OpenRaiser/Intern-Atlas huggingface dataset:
Fully Dynamic (Δ+1) Coloring Against Adaptive Adversaries
Venue: arXiv cs.DS 2025
Year: 2025

Over the years, there has been extensive work on fully dynamic algorithms for classic graph problems that admit greedy solutions. Examples include $(Δ+1)$ vertex coloring, maximal independent set, and maximal matching. For all three problems, there are randomized algorithms that maintain a valid solution after each edge insertion or deletion to the $n$-vertex graph by spending $\polylog n$ time, provided that the adversary is oblivious. However, none of these algorithms work against adaptive adversaries whose updates may depend on the output of the algorithm. In fact, even breaking the trivial bound of $O(n)$ against adaptive adversaries remains open for all three problems. For instance, in the case of $(Δ+1)$ vertex coloring, the main challenge is that an adaptive adversary can keep inserting edges between vertices of the same color, necessitating a recoloring of one of the endpoints. The trivial algorithm would simply scan all neighbors of one endpoint to find a new available color (which always exists) in $O(n)$ time. In this paper, we break this linear barrier for the $(Δ+1)$ vertex coloring problem. Our algorithm is randomized, and maintains a valid $(Δ+1)$ vertex coloring after each edge update by spending $\widetilde{O}(n^{8/9})$ time with high probability.
Political Hegemony, Imitation Isomorphism, and Project Familiarity: Instrumental Variables to Understand Funding Impact on Scholar Performance
Venue: arXiv cs.DL 2025
Year: 2025

This paper contributes a new idea for exploring research funding effects on scholar performance. By collecting details of 9,501 research grants received by principal investigators from universities in the U.S. social sciences from 2000 to 2019 and data on their publications and citations in the Microsoft Academic Graph and Web of Science bibliographic collections, we build a novel dataset of grants and article counts, citations, and journal CiteScore. Based on this dataset, we first introduce three instrumental variables (IVs) suitable for isolating endogeneity issues in the study of competing grant effects, namely scholars political hegemony in academia, imitation isomorphic behavior among scholars, and project familiarity. Then, this study explains the research funding effects by combining the three IVs with a two-stage least square (2SLS) model. Also, we provide validity and robustness tests of these three IVs and research funding effects. We find that our IVs serve the function of exogenizing and isolating endogeneity in capturing the research funding effect. Empirical findings show that receiving research funding increases a scholars research output and impact. While research funding doesn't significantly increase high CiteScore publications, it reduces submissions to low-prestige journals, reshaping journal selection strategies and raising the floor of academic performance.
Towards Unifying Interpretability and Control: Evaluation via Intervention
Venue: arXiv cs.LG 2025
Year: 2025

With the growing complexity and capability of large language models, a need to understand model reasoning has emerged, often motivated by an underlying goal of controlling and aligning models. While numerous interpretability and steering methods have been proposed as solutions, they are typically designed either for understanding or for control, seldom addressing both. Additionally, the lack of standardized applications, motivations, and evaluation metrics makes it difficult to assess methods' practical utility and efficacy. To address the aforementioned issues, we argue that intervention is a fundamental goal of interpretability and introduce success criteria to evaluate how well methods can control model behavior through interventions. To evaluate existing methods for this ability, we unify and extend four popular interpretability methods-sparse autoencoders, logit lens, tuned lens, and probing-into an abstract encoder-decoder framework, enabling interventions on interpretable features that can be mapped back to latent representations to control model outputs. We introduce two new evaluation metrics: intervention success rate and coherence-intervention tradeoff, designed to measure the accuracy of explanations and their utility in controlling model behavior. Our findings reveal that (1) while current methods allow for intervention, their effectiveness is inconsistent across features and models, (2) lens-based methods outperform SAEs and probes in achieving simple, concrete interventions, and (3) mechanistic interventions often compromise model coherence, underperforming simpler alternatives, such as prompting, and highlighting a critical shortcoming of current interpretability approaches in applications requiring control.
Tomato, Tomahto, Tomate: Do Multilingual Language Models Understand Based on Subword-Level Semantic Concepts?
Venue: arXiv cs.CL 2025
Year: 2025

Human understanding of text depends on general semantic concepts of words rather than their superficial forms. To what extent does our human intuition transfer to language models? In this work, we study the degree to which current multilingual language models (mLMs) understand based on subword-level semantic concepts. To this end, we form "semantic tokens" by merging the semantically similar subwords and their embeddings, and evaluate the updated mLMs on five heterogeneous multilingual downstream tasks. Results show that the general shared semantics could get the models a long way in making the predictions on mLMs with different tokenizers and model sizes. Inspections of the grouped subwords show that they exhibit a wide range of semantic similarities, including synonyms and translations across many languages and scripts. Lastly, we find that the zero-shot results with semantic tokens are on par with or even better than the original models on certain classification tasks, suggesting that the shared subword-level semantics may serve as the anchors for cross-lingual transfer.
Cross- and Intra-image Prototypical Learning for Multi-label Disease Diagnosis and Interpretation
Venue: arXiv cs.CV 2025
Year: 2025

Recent advances in prototypical learning have shown remarkable potential to provide useful decision interpretations associating activation maps and predictions with class-specific training prototypes. Such prototypical learning has been well-studied for various single-label diseases, but for quite relevant and more challenging multi-label diagnosis, where multiple diseases are often concurrent within an image, existing prototypical learning models struggle to obtain meaningful activation maps and effective class prototypes due to the entanglement of the multiple diseases. In this paper, we present a novel Cross- and Intra-image Prototypical Learning (CIPL) framework, for accurate multi-label disease diagnosis and interpretation from medical images. CIPL takes advantage of common cross-image semantics to disentangle the multiple diseases when learning the prototypes, allowing a comprehensive understanding of complicated pathological lesions. Furthermore, we propose a new two-level alignment-based regularisation strategy that effectively leverages consistent intra-image information to enhance interpretation robustness and predictive performance. Extensive experiments show that our CIPL attains the state-of-the-art (SOTA) classification accuracy in two public multi-label benchmarks of disease diagnosis: thoracic radiography and fundus images. Quantitative interpretability results show that CIPL also has superiority in weakly-supervised thoracic disease localisation over other leading saliency- and prototype-based explanation methods.
Complexity theory of orbit closure intersection for tensors: reductions, completeness, and graph isomorphism hardness
Venue: arXiv cs.CC 2025
Year: 2025

Many natural computational problems in computer science, mathematics, physics, and other sciences amount to deciding if two objects are equivalent. Often this equivalence is defined in terms of group actions. A natural question is to ask when two objects can be distinguished by polynomial functions that are invariant under the group action. For finite groups, this is the usual notion of equivalence, but for continuous groups like the general linear groups it gives rise to a new notion, called orbit closure intersection. It captures, among others, the graph isomorphism problem, noncommutative PIT, null cone problems in invariant theory, equivalence problems for tensor networks, and the classification of multiparty quantum states. Despite recent algorithmic progress in celebrated special cases, the computational complexity of general orbit closure intersection problems is currently quite unclear. In particular, tensors seem to give rise to the most difficult problems. In this work we start a systematic study of orbit closure intersection from the complexity-theoretic viewpoint. To this end, we define a complexity class TOCI that captures the power of orbit closure intersection problems for general tensor actions, give an appropriate notion of algebraic reductions that imply polynomial-time reductions in the usual sense, but are amenable to invariant-theoretic techniques, identify natural tensor problems that are complete for TOCI, including the equivalence of 2D tensor networks with constant physical dimension, and show that the graph isomorphism problem can be reduced to these complete problems, hence GI$\subseteq$TOCI. As such, our work establishes the first lower bound on the computational complexity of orbit closure intersection problems, and it explains the difficulty of finding unconditional polynomial-time algorithms beyond special cases, as has been observed in the literature.
Lightning IR: Straightforward Fine-tuning and Inference of Transformer-based Language Models for Information Retrieval
Venue: arXiv cs.IR 2025
Year: 2025

A wide range of transformer-based language models have been proposed for information retrieval tasks. However, including transformer-based models in retrieval pipelines is often complex and requires substantial engineering effort. In this paper, we introduce Lightning IR, an easy-to-use PyTorch Lightning-based framework for applying transformer-based language models in retrieval scenarios. Lightning IR provides a modular and extensible architecture that supports all stages of a retrieval pipeline: from fine-tuning and indexing to searching and re-ranking. Designed to be scalable and reproducible, Lightning IR is available as open-source: https://github.com/webis-de/lightning-ir.
The Pragmatic Frames of Spurious Correlations in Machine Learning: Interpreting How and Why They Matter
Venue: arXiv cs.LG 2025
Year: 2025

Learning correlations from data forms the foundation of today's machine learning (ML) and artificial intelligence (AI) research. While contemporary methods enable the automatic discovery of complex patterns, they are prone to failure when unintended correlations are captured. This vulnerability has spurred a growing interest in interrogating spuriousness, which is often seen as a threat to model performance, fairness, and robustness. In this article, we trace departures from the conventional statistical definition of spuriousness -- which denotes a non-causal relationship arising from coincidence or confounding -- to examine how its meaning is negotiated in ML research. Rather than relying solely on formal definitions, researchers assess spuriousness through what we call pragmatic frames: judgments based on what a correlation does in practice -- how it affects model behavior, supports or impedes task performance, or aligns with broader normative goals. Drawing on a broad survey of ML literature, we identify four such frames: relevance ("Models should use correlations that are relevant to the task"), generalizability ("Models should use correlations that generalize to unseen data"), human-likeness ("Models should use correlations that a human would use to perform the same task"), and harmfulness ("Models should use correlations that are not socially or ethically harmful"). These representations reveal that correlation desirability is not a fixed statistical property but a situated judgment informed by technical, epistemic, and ethical considerations. By examining how a foundational ML conundrum is problematized in research literature, we contribute to broader conversations on the contingent practices through which technical concepts like spuriousness are defined and operationalized.
Shared Heritage, Distinct Writing: Rethinking Resource Selection for East Asian Historical Documents
Venue: arXiv cs.CL 2025
Year: 2025

Historical documents in the Sinosphere are known to share common formats and practices, particularly in veritable records compiled by court historians. This shared linguistic heritage has led researchers to use Classical Chinese resources for cross-lingual transfer when processing historical documents from Korea and Japan, which remain relatively low-resource. In this paper, we question the assumption of cross-lingual transferability from Classical Chinese to Hanja and Kanbun, the ancient written languages of Korea and Japan, respectively. Our experiments across machine translation, named entity recognition, and punctuation restoration tasks show minimal impact of Classical Chinese datasets on language model performance for ancient Korean documents written in Hanja, with performance differences within $\pm{}0.0068$ F1-score for sequence labeling tasks and up to $+0.84$ BLEU score for translation. These limitations persist consistently across various model sizes, architectures, and domain-specific datasets. Our analysis reveals that the benefits of Classical Chinese resources diminish rapidly as local language data increases for Hanja, while showing substantial improvements only in extremely low-resource scenarios for both Korean and Japanese historical documents. These findings emphasize the need for careful empirical validation rather than assuming benefits from indiscriminate cross-lingual transfer.
OneProt: Towards Multi-Modal Protein Foundation Models
Venue: arXiv cs.LG 2025
Year: 2025

Recent advances in Artificial Intelligence have enabled multi-modal systems to model and translate diverse information spaces. Extending beyond text and vision, we introduce OneProt, a multi-modal AI for proteins that integrates structural, sequence, text, and binding site data. Using the ImageBind framework, OneProt aligns the latent spaces of protein modality encoders in a lightweight fine-tuning scheme that focuses on pairwise alignment with sequence data rather than requiring full matches. This novel approach comprises a mix of Graph Neural Networks and transformer architectures. It demonstrates strong performance in retrieval tasks and showcases the efficacy of multi-modal systems in Protein Machine Learning through a broad spectrum of downstream baselines, including enzyme function prediction and binding site analysis. Furthermore, OneProt enables the transfer of representational information from specialized encoders to the sequence encoder, enhancing capabilities for distinguishing evolutionarily related and unrelated sequences and exhibiting representational properties where evolutionarily related proteins align in similar directions within the latent space. In addition, we extensively investigate modality ablations to identify the encoders that contribute most to predictive performance, highlighting the significance of the binding site encoder, which has not been used in similar models previously. This work expands the horizons of multi-modal protein models, paving the way for transformative applications in drug discovery, biocatalytic reaction planning, and protein engineering.
Enabling LLM Knowledge Analysis via Extensive Materialization
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) have majorly advanced NLP and AI, and next to their ability to perform a wide range of procedural tasks, a major success factor is their internalized factual knowledge. Since Petroni et al. (2019), analyzing this knowledge has gained attention. However, most approaches investigate one question at a time via modest-sized pre-defined samples, introducing an ``availability bias'' (Tversky&Kahnemann, 1973) that prevents the analysis of knowledge (or beliefs) of LLMs beyond the experimenter's predisposition. To address this challenge, we propose a novel methodology to comprehensively materialize an LLM's factual knowledge through recursive querying and result consolidation. Our approach is a milestone for LLM research, for the first time providing constructive insights into the scope and structure of LLM knowledge (or beliefs). As a prototype, we build GPTKB, a knowledge base (KB) comprising 101 million relational triples for over 2.9 million entities from GPT-4o-mini. We use GPTKB to exemplarily analyze GPT-4o-mini's factual knowledge in terms of scale, accuracy, bias, cutoff and consistency, at the same time. GPTKB is accessible at https://gptkb.org
Scattered Forest Search: Smarter Code Space Exploration with LLMs
Venue: arXiv cs.SE 2025
Year: 2025

We frame code generation as a black-box optimization problem within the code space and demonstrate how optimization-inspired techniques can enhance inference scaling. Based on this perspective, we propose SCATTERED FOREST SEARCH (SFS), a novel approach that improves solution diversity and better exploits feedback during evolutionary search. Our theoretical analysis illustrates how these methods help avoid local optima during optimization, leading to more efficient exploration. Extensive experiments on HumanEval, MBPP, APPS, CodeContests, and Leetcode reveal significant performance gains. For instance, our method achieves a pass@1 rate of 67.1% on HumanEval+ and 87.2% on HumanEval with GPT-3.5, marking improvements of 8.6% and 4.3% over the state-of-the-art, while also halving the iterations needed to find the correct solution. Furthermore, our approach scales more efficiently than existing search techniques, including tree search, line search, and repeated sampling.
YouTube Comments Decoded: Leveraging LLMs for Low Resource Language Classification
Venue: arXiv cs.CL 2025
Year: 2025

Sarcasm detection is a significant challenge in sentiment analysis, particularly due to its nature of conveying opinions where the intended meaning deviates from the literal expression. This challenge is heightened in social media contexts where code-mixing, especially in Dravidian languages, is prevalent. Code-mixing involves the blending of multiple languages within a single utterance, often with non-native scripts, complicating the task for systems trained on monolingual data. This shared task introduces a novel gold standard corpus designed for sarcasm and sentiment detection within code-mixed texts, specifically in Tamil-English and Malayalam-English languages. The primary objective of this task is to identify sarcasm and sentiment polarity within a code-mixed dataset of Tamil-English and Malayalam-English comments and posts collected from social media platforms. Each comment or post is annotated at the message level for sentiment polarity, with particular attention to the challenges posed by class imbalance, reflecting real-world scenarios.In this work, we experiment with state-of-the-art large language models like GPT-3.5 Turbo via prompting to classify comments into sarcastic or non-sarcastic categories. We obtained a macro-F1 score of 0.61 for Tamil language. We obtained a macro-F1 score of 0.50 for Malayalam language.
Improving Radiology Report Conciseness and Structure via Local Large Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Radiology reports are often lengthy and unstructured, posing challenges for referring physicians to quickly identify critical imaging findings while increasing the risk of missed information. This retrospective study aimed to enhance radiology reports by making them concise and well-structured, with findings organized by relevant organs. To achieve this, we utilized private large language models (LLMs) deployed locally within our institution's firewall, ensuring data security and minimizing computational costs. Using a dataset of 814 radiology reports from seven board-certified body radiologists at Moffitt Cancer Center, we tested five prompting strategies within the LangChain framework. After evaluating several models, the Mixtral LLM demonstrated superior adherence to formatting requirements compared to alternatives like Llama. The optimal strategy involved condensing reports first and then applying structured formatting based on specific instructions, reducing verbosity while improving clarity. Across all radiologists and reports, the Mixtral LLM reduced redundant word counts by more than 53%. These findings highlight the potential of locally deployed, open-source LLMs to streamline radiology reporting. By generating concise, well-structured reports, these models enhance information retrieval and better meet the needs of referring physicians, ultimately improving clinical workflows.
Watermarking Language Models through Language Models
Venue: arXiv cs.LG 2025
Year: 2025

Watermarking the outputs of large language models (LLMs) is critical for provenance tracing, content regulation, and model accountability. Existing approaches often rely on access to model internals or are constrained by static rules and token-level perturbations. Moreover, the idea of steering generative behavior via prompt-based instruction control remains largely underexplored. We introduce a prompt-guided watermarking framework that operates entirely at the input level and requires no access to model parameters or decoding logits. The framework comprises three cooperating components: a Prompting LM that synthesizes watermarking instructions from user prompts, a Marking LM that generates watermarked outputs conditioned on these instructions, and a Detecting LM trained to classify whether a response carries an embedded watermark. This modular design enables dynamic watermarking that adapts to individual prompts while remaining compatible with diverse LLM architectures, including both proprietary and open-weight models. We evaluate the framework over 25 combinations of Prompting and Marking LMs, such as GPT-4o, Mistral, LLaMA3, and DeepSeek. Experimental results show that watermark signals generalize across architectures and remain robust under fine-tuning, model distillation, and prompt-based adversarial attacks, demonstrating the effectiveness and robustness of the proposed approach.