentally show that our metrics increase Kendall's Tau by up to 32% compared to the state-of-the-art baselines.
Downlink and Uplink ISAC in Continuous-Aperture Array (CAPA) Systems
Venue: arXiv cs.IT 2025
Year: 2025

A continuous-aperture array (CAPA)-based integrated sensing and communications (ISAC) framework is proposed for both downlink and uplink scenarios. Within this framework, continuous operator-based signal models are employed to describe the sensing and communication processes. The performance of communication and sensing is analyzed using two information-theoretic metrics: the communication rate (CR) and the sensing rate (SR). 1) For downlink ISAC, three continuous beamforming designs are proposed: i) the communications-centric (C-C) design that maximizes the CR, ii) the sensing-centric (S-C) design that maximizes the SR, and iii) the Pareto-optimal design that characterizes the Pareto boundary of the CR-SR region. A low-complexity signal subspace-based approach is proposed to derive the closed-form optimal beamformers for the considered designs. On this basis, closed-form expressions are derived for the achievable CRs and SRs, and the downlink rate region achieved by CAPAs is characterized. 2) For uplink ISAC, the C-C and S-C successive interference cancellation-based methods are proposed to manage inter-functionality interference. Using the subspace approach closed-form expressions for the optimal detectors as well as the achievable CRs and SRs are derived. The uplink SR-CR region is characterized based on the time-sharing technique. Numerical results demonstrate that, for both downlink and uplink, CAPA-based ISAC achieves higher CRs and SRs as well as larger CR-SR regions compared to conventional spatially discrete array-based ISAC.
Indoor Heat Estimation from a Single Visible-Light Panorama
Venue: arXiv cs.CV 2025
Year: 2025

This paper introduces a novel image-based rendering technique for jointly estimating indoor lighting and thermal conditions from paired indoor-outdoor high dynamic range (HDR) panoramas. Our method uses the indoor panorama to estimate the 3D floor layout, while the corresponding outdoor panorama serves as an environment map to infer spatially-varying illumination and material properties. Assuming indoor surfaces are Lambertian and that all heat originates from outdoor visible light, we model the relationship between light transport and heat transfer, and perform transient heat simulations to generate indoor temperature distributions. The simulated heat maps are validated against real-world thermal images captured with an infrared camera. This approach supports photorealistic and physically informed visualization, enabling integrated light and heat estimation to advance traditional virtual home staging.
Position: Episodic Memory is the Missing Piece for Long-Term LLM Agents
Venue: arXiv cs.AI 2025
Year: 2025

As Large Language Models (LLMs) evolve from text-completion tools into fully fledged agents operating in dynamic environments, they must address the challenge of continually learning and retaining long-term knowledge. Many biological systems solve these challenges with episodic memory, which supports single-shot learning of instance-specific contexts. Inspired by this, we present an episodic memory framework for LLM agents, centered around five key properties of episodic memory that underlie adaptive and context-sensitive behavior. With various research efforts already partially covering these properties, this position paper argues that now is the right time for an explicit, integrated focus on episodic memory to catalyze the development of long-term agents. To this end, we outline a roadmap that unites several research directions under the goal to support all five properties of episodic memory for more efficient long-term LLM agents.
Machine Learning Fleet Efficiency: Analyzing and Optimizing Large-Scale Google TPU Systems with ML Productivity Goodput
Venue: arXiv cs.LG 2025
Year: 2025

Recent years have seen the emergence of machine learning (ML) workloads deployed in warehouse-scale computing (WSC) settings, also known as ML fleets. As the computational demands placed on ML fleets have increased due to the rise of large models and growing demand for ML applications, it has become increasingly critical to measure and improve the efficiency of such systems. However, there is not yet an established methodology to characterize ML fleet performance and identify potential performance optimizations accordingly. This paper presents a large-scale analysis of an ML fleet based on Google's TPUs, introducing a framework to capture fleet-wide efficiency, systematically evaluate performance characteristics, and identify optimization strategies for the fleet. We begin by defining an ML fleet, outlining its components, and analyzing an example Google ML fleet in production comprising thousands of accelerators running diverse workloads. Our study reveals several critical insights: first, ML fleets extend beyond the hardware layer, with model, data, framework, compiler, and scheduling layers significantly impacting performance; second, the heterogeneous nature of ML fleets poses challenges in characterizing individual workload performance; and third, traditional utilization-based metrics prove insufficient for ML fleet characterization. To address these challenges, we present the "ML Productivity Goodput" (MPG) metric to measure ML fleet efficiency. We show how to leverage this metric to characterize the fleet across the ML system stack. We also present methods to identify and optimize performance bottlenecks using MPG, providing strategies for managing warehouse-scale ML systems in general. Lastly, we demonstrate quantitative evaluations from applying these methods to a real ML fleet for internal-facing Google TPU workloads, where we observed tangible improvements.
Representational Alignment with Chemical Induced Fit for Molecular Relational Learning
Venue: arXiv cs.LG 2025
Year: 2025

Molecular Relational Learning (MRL) is widely applied in natural sciences to predict relationships between molecular pairs by extracting structural features. The representational similarity between substructure pairs determines the functional compatibility of molecular binding sites. Nevertheless, aligning substructure representations by attention mechanisms lacks guidance from chemical knowledge, resulting in unstable model performance in chemical space (\textit{e.g.}, functional group, scaffold) shifted data. With theoretical justification, we propose the \textbf{Re}presentational \textbf{Align}ment with Chemical Induced \textbf{Fit} (ReAlignFit) to enhance the stability of MRL. ReAlignFit dynamically aligns substructure representation in MRL by introducing chemical Induced Fit-based inductive bias. In the induction process, we design the Bias Correction Function based on substructure edge reconstruction to align representations between substructure pairs by simulating chemical conformational changes (dynamic combination of substructures). ReAlignFit further integrates the Subgraph Information Bottleneck during fit process to refine and optimize substructure pairs exhibiting high chemical functional compatibility, leveraging them to generate molecular embeddings. Experimental results on nine datasets demonstrate that ReAlignFit outperforms state-of-the-art models in two tasks and significantly enhances model's stability in both rule-shifted and scaffold-shifted data distributions.
PrismAvatar: Real-time animated 3D neural head avatars on edge devices
Venue: arXiv cs.CV 2025
Year: 2025

We present PrismAvatar: a 3D head avatar model which is designed specifically to enable real-time animation and rendering on resource-constrained edge devices, while still enjoying the benefits of neural volumetric rendering at training time. By integrating a rigged prism lattice with a 3D morphable head model, we use a hybrid rendering model to simultaneously reconstruct a mesh-based head and a deformable NeRF model for regions not represented by the 3DMM. We then distill the deformable NeRF into a rigged mesh and neural textures, which can be animated and rendered efficiently within the constraints of the traditional triangle rendering pipeline. In addition to running at 60 fps with low memory usage on mobile devices, we find that our trained models have comparable quality to state-of-the-art 3D avatar models on desktop devices.
Scalable and Ethical Insider Threat Detection through Data Synthesis and Analysis by LLMs
Venue: arXiv cs.CR 2025
Year: 2025

Insider threats wield an outsized influence on organizations, disproportionate to their small numbers. This is due to the internal access insiders have to systems, information, and infrastructure. %One example of this influence is where anonymous respondents submit web-based job search site reviews, an insider threat risk to organizations. Signals for such risks may be found in anonymous submissions to public web-based job search site reviews. This research studies the potential for large language models (LLMs) to analyze and detect insider threat sentiment within job site reviews. Addressing ethical data collection concerns, this research utilizes synthetic data generation using LLMs alongside existing job review datasets. A comparative analysis of sentiment scores generated by LLMs is benchmarked against expert human scoring. Findings reveal that LLMs demonstrate alignment with human evaluations in most cases, thus effectively identifying nuanced indicators of threat sentiment. The performance is lower on human-generated data than synthetic data, suggesting areas for improvement in evaluating real-world data. Text diversity analysis found differences between human-generated and LLM-generated datasets, with synthetic data exhibiting somewhat lower diversity. Overall, the results demonstrate the applicability of LLMs to insider threat detection, and a scalable solution for insider sentiment testing by overcoming ethical and logistical barriers tied to data acquisition.
TOCTOU Resilient Attestation for IoT Networks (Full Version)
Venue: arXiv cs.CR 2025
Year: 2025

Internet-of-Things (IoT) devices are increasingly common in both consumer and industrial settings, often performing safety-critical functions. Although securing these devices is vital, manufacturers typically neglect security issues or address them as an afterthought. This is of particular importance in IoT networks, e.g., in the industrial automation settings. To this end, network attestation -- verifying the software state of all devices in a network -- is a promising mitigation approach. However, current network attestation schemes have certain shortcomings: (1) lengthy TOCTOU (Time-Of-Check-Time-Of-Use) vulnerability windows, (2) high latency and resource overhead, and (3) susceptibility to interference from compromised devices. To address these limitations, we construct TRAIN (TOCTOU-Resilient Attestation for IoT Networks), an efficient technique that minimizes TOCTOU windows, ensures constant-time per-device attestation, and maintains resilience even with multiple compromised devices. We demonstrate TRAIN's viability and evaluate its performance via a fully functional and publicly available prototype.
Tokenization Standards for Linguistic Integrity: Turkish as a Benchmark
Venue: arXiv cs.CL 2025
Year: 2025

Tokenization is a fundamental preprocessing step in NLP, directly impacting large language models' (LLMs) ability to capture syntactic, morphosyntactic, and semantic structures. This paper introduces a novel framework for systematically evaluating tokenization strategies, addressing challenges in morphologically rich and low-resource languages. Using a Turkish dataset of 6,200 multiple-choice questions from the Massive Multitask Language Understanding (MMLU) benchmark, the framework assesses tokenizers across five key metrics: vocabulary size, token count, processing time, language-specific token percentages (\%TR), and token purity. These metrics provide a structured approach to evaluating how well tokenizers preserve linguistic structures. While \%TR measures the proportion of valid words in the target language, \%Pure assesses the alignment of tokens with meaningful linguistic units, such as roots and valid morphemes, minimizing semantic fragmentation. The findings reveal that \%TR, introduced as a critical metric, exhibits a stronger correlation with downstream performance (e.g., MMLU scores) than token purity, emphasizing its role in improving model accuracy. Additionally, larger model parameters do not necessarily yield better tokenization quality or enhanced results, highlighting the importance of tailored tokenization strategies that prioritize linguistic alignment. This framework sets a new standard for developing robust tokenization methods optimized for morphologically complex and low-resource languages. Future work will refine morphological analysis, explore domain-specific customizations, and conduct cross-linguistic evaluations to further enhance tokenization practices.
IRepair: An Intent-Aware Approach to Repair Data-Driven Errors in Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Not a day goes by without hearing about the impressive feats of large language models (LLMs), and equally, not a day passes without hearing about their challenges. LLMs are notoriously vulnerable to biases in their dataset, leading to issues such as toxicity. While domain-adaptive training has been employed to mitigate these issues, these techniques often address all model parameters indiscriminately during the repair process, resulting in poor repair quality and reduced model versatility. In this paper, we introduce a novel dynamic slicing-based intent-aware LLM repair strategy, IRepair. This approach selectively targets the most error-prone sections of the model for repair. Specifically, we propose dynamically slicing the model's most sensitive layers that require immediate attention, concentrating repair efforts on those areas. This method enables more effective repairs with potentially less impact on the model's overall performance by altering a smaller portion of the model. We evaluated our technique on three models from the GPT2 and GPT-Neo families, with parameters ranging from 800M to 1.6B, in a toxicity mitigation setup. Our results show that IRepair repairs errors 43.6% more effectively while causing 46% less disruption to general performance compared to the closest baseline, direct preference optimization. Our empirical analysis also reveals that errors are more concentrated in a smaller section of the model, with the top 20% of layers exhibiting 773% more error density than the remaining 80\%. This highlights the need for selective repair. Additionally, we demonstrate that a dynamic selection approach is essential for addressing errors dispersed throughout the model, ensuring a robust and efficient repair.
Threat Me Right: A Human HARMS Threat Model for Technical Systems
Venue: arXiv cs.CR 2025
Year: 2025

Threat modelling is the process of identifying potential vulnerabilities in a system and prioritising them. Existing threat modelling tools focus primarily on technical systems and are not as well suited to interpersonal threats. In this paper, we discuss traditional threat modelling methods and their shortcomings, and propose a new threat modelling framework (HARMS) to identify non-technical and human factors harms. We also cover a case study of applying HARMS when it comes to IoT devices such as smart speakers with virtual assistants.
Unconstrained Body Recognition at Altitude and Range: Comparing Four Approaches
Venue: arXiv cs.CV 2025
Year: 2025

This study presents an investigation of four distinct approaches to long-term person identification using body shape. Unlike short-term re-identification systems that rely on temporary features (e.g., clothing), we focus on learning persistent body shape characteristics that remain stable over time. We introduce a body identification model based on a Vision Transformer (ViT) (Body Identification from Diverse Datasets, BIDDS) and on a Swin-ViT model (Swin-BIDDS). We also expand on previous approaches based on the Linguistic and Non-linguistic Core ResNet Identity Models (LCRIM and NLCRIM), but with improved training. All models are trained on a large and diverse dataset of over 1.9 million images of approximately 5k identities across 9 databases. Performance was evaluated on standard re-identification benchmark datasets (MARS, MSMT17, Outdoor Gait, DeepChange) and on an unconstrained dataset that includes images at a distance (from close-range to 1000m), at altitude (from an unmanned aerial vehicle, UAV), and with clothing change. A comparative analysis across these models provides insights into how different backbone architectures and input image sizes impact long-term body identification performance across real-world conditions.