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\n\n \n \n \n \n \n \n Impeding LLM-assisted Cheating in Introductory Programming Assignments via Adversarial Perturbation.\n \n \n \n \n\n\n \n Saiful Islam Salim; Rubin Yuchan Yang; Alexander Cooper; Suryashree Ray; Saumya Debray; and Sazzadur Rahaman.\n\n\n \n\n\n\n In
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP 2024), Miami, USA and virtual meeting, 2024. Association for Computational Linguistics\n
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@inproceedings{salim_2024_adversarial_perturbation,\n title={Impeding LLM-assisted Cheating in Introductory Programming Assignments via Adversarial Perturbation}, \n author={Saiful Islam Salim and Rubin Yuchan Yang and Alexander Cooper and Suryashree Ray and Saumya Debray and Sazzadur Rahaman},\n year = "2024",\n address = "Miami, USA and virtual meeting",\n publisher = "Association for Computational Linguistics",\n booktitle = "Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP 2024)",\n url={https://arxiv.org/abs/2410.09318},\n abstract = "While Large language model (LLM)-based programming assistants such as CoPilot and ChatGPT can help improve the productivity of professional software developers, they can also facilitate cheating in introductory computer programming courses. Assuming instructors have limited control over the industrial-strength models, this paper investigates the baseline performance of 5 widely used LLMs on a collection of introductory programming problems, examines adversarial perturbations to degrade their performance, and describes the results of a user study aimed at understanding the efficacy of such perturbations in hindering actual code generation for introductory programming assignments. The user study suggests that i) perturbations combinedly reduced the average correctness score by 77%, ii) the drop in correctness caused by these perturbations was affected based on their detectability."\n}\n\n\n
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\n While Large language model (LLM)-based programming assistants such as CoPilot and ChatGPT can help improve the productivity of professional software developers, they can also facilitate cheating in introductory computer programming courses. Assuming instructors have limited control over the industrial-strength models, this paper investigates the baseline performance of 5 widely used LLMs on a collection of introductory programming problems, examines adversarial perturbations to degrade their performance, and describes the results of a user study aimed at understanding the efficacy of such perturbations in hindering actual code generation for introductory programming assignments. The user study suggests that i) perturbations combinedly reduced the average correctness score by 77%, ii) the drop in correctness caused by these perturbations was affected based on their detectability.\n
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\n\n \n \n \n \n \n On the Contents and Utility of IoT Cybersecurity Guidelines.\n \n \n \n\n\n \n Jesse Chen; Dharun Anandayuvaraj; James C Davis; and Sazzadur Rahaman.\n\n\n \n\n\n\n
Proceedings of the ACM on Software Engineering, 1(FSE): 1400–1423. 2024.\n
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@article{chen2024contents,\n title={On the Contents and Utility of IoT Cybersecurity Guidelines},\n author={Chen, Jesse and Anandayuvaraj, Dharun and Davis, James C and Rahaman, Sazzadur},\n journal={Proceedings of the ACM on Software Engineering},\n volume={1},\n number={FSE},\n pages={1400--1423},\n year={2024},\n publisher={ACM New York, NY, USA}\n}\n\n\n
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\n\n \n \n \n \n \n Localized Evaluation for Constructing Discrete Vector Fields.\n \n \n \n\n\n \n Tanner Finken; Julien Tierny; and Joshua A. Levine.\n\n\n \n\n\n\n
IEEE TVCG. 2024.\n
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@article{finken2024OSA,\n author = {Tanner Finken and\n Julien Tierny and\n Joshua A. Levine},\n title = {Localized Evaluation for Constructing Discrete Vector Fields},\n journal = {IEEE TVCG},\n year = {2024}, \n doi = {10.1109/TVCG.2024.3456355}\n}\n\n
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\n\n \n \n \n \n \n Learning to Generate Rules for Realistic Few-Shot Relation Classification: An Encoder-Decoder Approach.\n \n \n \n\n\n \n Mayank Singh; and Eduardo Blanco.\n\n\n \n\n\n\n In
Findings of the Association for Computational Linguistics: EMNLP 2024, Miami, USA and virtual meeting, November 2024. Association for Computational Linguistics\n
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@inproceedings{singh-2024-learning,\n title = "Learning to Generate Rules for Realistic Few-Shot Relation Classification: An Encoder-Decoder Approach",\n author = "Singh, Mayank and Blanco, Eduardo",\n booktitle = "Findings of the Association for Computational Linguistics: EMNLP 2024",\n month = nov,\n year = "2024",\n address = "Miami, USA and virtual meeting",\n publisher = "Association for Computational Linguistics",\n abstract = "We propose a neuro-symbolic approach for realistic few-shot relation classification via rules. Instead of building neural models to predict relations, we design them to output straightforward rules that can be used to extract relations. The rules are generated using custom T5-style Encoder-Decoder Language Models. Crucially, our rules are fully interpretable and pliable (i.e., humans can easily modify them to boost performance). Through a combination of rules generated by these models along with a very effective, novel baseline, we demonstrate a few-shot relation-classification performance that is comparable to or stronger than the state of the art on the Few-Shot TACRED and NYT29 benchmarks while increasing interpretability and maintaining pliability.",\n}\n\n
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\n We propose a neuro-symbolic approach for realistic few-shot relation classification via rules. Instead of building neural models to predict relations, we design them to output straightforward rules that can be used to extract relations. The rules are generated using custom T5-style Encoder-Decoder Language Models. Crucially, our rules are fully interpretable and pliable (i.e., humans can easily modify them to boost performance). Through a combination of rules generated by these models along with a very effective, novel baseline, we demonstrate a few-shot relation-classification performance that is comparable to or stronger than the state of the art on the Few-Shot TACRED and NYT29 benchmarks while increasing interpretability and maintaining pliability.\n
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\n\n \n \n \n \n \n \n Change Is the Only Constant: Dynamic LLM Slicing based on Layer Redundancy.\n \n \n \n \n\n\n \n Razvan-Gabriel Dumitru; Paul Ioan Clotan; Vikas Yadav; Darius Peteleaza; and Mihai Surdeanu.\n\n\n \n\n\n\n In
Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP), September 2024. \n
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@inproceedings{dumitru2024slicing,\n title={Change Is the Only Constant: Dynamic LLM Slicing based on Layer Redundancy},\n author={Razvan-Gabriel Dumitru and Paul Ioan Clotan and Vikas Yadav and Darius Peteleaza and Mihai Surdeanu},\n booktitle={Proceedings of the 2024 Conference on Empirical Methods in Natural Language Processing (EMNLP)},\n year={2024},\n month={September},\n abstract={This paper introduces a novel model compression approach through dynamic layer-specific pruning in Large Language Models (LLMs), enhancing the traditional methodology established by SliceGPT. By transitioning from constant to dynamic slicing, our method leverages the newly proposed Layer Redundancy (LR) score, which assesses how much change each layer changes its input by measuring the cosine similarity of the input to the output of the layer. The method prunes parts of individual layers based on redundancy, maintaining performance while reducing model size.},\n url={https://openreview.net/forum?id=CHFf0AViDz}\n}\n\n
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\n This paper introduces a novel model compression approach through dynamic layer-specific pruning in Large Language Models (LLMs), enhancing the traditional methodology established by SliceGPT. By transitioning from constant to dynamic slicing, our method leverages the newly proposed Layer Redundancy (LR) score, which assesses how much change each layer changes its input by measuring the cosine similarity of the input to the output of the layer. The method prunes parts of individual layers based on redundancy, maintaining performance while reducing model size.\n
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\n\n \n \n \n \n \n \n Retrieval Augmented Generation of Subjective Explanations for Socioeconomic Scenarios.\n \n \n \n \n\n\n \n Razvan-Gabriel Dumitru; Maria Alexeeva; Keith Alcock; Nargiza Ludgate; Cheonkam Jeong; Zara Fatima Abdurahaman; Prateek Puri; Brian Kirchhoff; Santadarshan Sadhu; and Mihai Surdeanu.\n\n\n \n\n\n\n In
Sixth Workshop on NLP and Computational Social Science (at NAACL) 2024, 2024. \n
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@inproceedings{\n dumitru2024retrieval,\n title={Retrieval Augmented Generation of Subjective Explanations for Socioeconomic Scenarios},\n author={Dumitru, Razvan-Gabriel and Alexeeva, Maria and Alcock, Keith and Ludgate, Nargiza and Jeong, Cheonkam and Abdurahaman, Zara Fatima and Puri, Prateek and Kirchhoff, Brian and Sadhu, Santadarshan and Surdeanu, Mihai},\n booktitle={Sixth Workshop on NLP and Computational Social Science (at NAACL) 2024},\n year={2024},\n url={http://clulab.org/papers/naacl-css2024-rag.pdf}\n}\n\n
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\n\n \n \n \n \n \n \n Time Travel in LLMs: Tracing Data Contamination in Large Language Models.\n \n \n \n \n\n\n \n Shahriar Golchin; and Mihai Surdeanu.\n\n\n \n\n\n\n In
The Twelfth International Conference on Learning Representations (ICLR), 2024. \n
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@inproceedings{golchin2024time,\ntitle={Time Travel in {LLM}s: Tracing Data Contamination in Large Language Models},\nauthor={Shahriar Golchin and Mihai Surdeanu},\nbooktitle={The Twelfth International Conference on Learning Representations (ICLR)},\nyear={2024},\nurl={https://openreview.net/forum?id=2Rwq6c3tvr}\n}\n\n
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\n\n \n \n \n \n \n \n Building large-scale registries from unstructured clinical notes using a low-resource natural language processing pipeline.\n \n \n \n \n\n\n \n Nazgol Tavabi; James Pruneski; Shahriar Golchin; Mallika Singh; Ryan Sanborn; Benton Heyworth; Assaf Landschaft; Amir Kimia; and Ata Kiapour.\n\n\n \n\n\n\n
Artificial Intelligence in Medicine, 151: 102847. 2024.\n
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@article{TAVABI2024102847,\ntitle = {Building large-scale registries from unstructured clinical notes using a low-resource natural language processing pipeline},\njournal = {Artificial Intelligence in Medicine},\nvolume = {151},\npages = {102847},\nyear = {2024},\nissn = {0933-3657},\ndoi = {https://doi.org/10.1016/j.artmed.2024.102847},\nurl = {https://www.sciencedirect.com/science/article/pii/S0933365724000897},\nauthor = {Nazgol Tavabi and James Pruneski and Shahriar Golchin and Mallika Singh and Ryan Sanborn and Benton Heyworth and Assaf Landschaft and Amir Kimia and Ata Kiapour},\nkeywords = {Electronic health records, Natural language processing, Registry building, Clinical notes, ACL},\nabstract = {Building clinical registries is an important step in clinical research and improvement of patient care quality. Natural Language Processing (NLP) methods have shown promising results in extracting valuable information from unstructured clinical notes. However, the structure and nature of clinical notes are very different from regular text that state-of-the-art NLP models are trained and tested on, and they have their own set of challenges. In this study, we propose Sentence Extractor with Keywords (SE-K), an efficient and interpretable classification approach for extracting information from clinical notes and show that it outperforms more computationally expensive methods in text classification. Following the Institutional Review Board (IRB) approval, we used SE-K and two embedding based NLP approaches (Sentence Extractor with Embeddings (SE-E) and Bidirectional Encoder Representations from Transformers (BERT)) to develop comprehensive registry of anterior cruciate ligament surgeries from 20 years of unstructured clinical data at a multi-site tertiary-care regional children's hospital. The low-resource approach (SE-K) had better performance (average AUROC of 0.94 ± 0.04) than the embedding-based approaches (SE-E: 0.93 ± 0.04 and BERT: 0.87 ± 0.09) for out of sample validation, in addition to minimum performance drop between test and out-of-sample validation. Moreover, the SE-K approach was at least six times faster (on CPU) than SE-E (on CPU) and BERT (on GPU) and provides interpretability. Our proposed approach, SE-K, can be effectively used to extract relevant variables from clinic notes to build large-scale registries, with consistently better performance compared to the more resource-intensive approaches (e.g., BERT). Such approaches can facilitate information extraction from unstructured notes for registry building, quality improvement and adverse event monitoring.}\n}\n\n
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\n Building clinical registries is an important step in clinical research and improvement of patient care quality. Natural Language Processing (NLP) methods have shown promising results in extracting valuable information from unstructured clinical notes. However, the structure and nature of clinical notes are very different from regular text that state-of-the-art NLP models are trained and tested on, and they have their own set of challenges. In this study, we propose Sentence Extractor with Keywords (SE-K), an efficient and interpretable classification approach for extracting information from clinical notes and show that it outperforms more computationally expensive methods in text classification. Following the Institutional Review Board (IRB) approval, we used SE-K and two embedding based NLP approaches (Sentence Extractor with Embeddings (SE-E) and Bidirectional Encoder Representations from Transformers (BERT)) to develop comprehensive registry of anterior cruciate ligament surgeries from 20 years of unstructured clinical data at a multi-site tertiary-care regional children's hospital. The low-resource approach (SE-K) had better performance (average AUROC of 0.94 ± 0.04) than the embedding-based approaches (SE-E: 0.93 ± 0.04 and BERT: 0.87 ± 0.09) for out of sample validation, in addition to minimum performance drop between test and out-of-sample validation. Moreover, the SE-K approach was at least six times faster (on CPU) than SE-E (on CPU) and BERT (on GPU) and provides interpretability. Our proposed approach, SE-K, can be effectively used to extract relevant variables from clinic notes to build large-scale registries, with consistently better performance compared to the more resource-intensive approaches (e.g., BERT). Such approaches can facilitate information extraction from unstructured notes for registry building, quality improvement and adverse event monitoring.\n
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\n\n \n \n \n \n \n Best of Both Worlds: A Pliable and Generalizable Neuro-Symbolic Approach for Relation Classification.\n \n \n \n\n\n \n Robert Vacareanu; Fahmida Alam; Md Asiful Islam; Haris Riaz; and Mihai Surdeanu.\n\n\n \n\n\n\n In
Findings of the Association for Computational Linguistics: NAACL 2024, Mexico City, Mexico, June 2024. Association for Computational Linguistics\n
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@inproceedings{vacareanu2024softrules,\n title = "Best of Both Worlds: A Pliable and Generalizable Neuro-Symbolic Approach for Relation Classification",\n author = "Robert Vacareanu and Fahmida Alam and Md Asiful Islam and Haris Riaz and Mihai Surdeanu",\n booktitle = "Findings of the Association for Computational Linguistics: NAACL 2024",\n month = jun,\n year = "2024",\n address = "Mexico City, Mexico",\n publisher = "Association for Computational Linguistics",\n abstract = "This paper introduces a novel neuro-symbolic architecture for relation classification (RC) that combines rule-based methods with contemporary deep learning techniques. This approach capitalizes on the strengths of both paradigms: the adaptability of rule-based systems and the generalization power of neural networks. Our architecture consists of two components: a declarative rule-based model for transparent classification and a neural component to enhance rule generalizability through semantic text matching. Notably, our semantic matcher is trained in an unsupervised domain-agnostic way, solely with synthetic data. Further, these components are loosely coupled, allowing for rule modifications without retraining the semantic matcher. In our evaluation, we focused on two few-shot relation classification datasets: Few-Shot TACRED and a Few-Shot version of NYT29. We show that our proposed method outperforms previous state-of-the-art models in three out of four settings, despite not seeing any human-annotated training data. Further, we show that our approach remains modular and pliable, i.e., the corresponding rules can be locally modified to improve the overall model. Human interventions to the rules for the TACRED relation \\texttt{org:parents} boost the performance on that relation by as much as 26\\% relative improvement, without negatively impacting the other relations, and without retraining the semantic matching component.",\n}\n\n
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\n This paper introduces a novel neuro-symbolic architecture for relation classification (RC) that combines rule-based methods with contemporary deep learning techniques. This approach capitalizes on the strengths of both paradigms: the adaptability of rule-based systems and the generalization power of neural networks. Our architecture consists of two components: a declarative rule-based model for transparent classification and a neural component to enhance rule generalizability through semantic text matching. Notably, our semantic matcher is trained in an unsupervised domain-agnostic way, solely with synthetic data. Further, these components are loosely coupled, allowing for rule modifications without retraining the semantic matcher. In our evaluation, we focused on two few-shot relation classification datasets: Few-Shot TACRED and a Few-Shot version of NYT29. We show that our proposed method outperforms previous state-of-the-art models in three out of four settings, despite not seeing any human-annotated training data. Further, we show that our approach remains modular and pliable, i.e., the corresponding rules can be locally modified to improve the overall model. Human interventions to the rules for the TACRED relation \\textttorg:parents boost the performance on that relation by as much as 26% relative improvement, without negatively impacting the other relations, and without retraining the semantic matching component.\n
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\n\n \n \n \n \n \n \n A Weak Supervision Approach for Few-Shot Aspect Based Sentiment Analysis.\n \n \n \n \n\n\n \n Robert Vacareanu; Siddharth Varia; Kishaloy Halder; Shuai Wang; Giovanni Paolini; Neha Anna John; Miguel Ballesteros; and Smaranda Muresan.\n\n\n \n\n\n\n In Yvette Graham; and Matthew Purver., editor(s),
Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics (Volume 1: Long Papers), pages 2734–2752, St. Julian's, Malta, March 2024. Association for Computational Linguistics\n
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@inproceedings{vacareanu-etal-2024-weak,\n title = "A Weak Supervision Approach for Few-Shot Aspect Based Sentiment Analysis",\n author = "Vacareanu, Robert and\n Varia, Siddharth and\n Halder, Kishaloy and\n Wang, Shuai and\n Paolini, Giovanni and\n Anna John, Neha and\n Ballesteros, Miguel and\n Muresan, Smaranda",\n editor = "Graham, Yvette and\n Purver, Matthew",\n booktitle = "Proceedings of the 18th Conference of the European Chapter of the Association for Computational Linguistics (Volume 1: Long Papers)",\n month = mar,\n year = "2024",\n address = "St. Julian{'}s, Malta",\n publisher = "Association for Computational Linguistics",\n url = "https://aclanthology.org/2024.eacl-long.167",\n pages = "2734--2752",\n abstract = "We explore how weak supervision on abundant unlabeled data can be leveraged to improve few-shot performance in aspect-based sentiment analysis (ABSA) tasks. We propose a pipeline approach to construct a noisy ABSA dataset, and we use it to adapt a pre-trained sequence-to-sequence model to the ABSA tasks. We test the resulting model on three widely used ABSA datasets, before and after fine-tuning. Our proposed method preserves the full fine-tuning performance while showing significant improvements (15.84 absolute F1) in the few-shot learning scenario for the harder tasks. In zero-shot (i.e., without fine-tuning), our method outperforms the previous state of the art on the aspect extraction sentiment classification (AESC) task and is, additionally, capable of performing the harder aspect sentiment triplet extraction (ASTE) task.",\n}\n\n
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\n We explore how weak supervision on abundant unlabeled data can be leveraged to improve few-shot performance in aspect-based sentiment analysis (ABSA) tasks. We propose a pipeline approach to construct a noisy ABSA dataset, and we use it to adapt a pre-trained sequence-to-sequence model to the ABSA tasks. We test the resulting model on three widely used ABSA datasets, before and after fine-tuning. Our proposed method preserves the full fine-tuning performance while showing significant improvements (15.84 absolute F1) in the few-shot learning scenario for the harder tasks. In zero-shot (i.e., without fine-tuning), our method outperforms the previous state of the art on the aspect extraction sentiment classification (AESC) task and is, additionally, capable of performing the harder aspect sentiment triplet extraction (ASTE) task.\n
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\n\n \n \n \n \n \n Interpreting Answers to Yes-No Questions in Dialogues from Multiple Domains.\n \n \n \n\n\n \n Zijie Wang; Farzana Rashid; and Eduardo Blanco.\n\n\n \n\n\n\n In
Findings of the Association for Computational Linguistics: NAACL 2024, Mexico City, Mexico, June 2024. Association for Computational Linguistics\n
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@inproceedings{wang2024naaclfindings,\n title = "Interpreting Answers to Yes-No Questions in Dialogues from Multiple Domains",\n author = "Wang, Zijie and Rashid, Farzana and Blanco, Eduardo",\n booktitle = "Findings of the Association for Computational Linguistics: NAACL 2024",\n month = jun,\n year = "2024",\n address = "Mexico City, Mexico",\n publisher = "Association for Computational Linguistics",\n abstract = "People often answer yes-no questions without explicitly saying yes, no, or similar polar keywords. Figuring out the meaning of indirect answers is challenging, even for large language models. In this paper, we investigate this problem working with dialogues from multiple domains. We present new benchmarks in three diverse domains: movie scripts, tennis interviews, and airline customer service. We present an approach grounded on distant supervision and blended training to quickly adapt to a new dialogue domain. Experimental results show that our approach is never detrimental and yields F1 improvements as high as 11-34%.",\n}\n\n
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\n People often answer yes-no questions without explicitly saying yes, no, or similar polar keywords. Figuring out the meaning of indirect answers is challenging, even for large language models. In this paper, we investigate this problem working with dialogues from multiple domains. We present new benchmarks in three diverse domains: movie scripts, tennis interviews, and airline customer service. We present an approach grounded on distant supervision and blended training to quickly adapt to a new dialogue domain. Experimental results show that our approach is never detrimental and yields F1 improvements as high as 11-34%.\n
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\n\n \n \n \n \n \n ELLEN: Extremely Lightly Supervised Learning For Efficient Named Entity Recognition.\n \n \n \n\n\n \n Haris Riaz; Razvan-Gabriel Dumitru; and Mihai Surdeanu.\n\n\n \n\n\n\n In
Proceedings of the Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING), Torino, Italy, May 2024. European Language Resources Association\n
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@inproceedings{riaz2024ellen,\n title = "ELLEN: Extremely Lightly Supervised Learning For Efficient Named Entity Recognition",\n author = "Haris Riaz and Razvan-Gabriel Dumitru and Mihai Surdeanu",\n booktitle = "Proceedings of the Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING)",\n month = may,\n year = "2024",\n address = "Torino, Italy",\n publisher = "European Language Resources Association",\n abstract = "In this work, we revisit the problem of semi-supervised named entity recognition (NER) focusing on extremely light supervision, consisting of a lexicon containing only 10 examples per class. We introduce ELLEN, a simple, fully modular, neuro-symbolic method that blends fine-tuned language models with linguistic rules. These rules include insights such as ''One Sense Per Discourse'', using a Masked Language Model as an unsupervised NER, leveraging part-of-speech tags to identify and eliminate unlabeled entities as false negatives, and other intuitions about classifier confidence scores in local and global context. ELLEN achieves very strong performance on the CoNLL-2003 dataset when using the minimal supervision from the lexicon above. It also outperforms most existing (and considerably more complex) semi-supervised NER methods under the same supervision settings commonly used in the literature (i.e., 5% of the training data). Further, we evaluate our CoNLL-2003 model in a zero-shot scenario on WNUT-17 where we find that it outperforms GPT-3.5 and achieves comparable performance to GPT-4. In a zero-shot setting, ELLEN also achieves over 75% of the performance of a strong, fully supervised model trained on gold data. Our code is available at: https://github.com/hriaz17/ELLEN",\n}\n\n
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\n In this work, we revisit the problem of semi-supervised named entity recognition (NER) focusing on extremely light supervision, consisting of a lexicon containing only 10 examples per class. We introduce ELLEN, a simple, fully modular, neuro-symbolic method that blends fine-tuned language models with linguistic rules. These rules include insights such as ''One Sense Per Discourse'', using a Masked Language Model as an unsupervised NER, leveraging part-of-speech tags to identify and eliminate unlabeled entities as false negatives, and other intuitions about classifier confidence scores in local and global context. ELLEN achieves very strong performance on the CoNLL-2003 dataset when using the minimal supervision from the lexicon above. It also outperforms most existing (and considerably more complex) semi-supervised NER methods under the same supervision settings commonly used in the literature (i.e., 5% of the training data). Further, we evaluate our CoNLL-2003 model in a zero-shot scenario on WNUT-17 where we find that it outperforms GPT-3.5 and achieves comparable performance to GPT-4. In a zero-shot setting, ELLEN also achieves over 75% of the performance of a strong, fully supervised model trained on gold data. Our code is available at: https://github.com/hriaz17/ELLEN\n
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\n\n \n \n \n \n \n \n Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria.\n \n \n \n \n\n\n \n Aditya AND Tran Kamat; Mohak AND Sontakke Ngat T. Sharda; and Tung B. K. AND Badrinarayanan Neha Le.\n\n\n \n\n\n\n
PLOS Biology, 22(3): 1-25. 03 2024.\n
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@article{10.1371/journal.pbio.3002540,\n doi = {10.1371/journal.pbio.3002540},\n author = {Kamat, Aditya AND Tran, Ngat T. AND Sharda, Mohak AND Sontakke, Neha AND Le, Tung B. K. AND Badrinarayanan, Anjana},\n journal = {PLOS Biology},\n publisher = {Public Library of Science},\n title = {Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria},\n year = {2024},\n month = {03},\n volume = {22},\n url = {https://doi.org/10.1371/journal.pbio.3002540},\n pages = {1-25},\n abstract = {DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.},\n number = {3},\n}\n\n
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\n DNA methylation plays central roles in diverse cellular processes, ranging from error-correction during replication to regulation of bacterial defense mechanisms. Nevertheless, certain aberrant methylation modifications can have lethal consequences. The mechanisms by which bacteria detect and respond to such damage remain incompletely understood. Here, we discover a highly conserved but previously uncharacterized transcription factor (Cada2), which orchestrates a methylation-dependent adaptive response in Caulobacter. This response operates independently of the SOS response, governs the expression of genes crucial for direct repair, and is essential for surviving methylation-induced damage. Our molecular investigation of Cada2 reveals a cysteine methylation-dependent posttranslational modification (PTM) and mode of action distinct from its Escherichia coli counterpart, a trait conserved across all bacteria harboring a Cada2-like homolog instead. Extending across the bacterial kingdom, our findings support the notion of divergence and coevolution of adaptive response transcription factors and their corresponding sequence-specific DNA motifs. Despite this diversity, the ubiquitous prevalence of adaptive response regulators underscores the significance of a transcriptional switch, mediated by methylation PTM, in driving a specific and essential bacterial DNA damage response.\n
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\n\n \n \n \n \n \n ASSOCIATION OF MRI-DEFINED STRUCTURE FEATURES AT BASELINE WITH KNEE PAIN TRAJECTORIES.\n \n \n \n\n\n \n S Liu; X Sun; Y Ge; TN Duong; and CK Kwoh.\n\n\n \n\n\n\n
Osteoarthritis Imaging, 4: 100187. 2024.\n
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@article{liu2024association,\n title={ASSOCIATION OF MRI-DEFINED STRUCTURE FEATURES AT BASELINE WITH KNEE PAIN TRAJECTORIES},\n author={Liu, S and Sun, X and Ge, Y and Duong, TN and Kwoh, CK},\n journal={Osteoarthritis Imaging},\n volume={4},\n pages={100187},\n year={2024},\n publisher={Elsevier}\n}\n\n
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\n\n \n \n \n \n \n Beyond task diversity: provable representation transfer for sequential multi-task linear bandits.\n \n \n \n\n\n \n Thang Duong; Zhi Wang; and Chicheng Zhang.\n\n\n \n\n\n\n In
Advances in Neural Information Processing Systems 37 (NeurIPS 2024), 2024. NeurIPS\n
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@inproceedings{duong2024beyond,\n title={Beyond task diversity: provable representation transfer for sequential multi-task linear bandits},\n author={Duong, Thang and Wang, Zhi and Zhang, Chicheng},\n booktitle={Advances in Neural Information Processing Systems 37 (NeurIPS 2024)},\n year={2024},\n publisher={NeurIPS}\n}\n\n
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