OpenRaiser/Intern-Atlas huggingface dataset:
PERC: a suite of software tools for the curation of cryoEM data with application to simulation, modelling and machine learning
Venue: arXiv cs.LG 2025
Year: 2025

Ease of access to data, tools and models expedites scientific research. In structural biology there are now numerous open repositories of experimental and simulated datasets. Being able to easily access and utilise these is crucial for allowing researchers to make optimal use of their research effort. The tools presented here are useful for collating existing public cryoEM datasets and/or creating new synthetic cryoEM datasets to aid the development of novel data processing and interpretation algorithms. In recent years, structural biology has seen the development of a multitude of machine-learning based algorithms for aiding numerous steps in the processing and reconstruction of experimental datasets and the use of these approaches has become widespread. Developing such techniques in structural biology requires access to large datasets which can be cumbersome to curate and unwieldy to make use of. In this paper we present a suite of Python software packages which we collectively refer to as PERC (profet, EMPIARreader and CAKED). These are designed to reduce the burden which data curation places upon structural biology research. The protein structure fetcher (profet) package allows users to conveniently download and cleave sequences or structures from the Protein Data Bank or Alphafold databases. EMPIARreader allows lazy loading of Electron Microscopy Public Image Archive datasets in a machine-learning compatible structure. The Class Aggregator for Key Electron-microscopy Data (CAKED) package is designed to seamlessly facilitate the training of machine learning models on electron microscopy data, including electron-cryo-microscopy-specific data augmentation and labelling. These packages may be utilised independently or as building blocks in workflows. All are available in open source repositories and designed to be easily extensible to facilitate more advanced workflows if required.
STEP: Simultaneous Tracking and Estimation of Pose for Animals and Humans
Venue: arXiv cs.CV 2025
Year: 2025

We introduce STEP, a novel framework utilizing Transformer-based discriminative model prediction for simultaneous tracking and estimation of pose across diverse animal species and humans. We are inspired by the fact that the human brain exploits spatiotemporal continuity and performs concurrent localization and pose estimation despite the specialization of brain areas for form and motion processing. Traditional discriminative models typically require predefined target states for determining model weights, a challenge we address through Gaussian Map Soft Prediction (GMSP) and Offset Map Regression Adapter (OMRA) Modules. These modules remove the necessity of keypoint target states as input, streamlining the process. Our method starts with a known target state in the initial frame of a given video sequence. It then seamlessly tracks the target and estimates keypoints of anatomical importance as output for subsequent frames. Unlike prevalent top-down pose estimation methods, our approach doesn't rely on per-frame target detections due to its tracking capability. This facilitates a significant advancement in inference efficiency and potential applications. We train and validate our approach on datasets encompassing diverse species. Our experiments demonstrate superior results compared to existing methods, opening doors to various applications, including but not limited to action recognition and behavioral analysis.
Sightation Counts: Leveraging Sighted User Feedback in Building a BLV-aligned Dataset of Diagram Descriptions
Venue: arXiv cs.AI 2025
Year: 2025

Often, the needs and visual abilities differ between the annotator group and the end user group. Generating detailed diagram descriptions for blind and low-vision (BLV) users is one such challenging domain. Sighted annotators could describe visuals with ease, but existing studies have shown that direct generations by them are costly, bias-prone, and somewhat lacking by BLV standards. In this study, we ask sighted individuals to assess -- rather than produce -- diagram descriptions generated by vision-language models (VLM) that have been guided with latent supervision via a multi-pass inference. The sighted assessments prove effective and useful to professional educators who are themselves BLV and teach visually impaired learners. We release Sightation, a collection of diagram description datasets spanning 5k diagrams and 137k samples for completion, preference, retrieval, question answering, and reasoning training purposes and demonstrate their fine-tuning potential in various downstream tasks.
Causal Emergence 2.0: Quantifying emergent complexity
Venue: arXiv cs.IT 2025
Year: 2025

Complex systems can be described at myriad different scales, and their causal workings often have multiscale structure (e.g., a computer can be described at the microscale of its hardware circuitry, the mesoscale of its machine code, and the macroscale of its operating system). While scientists study and model systems across the full hierarchy of their scales, from microphysics to macroeconomics, there is debate about what the macroscales of systems can possibly add beyond mere compression. To resolve this longstanding issue, here a new theory of emergence is introduced wherein the different scales of a system are treated like slices of a higher-dimensional object. The theory can distinguish which of these scales possess unique causal contributions, and which are not causally relevant. Constructed from an axiomatic notion of causation, the theory's application is demonstrated in coarse-grains of Markov chains. It identifies all cases of macroscale causation: instances where reduction to a microscale is possible, yet lossy about causation. Furthermore, the theory posits a causal apportioning schema that calculates the causal contribution of each scale, showing what each uniquely adds. Finally, it reveals a novel measure of emergent complexity: how widely distributed a system's causal workings are across its hierarchy of scales.
Levels of Analysis for Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Modern artificial intelligence systems, such as large language models, are increasingly powerful but also increasingly hard to understand. Recognizing this problem as analogous to the historical difficulties in understanding the human mind, we argue that methods developed in cognitive science can be useful for understanding large language models. We propose a framework for applying these methods based on the levels of analysis that David Marr proposed for studying information processing systems. By revisiting established cognitive science techniques relevant to each level and illustrating their potential to yield insights into the behavior and internal organization of large language models, we aim to provide a toolkit for making sense of these new kinds of minds.
DLPO: Towards a Robust, Efficient, and Generalizable Prompt Optimization Framework from a Deep-Learning Perspective
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) have achieved remarkable success across diverse tasks, largely driven by well-designed prompts. However, crafting and selecting such prompts often requires considerable human effort, significantly limiting its scalability. To mitigate this, recent studies have explored automated prompt optimization as a promising solution. Despite these efforts, existing methods still face critical challenges in robustness, efficiency, and generalization. To systematically address these challenges, we first conduct an empirical analysis to identify the limitations of current reflection-based prompt optimization paradigm. Building on these insights, we propose 7 innovative approaches inspired by traditional deep learning paradigms for prompt optimization (DLPO), seamlessly integrating these concepts into text-based gradient optimization. Through these advancements, we progressively tackle the aforementioned challenges and validate our methods through extensive experimentation. We hope our study not only provides valuable guidance for future research but also offers a comprehensive understanding of the challenges and potential solutions in prompt optimization. Our code is available at https://github.com/sfasfaffa/DLPO.
Interpretable 3D Neural Object Volumes for Robust Conceptual Reasoning
Venue: arXiv cs.CV 2025
Year: 2025

With the rise of deep neural networks, especially in safety-critical applications, robustness and interpretability are crucial to ensure their trustworthiness. Recent advances in 3D-aware classifiers that map image features to volumetric representation of objects, rather than relying solely on 2D appearance, have greatly improved robustness on out-of-distribution (OOD) data. Such classifiers have not yet been studied from the perspective of interpretability. Meanwhile, current concept-based XAI methods often neglect OOD robustness. We aim to address both aspects with CAVE - Concept Aware Volumes for Explanations - a new direction that unifies interpretability and robustness in image classification. We design CAVE as a robust and inherently interpretable classifier that learns sparse concepts from 3D object representation. We further propose 3D Consistency (3D-C), a metric to measure spatial consistency of concepts. Unlike existing metrics that rely on human-annotated parts on images, 3D-C leverages ground-truth object meshes as a common surface to project and compare explanations across concept-based methods. CAVE achieves competitive classification performance while discovering consistent and meaningful concepts across images in various OOD settings. Code available at https://github.com/phamleyennhi/CAVE.
Unified Autoregressive Visual Generation and Understanding with Continuous Tokens
Venue: arXiv cs.CV 2025
Year: 2025

We present UniFluid, a unified autoregressive framework for joint visual generation and understanding leveraging continuous visual tokens. Our unified autoregressive architecture processes multimodal image and text inputs, generating discrete tokens for text and continuous tokens for image. We find though there is an inherent trade-off between the image generation and understanding task, a carefully tuned training recipe enables them to improve each other. By selecting an appropriate loss balance weight, the unified model achieves results comparable to or exceeding those of single-task baselines on both tasks. Furthermore, we demonstrate that employing stronger pre-trained LLMs and random-order generation during training is important to achieve high-fidelity image generation within this unified framework. Built upon the Gemma model series, UniFluid exhibits competitive performance across both image generation and understanding, demonstrating strong transferability to various downstream tasks, including image editing for generation, as well as visual captioning and question answering for understanding.
Self-Citations in Academic Excellence: Analysis of the Top 1% Highly Cited India-Affiliated Research Papers
Venue: arXiv cs.DL 2025
Year: 2025

Citations demonstrate the credibility, impact, and connection of a paper with the academic community. Self-citations support research continuity but, if excessive, may inflate metrics and raise bias concerns. The aim of the study is to examine the role of self-citations towards the research impact of India. To study this, 3.58 million papers affiliated with India from 1947 to 2024 in the Scopus database were downloaded, and 2.96 million were filtered according to document type and publication year up to 2023. Further filtering based on high citation counts identified the top 1% of highly cited papers, totaling 29,556. The results indicate that the impact of Indian research, measured by highly cited papers, has grown exponentially since 2000, reaching a peak during the 2011-2020 decade. Among the citations received by these 29,556 papers, 6% are self-citations. Papers with a high proportion of self-citations (>90%) are predominantly from recent decades and are associated with smaller team sizes. The findings also reveal that smaller teams are primarily domestic, whereas larger teams are more likely to involve international collaborations. Domestic collaborations dominate smaller team sizes in terms of both self-citations and publications, whereas international collaborations gain prominence as team sizes increase. The results indicate that while domestic collaborations produce a higher number of highly cited papers, international collaborations are more likely to generate self-citations. The top international collaborators in highly cited papers are the USA, followed by UK, and Germany.
A Causal Inference Approach for Quantifying Research Impact
Venue: arXiv cs.DL 2025
Year: 2025

Deep learning has had a great impact on various fields of computer science by enabling data-driven representation learning in a decade. Because science and technology policy decisions for a nation can be made on the impact of each technology, quantifying research impact is an important task. The number of citations and impact factor can be used to measure the impact for individual research. What would have happened without the research, however, is fundamentally a counterfactual phenomenon. Thus, we propose an approach based on causal inference to quantify the research impact of a specific technical topic. We leverage difference-in-difference to quantify the research impact by applying to bibliometric data. First, we identify papers of a specific technical topic using keywords or category tags from Microsoft Academic Graph, which is one of the largest academic publication dataset. Next, we build a paper citation network between each technical field. Then, we aggregate the cross-field citation count for each research field. Finally, the impact of a specific technical topic for each research field is estimated by applying difference-in-difference. Evaluation results show that deep learning significantly affects computer vision and natural language processing. Besides, deep learning significantly affects cross-field citation especially for speech recognition to computer vision and natural language processing to computer vision. Moreover, our method revealed that the impact of deep learning was 3.1 times of the impact of interpretability for ML models.
NeurIPS 2023 LLM Efficiency Fine-tuning Competition
Venue: arXiv cs.CL 2025
Year: 2025

Our analysis of the NeurIPS 2023 large language model (LLM) fine-tuning competition revealed the following trend: top-performing models exhibit significant overfitting on benchmark datasets, mirroring the broader issue of benchmark overfitting on popular leaderboards and that data curation is essential in order to get a high performing LLM. The competition, which consisted of two stages - an open evaluation stage with publicly available tasks and a closed evaluation stage with unseen tasks - allowed us to assess the generalizability of fine-tuned LLMs. Our results highlight the limitations of current benchmark-based evaluation schemes for generative models and demonstrate the need for more robust evaluation methods. Notably, the winning submissions utilized standard open-source libraries and focused primarily on data curation. To facilitate further research and promote reproducibility, we release all competition entries, Docker files, and evaluation infrastructure, providing a valuable resource for the community to explore fine-tuning, overfitting, and reproducibility in LLMs.
Towards a Digital Twin Modeling Method for Container Terminal Port
Venue: arXiv cs.SE 2025
Year: 2025

This paper introduces a novel strategy aimed at enhancing productivity and minimizing non-productive movements within container terminals, specifically focusing on container yards. It advocates for the implementation of a digital twin-based methodology to streamline the operations of stacking cranes (SCs) responsible for container handling. The proposed approach entails the creation of a virtual container yard that mirrors the physical yard within a digital twin system, facilitating real-time observation and validation. In addition, this article demonstrates the effectiveness of using a digital twin to reduce unproductive movements and improve productivity through simulation. It defines various operational strategies and takes into account different yard contexts, providing a comprehensive understanding of optimisation possibilities. By exploiting the capabilities of the digital twin, managers and operators are provided with crucial information on operational dynamics, enabling them to identify areas for improvement. This visualisation helps decision-makers to make informed choices about their stacking strategies, thereby improving the efficiency of overall container terminal operations. Overall, this paper present a digital twin solution in container terminal operations, offering a powerful tool for optimising productivity and minimising inefficiencies.
Examples as the Prompt: A Scalable Approach for Efficient LLM Adaptation in E-Commerce
Venue: arXiv cs.CL 2025
Year: 2025

Prompting LLMs offers an efficient way to guide output generation without explicit model training. In the e-commerce domain, prompting-based applications are widely used for tasks such as query understanding, recommender systems, and customer support. However, adapting LLMs to different tasks often requires extensive prompt engineering by domain experts, along with frequent updates to align with evolving business needs. Additionally, crafting fully unbiased natural language prompts remains a challenge for humans. To address these challenges, we propose a novel framework, Examples as the Prompt (EaP) which leverages labeled data to enhance prompts. Specifically, EaP automatically selects the most representative examples to maximize the few-shot capability of LLMs. It is efficient due to its unsupervised example selection and adaptive to potential data distribution shifts. We validate EaP on four real-world production use cases, demonstrating that it achieves comparable or even superior performance comparing to hand-crafted prompts designed by domain experts. Additionally, we introduce EaP_lite, which entirely replaces the natural language components of prompts with labeled examples. EaP_lite improves LLM inference speed by up to 70% without compromising performance. Latest online A/B test shows that using EaP and EaP_lite for data labeling can bring significant composite revenue gain by 0.06%.
Unlocking Learning Potentials: The Transformative Effect of Generative AI in Education Across Grade Levels
Venue: arXiv cs.CY 2025
Year: 2025

The advent of generative artificial intelligence (GAI) has brought about a notable surge in the field of education. The use of GAI to support learning is becoming increasingly prevalent among students. However, the manner and extent of its utilisation vary considerably from one individual to another. And researches about student's utilisation and perceptions of GAI remains relatively scarce. To gain insight into the issue, this paper proposed a hybrid-survey method to examine the impact of GAI on students across four different grades in six key areas (LIPSAL): learning interest, independent learning, problem solving, self-confidence, appropriate use, and learning enjoyment. Firstly, through questionnaire, we found that among LIPSAL, GAI has the greatest impact on the concept of appropriate use, the lowest level of learning interest and self-confidence. Secondly, a comparison of four grades revealed that the high and low factors of LIPSAL exhibited grade-related variation, and college students exhibited a higher level than high school students across LIPSAL. Thirdly, through interview, the students demonstrated a comprehensive understanding of the application of GAI. We found that students have a positive attitude towards GAI and are very willing to use it, which is why GAI has grown so rapidly in popularity. They also told us prospects and challenges in using GAI. In the future, as GAI matures technologically, it will have an greater impact on students. These findings may help better understand usage by different students and inform future research in digital education.
Decision by Supervised Learning with Deep Ensembles: A Practical Framework for Robust Portfolio Optimization
Venue: arXiv cs.LG 2025
Year: 2025

We propose Decision by Supervised Learning (DSL), a practical framework for robust portfolio optimization. DSL reframes portfolio construction as a supervised learning problem: models are trained to predict optimal portfolio weights, using cross-entropy loss and portfolios constructed by maximizing the Sharpe or Sortino ratio. To further enhance stability and reliability, DSL employs Deep Ensemble methods, substantially reducing variance in portfolio allocations. Through comprehensive backtesting across diverse market universes and neural architectures, shows superior performance compared to both traditional strategies and leading machine learning-based methods, including Prediction-Focused Learning and End-to-End Learning. We show that increasing the ensemble size leads to higher median returns and more stable risk-adjusted performance. The code is available at https://github.com/DSLwDE/DSLwDE.
LLM Test Generation via Iterative Hybrid Program Analysis
Venue: arXiv cs.SE 2025
Year: 2025

Automating unit test generation remains a significant challenge, particularly for complex methods in real-world projects. While Large Language Models (LLMs) have made strides in code generation, they struggle to achieve high branch coverage due to their limited ability to reason about intricate control flow structures. To address this limitation, we introduce Panta, a technique that emulates the iterative process human developers follow when analyzing code and constructing test cases. Panta integrates static control flow analysis and dynamic code coverage analysis to systematically guide LLMs in identifying uncovered execution paths and generating better test cases. By incorporating an iterative feedback-driven mechanism, our technique continuously refines test generation based on static and dynamic path coverage insights, ensuring more comprehensive and effective testing. Our empirical evaluation, conducted on classes with high cyclomatic complexity from open-source projects, demonstrates that Panta achieves 26% higher line coverage and 23% higher branch coverage compared to the state-of-the-art.
Stable Task Allocation in Multi-Agent Systems with Lexicographic Preferences
Venue: arXiv cs.MA 2025
Year: 2025

Motivated by the increasing interest in the explicit representation and handling of various "preference" structures arising in modern digital economy, this work introduces a new class of "one-to-many stable-matching" problems where a set of atomic tasks must be stably allocated to a set of agents. An important characteristic of these stable-matching problems is the very arbitrary specification of the task subsets constituting "feasible" allocations for each agent. It is shown that as long as the agents rank their feasible task allocations lexicographically with respect to their stated preferences for each atomic task, matching stability reduces to the absence of blocking agent-task pairs. This result, together with a pertinent graphical representation of feasible allocations, enable (i) the representation of the space of stable matchings as a set of linear constraints with binary variables, and (ii) the specification and handling of certain notions of optimality within this space of stable matchings. The last part of the paper also addresses the notion of "substitutability" in the considered problem context.