OpenRaiser/Intern-Atlas huggingface dataset:
ChemMiner: A Large Language Model Agent System for Chemical Literature Data Mining
Venue: arXiv cs.IR 2025
Year: 2025

The development of AI-assisted chemical synthesis tools requires comprehensive datasets covering diverse reaction types, yet current high-throughput experimental (HTE) approaches are expensive and limited in scope. Chemical literature represents a vast, underexplored data source containing thousands of reactions published annually. However, extracting reaction information from literature faces significant challenges including varied writing styles, complex coreference relationships, and multimodal information presentation. This paper proposes ChemMiner, a novel end-to-end framework leveraging multiple agents powered by large language models (LLMs) to extract high-fidelity chemical data from literature. ChemMiner incorporates three specialized agents: a text analysis agent for coreference mapping, a multimodal agent for non-textual information extraction, and a synthesis analysis agent for data generation. Furthermore, we developed a comprehensive benchmark with expert-annotated chemical literature to evaluate both extraction efficiency and precision. Experimental results demonstrate reaction identification rates comparable to human chemists while significantly reducing processing time, with high accuracy, recall, and F1 scores. Our open-sourced benchmark facilitates future research in chemical literature data mining.
How Important is Domain Specificity in Language Models and Instruction Finetuning for Biomedical Relation Extraction?
Venue: arXiv cs.CL 2025
Year: 2025

Cutting edge techniques developed in the general NLP domain are often subsequently applied to the high-value, data-rich biomedical domain. The past few years have seen generative language models (LMs), instruction finetuning, and few-shot learning become foci of NLP research. As such, generative LMs pretrained on biomedical corpora have proliferated and biomedical instruction finetuning has been attempted as well, all with the hope that domain specificity improves performance on downstream tasks. Given the nontrivial effort in training such models, we investigate what, if any, benefits they have in the key biomedical NLP task of relation extraction. Specifically, we address two questions: (1) Do LMs trained on biomedical corpora outperform those trained on general domain corpora? (2) Do models instruction finetuned on biomedical datasets outperform those finetuned on assorted datasets or those simply pretrained? We tackle these questions using existing LMs, testing across four datasets. In a surprising result, general-domain models typically outperformed biomedical-domain models. However, biomedical instruction finetuning improved performance to a similar degree as general instruction finetuning, despite having orders of magnitude fewer instructions. Our findings suggest it may be more fruitful to focus research effort on larger-scale biomedical instruction finetuning of general LMs over building domain-specific biomedical LMs
Round Trip Translation Defence against Large Language Model Jailbreaking Attacks
Venue: arXiv cs.CL 2025
Year: 2025

Large language models (LLMs) are susceptible to social-engineered attacks that are human-interpretable but require a high level of comprehension for LLMs to counteract. Existing defensive measures can only mitigate less than half of these attacks at most. To address this issue, we propose the Round Trip Translation (RTT) method, the first algorithm specifically designed to defend against social-engineered attacks on LLMs. RTT paraphrases the adversarial prompt and generalizes the idea conveyed, making it easier for LLMs to detect induced harmful behavior. This method is versatile, lightweight, and transferrable to different LLMs. Our defense successfully mitigated over 70% of Prompt Automatic Iterative Refinement (PAIR) attacks, which is currently the most effective defense to the best of our knowledge. We are also the first to attempt mitigating the MathsAttack and reduced its attack success rate by almost 40%. Our code is publicly available at https://github.com/Cancanxxx/Round_Trip_Translation_Defence This version of the article has been accepted for publication, after peer review (when applicable) but is not the Version of Record and does not reflect post-acceptance improvements, or any corrections. The Version of Record is available online at: https://doi.org/10.48550/arXiv.2402.13517 Use of this Accepted Version is subject to the publisher's Accepted Manuscript terms of use https://www.springernature.com/gp/open-research/policies/accepted-manuscript-terms
Exploiting Adaptive Contextual Masking for Aspect-Based Sentiment Analysis
Venue: arXiv cs.CL 2025
Year: 2025

Aspect-Based Sentiment Analysis (ABSA) is a fine-grained linguistics problem that entails the extraction of multifaceted aspects, opinions, and sentiments from the given text. Both standalone and compound ABSA tasks have been extensively used in the literature to examine the nuanced information present in online reviews and social media posts. Current ABSA methods often rely on static hyperparameters for attention-masking mechanisms, which can struggle with context adaptation and may overlook the unique relevance of words in varied situations. This leads to challenges in accurately analyzing complex sentences containing multiple aspects with differing sentiments. In this work, we present adaptive masking methods that remove irrelevant tokens based on context to assist in Aspect Term Extraction and Aspect Sentiment Classification subtasks of ABSA. We show with our experiments that the proposed methods outperform the baseline methods in terms of accuracy and F1 scores on four benchmark online review datasets. Further, we show that the proposed methods can be extended with multiple adaptations and demonstrate a qualitative analysis of the proposed approach using sample text for aspect term extraction.
Accuracy-Preserving Calibration via Statistical Modeling on Probability Simplex
Venue: arXiv cs.LG 2025
Year: 2025

Classification models based on deep neural networks (DNNs) must be calibrated to measure the reliability of predictions. Some recent calibration methods have employed a probabilistic model on the probability simplex. However, these calibration methods cannot preserve the accuracy of pre-trained models, even those with a high classification accuracy. We propose an accuracy-preserving calibration method using the Concrete distribution as the probabilistic model on the probability simplex. We theoretically prove that a DNN model trained on cross-entropy loss has optimality as the parameter of the Concrete distribution. We also propose an efficient method that synthetically generates samples for training probabilistic models on the probability simplex. We demonstrate that the proposed method can outperform previous methods in accuracy-preserving calibration tasks using benchmarks. The code is available at https://github.com/ToyotaCRDL/SimplexTS.
Large Language Models are Advanced Anonymizers
Venue: arXiv cs.AI 2025
Year: 2025

Recent privacy research on large language models (LLMs) has shown that they achieve near-human-level performance at inferring personal data from online texts. With ever-increasing model capabilities, existing text anonymization methods are currently lacking behind regulatory requirements and adversarial threats. In this work, we take two steps to bridge this gap: First, we present a new setting for evaluating anonymization in the face of adversarial LLM inferences, allowing for a natural measurement of anonymization performance while remedying some of the shortcomings of previous metrics. Then, within this setting, we develop a novel LLM-based adversarial anonymization framework leveraging the strong inferential capabilities of LLMs to inform our anonymization procedure. We conduct a comprehensive experimental evaluation of adversarial anonymization across 13 LLMs on real-world and synthetic online texts, comparing it against multiple baselines and industry-grade anonymizers. Our evaluation shows that adversarial anonymization outperforms current commercial anonymizers both in terms of the resulting utility and privacy. We support our findings with a human study (n=50) highlighting a strong and consistent human preference for LLM-anonymized texts.
Partially Frozen Random Networks Contain Compact Strong Lottery Tickets
Venue: arXiv cs.LG 2025
Year: 2025

Randomly initialized dense networks contain subnetworks that achieve high accuracy without weight learning--strong lottery tickets (SLTs). Recently, Gadhikar et al. (2023) demonstrated that SLTs could also be found within a randomly pruned source network. This phenomenon can be exploited to further compress the small memory size required by SLTs. However, their method is limited to SLTs that are even sparser than the source, leading to worse accuracy due to unintentionally high sparsity. This paper proposes a method for reducing the SLT memory size without restricting the sparsity of the SLTs that can be found. A random subset of the initial weights is frozen by either permanently pruning them or locking them as a fixed part of the SLT, resulting in a smaller model size. Experimental results show that Edge-Popup (Ramanujan et al., 2020; Sreenivasan et al., 2022) finds SLTs with better accuracy-to-model size trade-off within frozen networks than within dense or randomly pruned source networks. In particular, freezing $70\%$ of a ResNet on ImageNet provides $3.3 \times$ compression compared to the SLT found within a dense counterpart, raises accuracy by up to $14.12$ points compared to the SLT found within a randomly pruned counterpart, and offers a better accuracy-model size trade-off than both.
Rethinking Scientific Summarization Evaluation: Grounding Explainable Metrics on Facet-aware Benchmark
Venue: arXiv cs.CL 2025
Year: 2025

The summarization capabilities of pretrained and large language models (LLMs) have been widely validated in general areas, but their use in scientific corpus, which involves complex sentences and specialized knowledge, has been less assessed. This paper presents conceptual and experimental analyses of scientific summarization, highlighting the inadequacies of traditional evaluation methods, such as $n$-gram, embedding comparison, and QA, particularly in providing explanations, grasping scientific concepts, or identifying key content. Subsequently, we introduce the Facet-aware Metric (FM), employing LLMs for advanced semantic matching to evaluate summaries based on different aspects. This facet-aware approach offers a thorough evaluation of abstracts by decomposing the evaluation task into simpler subtasks.Recognizing the absence of an evaluation benchmark in this domain, we curate a Facet-based scientific summarization Dataset (FD) with facet-level annotations. Our findings confirm that FM offers a more logical approach to evaluating scientific summaries. In addition, fine-tuned smaller models can compete with LLMs in scientific contexts, while LLMs have limitations in learning from in-context information in scientific domains. This suggests an area for future enhancement of LLMs.
Global Safe Sequential Learning via Efficient Knowledge Transfer
Venue: arXiv cs.LG 2025
Year: 2025

Sequential learning methods, such as active learning and Bayesian optimization, aim to select the most informative data for task learning. In many applications, however, data selection is constrained by unknown safety conditions, motivating the development of safe learning approaches. A promising line of safe learning methods uses Gaussian processes to model safety conditions, restricting data selection to areas with high safety confidence. However, these methods are limited to local exploration around an initial seed dataset, as safety confidence centers around observed data points. As a consequence, task exploration is slowed down and safe regions disconnected from the initial seed dataset remain unexplored. In this paper, we propose safe transfer sequential learning to accelerate task learning and to expand the explorable safe region. By leveraging abundant offline data from a related source task, our approach guides exploration in the target task more effectively. We also provide a theoretical analysis to explain why single-task method cannot cope with disconnected regions. Finally, we introduce a computationally efficient approximation of our method that reduces runtime through pre-computations. Our experiments demonstrate that this approach, compared to state-of-the-art methods, learns tasks with lower data consumption and enhances global exploration across multiple disjoint safe regions, while maintaining comparable computational efficiency.
A new sociology of humans and machines
Venue: arXiv cs.SI 2025
Year: 2025

From fake social media accounts and generative artificial intelligence chatbots to trading algorithms and self-driving vehicles, robots, bots and algorithms are proliferating and permeating our communication channels, social interactions, economic transactions and transportation arteries. Networks of multiple interdependent and interacting humans and intelligent machines constitute complex social systems for which the collective outcomes cannot be deduced from either human or machine behaviour alone. Under this paradigm, we review recent research and identify general dynamics and patterns in situations of competition, coordination, cooperation, contagion and collective decision-making, with context-rich examples from high-frequency trading markets, a social media platform, an open collaboration community and a discussion forum. To ensure more robust and resilient human-machine communities, we require a new sociology of humans and machines. Researchers should study these communities using complex system methods; engineers should explicitly design artificial intelligence for human-machine and machine-machine interactions; and regulators should govern the ecological diversity and social co-development of humans and machines.
Federated Learning in Genetics: Extended Analysis of Accuracy, Performance and Privacy Trade-offs
Venue: arXiv cs.LG 2025
Year: 2025

Machine learning on large-scale genomic or transcriptomic data is important for many novel health applications. For example, precision medicine tailors medical treatments to patients on the basis of individual biomarkers, cellular and molecular states, etc. However, the data required is sensitive, voluminous, heterogeneous, and typically distributed across locations where dedicated machine learning hardware is not available. Due to privacy and regulatory reasons, it is also problematic to aggregate all data at a trusted third party. Federated learning is a promising solution to this dilemma, because it enables decentralized, collaborative machine learning without exchanging raw data. In this paper, we perform comparative experiments with the federated learning frameworks TensorFlow Federated and Flower. Our test case is the training of disease prognosis and cell type classification models. We train the models with distributed transcriptomic data, considering both data heterogeneity and architectural heterogeneity. We measure model quality, robustness against privacy-enhancing noise and computational performance. We evaluate the resource overhead of a federated system from both client and global perspectives and assess benefits and limitations. Each of the federated learning frameworks has different strengths. However, our experiments confirm that both frameworks can readily build models on transcriptomic data, without transferring personal raw data to a third party with abundant computational resources. This paper is the extended version of https://link.springer.com/chapter/10.1007/978-3-031-63772-8_26.
COBIAS: Assessing the Contextual Reliability of Bias Benchmarks for Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Large Language Models (LLMs) often inherit biases from the web data they are trained on, which contains stereotypes and prejudices. Current methods for evaluating and mitigating these biases rely on bias-benchmark datasets. These benchmarks measure bias by observing an LLM's behavior on biased statements. However, these statements lack contextual considerations of the situations they try to present. To address this, we introduce a contextual reliability framework, which evaluates model robustness to biased statements by considering the various contexts in which they may appear. We develop the Context-Oriented Bias Indicator and Assessment Score (COBIAS) to measure a biased statement's reliability in detecting bias, based on the variance in model behavior across different contexts. To evaluate the metric, we augmented 2,291 stereotyped statements from two existing benchmark datasets by adding contextual information. We show that COBIAS aligns with human judgment on the contextual reliability of biased statements (Spearman's $ρ= 0.65, p = 3.4 * 10^{-60}$) and can be used to create reliable benchmarks, which would assist bias mitigation works.
GenCeption: Evaluate Vision LLMs with Unlabeled Unimodal Data
Venue: arXiv cs.CL 2025
Year: 2025

Multimodal Large Language Models (MLLMs) are typically assessed using expensive annotated multimodal benchmarks, which often lag behind the rapidly evolving demands of MLLM evaluation. This paper outlines and validates GenCeption, a novel, annotation-free evaluation method that requires only unimodal data to measure inter-modality semantic coherence and inversely assesses MLLMs' tendency to hallucinate. This approach eliminates the need for costly data annotation, minimizes the risk of training data contamination, is expected to result in slower benchmark saturation, and avoids the illusion of emerging abilities. Inspired by the DrawCeption game, GenCeption begins with a non-textual sample and proceeds through iterative description and generation steps. The semantic drift across iterations is quantified using the GC@T metric. While GenCeption is principally applicable to MLLMs across various modalities, this paper focuses on its implementation and validation for Vision LLMs (VLLMs). Based on the GenCeption method, we establish the MMECeption benchmark for evaluating VLLMs, and compare the performance of several popular VLLMs and human annotators. Our empirical results validate GenCeption's effectiveness, demonstrating strong correlations with established VLLM benchmarks. VLLMs still significantly lag behind human performance and struggle especially with text-intensive tasks.
Efficient State Space Model via Fast Tensor Convolution and Block Diagonalization
Venue: arXiv cs.LG 2025
Year: 2025

Existing models encounter bottlenecks in balancing performance and computational efficiency when modeling long sequences. Although the state space model (SSM) has achieved remarkable success in handling long sequence tasks, it still faces the problem of large number of parameters. In order to further improve the efficiency of SSM, we propose a new state space layer based on multiple-input multiple-output SSM, called efficient SSM (eSSM). Our eSSM is built on the convolutional representation of multi-input and multi-input (MIMO) SSM. We propose a variety of effective strategies to improve the computational efficiency. The diagonalization of the system matrix first decouples the original system. Then a fast tensor convolution is proposed based on the fast Fourier transform. In addition, the block diagonalization of the SSM further reduces the model parameters and improves the model flexibility. Extensive experimental results show that the performance of the proposed model on multiple databases matches the performance of state-of-the-art models, such as S4, and is significantly better than Transformers and LSTM. In the model efficiency benchmark, the parameters of eSSM are only 12.89\% of LSTM and 13.24\% of Mamba. The training speed of eSSM is 3.94 times faster than LSTM and 1.35 times faster than Mamba. Code is available at: \href{https://github.com/leonty1/essm}{https://github.com/leonty1/essm}.
Closed-loop Multi-step Planning
Venue: arXiv cs.RO 2025
Year: 2025

Living organisms interact with their surroundings in a closed-loop fashion, where sensory inputs dictate the initiation and termination of behaviours. Even simple animals are able to develop and execute complex plans, which has not yet been replicated in robotics using pure closed-loop input control. We propose a solution to this problem by defining a set of discrete and temporary closed-loop controllers, called ``Tasks'', each representing a closed-loop behaviour. We further introduce a supervisory module which has an innate understanding of physics and causality, through which it can simulate the execution of Task sequences over time and store the results in a model of the environment. On the basis of this model, plans can be made by chaining temporary closed-loop controllers. Our proposed framework was implemented for a real robot and tested in two scenarios as proof of concept.
Bias and Volatility: A Statistical Framework for Evaluating Large Language Model's Stereotypes and the Associated Generation Inconsistency
Venue: arXiv cs.CL 2025
Year: 2025

We present a novel statistical framework for analyzing stereotypes in large language models (LLMs) by systematically estimating the bias and variation in their generation. Current alignment evaluation metrics often overlook stereotypes' randomness caused by LLMs' inconsistent generative behavior. For instance, LLMs may display contradictory stereotypes, such as those related to gender or race, for identical professions in different contexts. Ignoring this inconsistency risks misleading conclusions in alignment assessments and undermines efforts to evaluate the potential of LLMs to perpetuate or amplify social biases and unfairness. To address this, we propose the Bias-Volatility Framework (BVF), which estimates the probability distribution of stereotypes in LLM outputs. By capturing the variation in generative behavior, BVF assesses both the likelihood and degree to which LLM outputs negatively impact vulnerable groups, enabling a quantification of aggregated discrimination risk. Additionally, we introduce a mathematical framework to decompose this risk into bias risk (from the mean of the stereotype distribution) and volatility risk (from its variation). Applying BVF to 12 widely used LLMs, we find: i) Bias risk is the dominant contributor to discrimination; ii) Most LLMs exhibit substantial pro-male stereotypes across nearly all professions; iii) Reinforcement learning from human feedback reduces bias but increases volatility; iv) Discrimination risk correlates with socio-economic factors, such as professional salaries. Finally, we highlight BVF's broader applicability for assessing how generation inconsistencies in LLMs impact behavior beyond stereotypes.
Data-Efficient Operator Learning via Unsupervised Pretraining and In-Context Learning
Venue: arXiv cs.LG 2025
Year: 2025

Recent years have witnessed the promise of coupling machine learning methods and physical domain-specific insights for solving scientific problems based on partial differential equations (PDEs). However, being data-intensive, these methods still require a large amount of PDE data. This reintroduces the need for expensive numerical PDE solutions, partially undermining the original goal of avoiding these expensive simulations. In this work, seeking data efficiency, we design unsupervised pretraining for PDE operator learning. To reduce the need for training data with heavy simulation costs, we mine unlabeled PDE data without simulated solutions, and we pretrain neural operators with physics-inspired reconstruction-based proxy tasks. To improve out-of-distribution performance, we further assist neural operators in flexibly leveraging a similarity-based method that learns in-context examples, without incurring extra training costs or designs. Extensive empirical evaluations on a diverse set of PDEs demonstrate that our method is highly data-efficient, more generalizable, and even outperforms conventional vision-pretrained models. We provide our code at https://github.com/delta-lab-ai/data_efficient_nopt.