arXiv subjects

Arzucan Özgür

Publications and source records attributed to Arzucan Özgür.

At least 19 recordsLinked to original sources

arXiv2026

PUMA: Learning a Mutation-Aware Vocabulary of Protein Units

Modeling protein sequences as a language has made language models a powerful tool in computational biology, yet the language itself remains poorly understood. A key step toward understanding it is identifying its constituent units. In natural languages, morphemes can occur in multiple forms; similarly, in proteins, mutations can give rise to variations of a unit that persist through evolution, forming families of related units. We introduce PUMA (Protein Units via Mutation-Aware Merging), an algorithm that learns protein units from sequence and explores their mutational variants using substitution matrices, forming a genealogy of unit families. Our results show that mutations remaining within a PUMA family are more often benign than the substitution matrix alone predicts, and that PUMA genealogy improves molecular function representations compared to treating units independently. A case study of a unit family demonstrates relatedness beyond homology. PUMA achieves competitive performance on downstream tasks when used as a protein language model tokenizer. Moreover, collapsing units into families results in a smaller embedding table and faster training. Together, these results support PUMA as a biologically grounded protein vocabulary that organizes protein units into plausible families of mutational variants. The source code is available at https://github.com/boun-tabi-lifelu/PUMA.

cs.CL↗

arXiv2026

Hate Speech Detection in Turkish and Arabic: A Comprehensive Study

Online hate speech has been linked to a global rise in violence against minorities, including incidents such as mass shootings, lynchings, and ethnic cleansing. Societies grappling with this issue, particularly when hate speech targets specific groups based on religion, race, ethnicity, culture, nationality, or migration status, face the challenge of balancing freedom of expression with the need for effective content moderation on widely used online platforms. In response to this challenge, we introduce a comprehensive hate speech dataset covering five distinct topics in Turkish: refugees, the Israel-Palestine conflict, anti-Greek sentiment in Turkey, ethnic or religious communities (Alevis, Armenians, Arabs, Jews, and Kurds), and LGBTI+, alongside one topic in Arabic (refugees). In addition, we develop state-of-the-art BERT-based models to address multiple dimensions of hate speech analysis, including hate category classification, hate intensity prediction, target identification, and hate speech span detection, enabling a comprehensive understanding of hateful content in online discourse.

cs.CL↗

arXiv2026

PUFFIN: Protein Unit Discovery with Functional Supervision

Proteins carry out biological functions through the coordinated action of groups of residues organized into structural arrangements. These arrangements, which we refer to as protein units, exist at an intermediate scale, being larger than individual residues yet smaller than entire proteins. A deeper understanding of protein function can be achieved by identifying these units and their associations with function. However, existing approaches either focus on residue-level signals, rely on curated annotations, or segment protein structures without incorporating functional information, thereby limiting interpretable analysis of structure-function relationships. We introduce PUFFIN, a data-driven framework for discovering protein units by jointly learning structural partitioning and functional supervision. PUFFIN represents proteins as residue-level structure graphs and applies a graph neural network with a structure-aware pooling mechanism that partitions each protein into multi-residue units, with functional supervision that shapes the partition. We show that the learned units are structurally coherent, exhibit organized associations with molecular function, and show meaningful correspondence with curated InterPro annotations. Together, these results demonstrate that PUFFIN provides an interpretable framework for analyzing structure-function relationships using learned protein units and their statistical function associations. We made our source code available at https://github.com/boun-tabi-lifelu/puffin.

q-bio.BM↗

arXiv2026

STAR-GO: Improving Protein Function Prediction by Learning to Hierarchically Integrate Ontology-Informed Semantic Embeddings

Accurate prediction of protein function is essential for elucidating molecular mechanisms and advancing biological and therapeutic discovery. Yet experimental annotation lags far behind the rapid growth of protein sequence data. Computational approaches address this gap by associating proteins with Gene Ontology (GO) terms, which encode functional knowledge through hierarchical relations and textual definitions. However, existing models often emphasize one modality over the other, limiting their ability to generalize, particularly to unseen or newly introduced GO terms that frequently arise as the ontology evolves, and making the previously trained models outdated. We present STAR-GO, a Transformer-based framework that jointly models the semantic and structural characteristics of GO terms to enhance zero-shot protein function prediction. STAR-GO integrates textual definitions with ontology graph structure to learn unified GO representations, which are processed in hierarchical order to propagate information from general to specific terms. These representations are then aligned with protein sequence embeddings to capture sequence-function relationships. STAR-GO achieves state-of-the-art performance and superior zero-shot generalization, demonstrating the utility of integrating semantics and structure for robust and adaptable protein function prediction. Code is available at https://github.com/boun-tabi-lifelu/stargo.

q-bio.BM↗

arXiv2025

Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models

Motivation: An adjuvant is a chemical incorporated into vaccines that enhances their efficacy by improving the immune response. Identifying adjuvant names from cancer vaccine studies is essential for furthering research and enhancing immunotherapies. However, the manual curation from the constantly expanding biomedical literature poses significant challenges. This study explores the automated recognition of vaccine adjuvant names using Large Language Models (LLMs), specifically Generative Pretrained Transformers (GPT) and Large Language Model Meta AI (Llama). Methods: We utilized two datasets: 97 clinical trial records from AdjuvareDB and 290 abstracts annotated with the Vaccine Adjuvant Compendium (VAC). GPT-4o and Llama 3.2 were employed in zero-shot and few-shot learning paradigms with up to four examples per prompt. Prompts explicitly targeted adjuvant names, testing the impact of contextual information such as substances or interventions. Outputs underwent automated and manual validation for accuracy and consistency. Results: GPT-4o attained 100% Precision across all situations while exhibiting notable improve in Recall and F1-scores, particularly with incorporating interventions. On the VAC dataset, GPT-4o achieved a maximum F1-score of 77.32% with interventions, surpassing Llama-3.2-3B by approximately 2%. On the AdjuvareDB dataset, GPT-4o reached an F1-score of 81.67% for three-shot prompting with interventions, surpassing Llama-3.2-3 B's maximum F1-score of 65.62%. Conclusion: Our findings demonstrate that LLMs excel at identifying adjuvant names, including rare variations of naming representation. This study emphasizes the capability of LLMs to enhance cancer vaccine development by efficiently extracting insights. Future work aims to broaden the framework to encompass various biomedical literature and enhance model generalizability across various vaccines and adjuvants.

cs.CL↗

arXiv2024

Linguistic Laws Meet Protein Sequences: A Comparative Analysis of Subword Tokenization Methods

Tokenization is a crucial step in processing protein sequences for machine learning models, as proteins are complex sequences of amino acids that require meaningful segmentation to capture their functional and structural properties. However, existing subword tokenization methods, developed primarily for human language, may be inadequate for protein sequences, which have unique patterns and constraints. This study evaluates three prominent tokenization approaches, Byte-Pair Encoding (BPE), WordPiece, and SentencePiece, across varying vocabulary sizes (400-6400), analyzing their effectiveness in protein sequence representation, domain boundary preservation, and adherence to established linguistic laws. Our comprehensive analysis reveals distinct behavioral patterns among these tokenizers, with vocabulary size significantly influencing their performance. BPE demonstrates better contextual specialization and marginally better domain boundary preservation at smaller vocabularies, while SentencePiece achieves better encoding efficiency, leading to lower fertility scores. WordPiece offers a balanced compromise between these characteristics. However, all tokenizers show limitations in maintaining protein domain integrity, particularly as vocabulary size increases. Analysis of linguistic law adherence shows partial compliance with Zipf's and Brevity laws but notable deviations from Menzerath's law, suggesting that protein sequences may follow distinct organizational principles from natural languages. These findings highlight the limitations of applying traditional NLP tokenization methods to protein sequences and emphasize the need for developing specialized tokenization strategies that better account for the unique characteristics of proteins.

cs.CL↗

arXiv2023

Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and accurate extraction of PPIs to facilitate scientific knowledge discovery. Pre-trained language models, such as generative pre-trained transformers (GPT) and bidirectional encoder representations from transformers (BERT), have shown promising results in natural language processing (NLP) tasks. We evaluated the performance of PPI identification of multiple GPT and BERT models using three manually curated gold-standard corpora: Learning Language in Logic (LLL) with 164 PPIs in 77 sentences, Human Protein Reference Database with 163 PPIs in 145 sentences, and Interaction Extraction Performance Assessment with 335 PPIs in 486 sentences. BERT-based models achieved the best overall performance, with BioBERT achieving the highest recall (91.95%) and F1-score (86.84%) and PubMedBERT achieving the highest precision (85.25%). Interestingly, despite not being explicitly trained for biomedical texts, GPT-4 achieved commendable performance, comparable to the top-performing BERT models. It achieved a precision of 88.37%, a recall of 85.14%, and an F1-score of 86.49% on the LLL dataset. These results suggest that GPT models can effectively detect PPIs from text data, offering promising avenues for application in biomedical literature mining. Further research could explore how these models might be fine-tuned for even more specialized tasks within the biomedical domain.

cs.CL↗

arXiv2023

Exploring Data-Driven Chemical SMILES Tokenization Approaches to Identify Key Protein-Ligand Binding Moieties

Machine learning models have found numerous successful applications in computational drug discovery. A large body of these models represents molecules as sequences since molecular sequences are easily available, simple, and informative. The sequence-based models often segment molecular sequences into pieces called chemical words (analogous to the words that make up sentences in human languages) and then apply advanced natural language processing techniques for tasks such as $\textit{de novo}$ drug design, property prediction, and binding affinity prediction. However, the chemical characteristics and significance of these building blocks, chemical words, remain unexplored. This study aims to investigate the chemical vocabularies generated by popular subword tokenization algorithms, namely Byte Pair Encoding (BPE), WordPiece, and Unigram, and identify key chemical words associated with protein-ligand binding. To this end, we build a language-inspired pipeline that treats high affinity ligands of protein targets as documents and selects key chemical words making up those ligands based on tf-idf weighting. Further, we conduct case studies on a number of protein families to analyze the impact of key chemical words on binding. Through our analysis, we find that these key chemical words are specific to protein targets and correspond to known pharmacophores and functional groups. Our findings will help shed light on the chemistry captured by the chemical words, and by machine learning models for drug discovery at large.

q-bio.BM↗

arXiv2023

PEAK: Explainable Privacy Assistant through Automated Knowledge Extraction

In the realm of online privacy, privacy assistants play a pivotal role in empowering users to manage their privacy effectively. Although recent studies have shown promising progress in tackling tasks such as privacy violation detection and personalized privacy recommendations, a crucial aspect for widespread user adoption is the capability of these systems to provide explanations for their decision-making processes. This paper presents a privacy assistant for generating explanations for privacy decisions. The privacy assistant focuses on discovering latent topics, identifying explanation categories, establishing explanation schemes, and generating automated explanations. The generated explanations can be used by users to understand the recommendations of the privacy assistant. Our user study of real-world privacy dataset of images shows that users find the generated explanations useful and easy to understand. Additionally, the generated explanations can be used by privacy assistants themselves to improve their decision-making. We show how this can be realized by incorporating the generated explanations into a state-of-the-art privacy assistant.

cs.AI↗

arXiv2023

DebiasedDTA: A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models

Computational models that accurately predict the binding affinity of an input protein-chemical pair can accelerate drug discovery studies. These models are trained on available protein-chemical interaction datasets, which may contain dataset biases that may lead the model to learn dataset-specific patterns, instead of generalizable relationships. As a result, the prediction performance of models drops for previously unseen biomolecules, $\textit{i.e.}$ the prediction models cannot generalize to biomolecules outside of the dataset. The latest approaches that aim to improve model generalizability either have limited applicability or introduce the risk of degrading prediction performance. Here, we present DebiasedDTA, a novel drug-target affinity (DTA) prediction model training framework that addresses dataset biases to improve the generalizability of affinity prediction models. DebiasedDTA reweights the training samples to mitigate the effect of dataset biases and is applicable to most DTA prediction models. The results suggest that models trained in the DebiasedDTA framework can achieve improved generalizability in predicting the interactions of the previously unseen biomolecules, as well as performance improvements on those previously seen. Extensive experiments with different biomolecule representations, model architectures, and datasets demonstrate that DebiasedDTA can upgrade DTA prediction models irrespective of the biomolecule representation, model architecture, and training dataset. Last but not least, we release DebiasedDTA as an open-source python library to enable other researchers to debias their own predictors and/or develop their own debiasing methods. We believe that this python library will corroborate and foster research to develop more generalizable DTA prediction models.

q-bio.QM↗

arXiv2022

Exploiting Pretrained Biochemical Language Models for Targeted Drug Design

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145

cs.LG↗

arXiv2022

Uncertainty-aware Personal Assistant for Making Personalized Privacy Decisions

Many software systems, such as online social networks enable users to share information about themselves. While the action of sharing is simple, it requires an elaborate thought process on privacy: what to share, with whom to share, and for what purposes. Thinking about these for each piece of content to be shared is tedious. Recent approaches to tackle this problem build personal assistants that can help users by learning what is private over time and recommending privacy labels such as private or public to individual content that a user considers sharing. However, privacy is inherently ambiguous and highly personal. Existing approaches to recommend privacy decisions do not address these aspects of privacy sufficiently. Ideally, a personal assistant should be able to adjust its recommendation based on a given user, considering that user's privacy understanding. Moreover, the personal assistant should be able to assess when its recommendation would be uncertain and let the user make the decision on her own. Accordingly, this paper proposes a personal assistant that uses evidential deep learning to classify content based on its privacy label. An important characteristic of the personal assistant is that it can model its uncertainty in its decisions explicitly, determine that it does not know the answer, and delegate from making a recommendation when its uncertainty is high. By factoring in the user's own understanding of privacy, such as risk factors or own labels, the personal assistant can personalize its recommendations per user. We evaluate our proposed personal assistant using a well-known data set. Our results show that our personal assistant can accurately identify uncertain cases, personalize them to its user's needs, and thus helps users preserve their privacy well.

cs.AI↗

arXiv2022

Enhancements to the BOUN Treebank Reflecting the Agglutinative Nature of Turkish

In this study, we aim to offer linguistically motivated solutions to resolve the issues of the lack of representation of null morphemes, highly productive derivational processes, and syncretic morphemes of Turkish in the BOUN Treebank without diverging from the Universal Dependencies framework. In order to tackle these issues, new annotation conventions were introduced by splitting certain lemmas and employing the MISC (miscellaneous) tab in the UD framework to denote derivation. Representational capabilities of the re-annotated treebank were tested on a LSTM-based dependency parser and an updated version of the BoAT Tool is introduced.

cs.CL↗

arXiv2022

A Dataset and BERT-based Models for Targeted Sentiment Analysis on Turkish Texts

Targeted Sentiment Analysis aims to extract sentiment towards a particular target from a given text. It is a field that is attracting attention due to the increasing accessibility of the Internet, which leads people to generate an enormous amount of data. Sentiment analysis, which in general requires annotated data for training, is a well-researched area for widely studied languages such as English. For low-resource languages such as Turkish, there is a lack of such annotated data. We present an annotated Turkish dataset suitable for targeted sentiment analysis. We also propose BERT-based models with different architectures to accomplish the task of targeted sentiment analysis. The results demonstrate that the proposed models outperform the traditional sentiment analysis models for the targeted sentiment analysis task.

cs.CL↗

arXiv2021

Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution

Multi-label text classification is a challenging task because it requires capturing label dependencies. It becomes even more challenging when class distribution is long-tailed. Resampling and re-weighting are common approaches used for addressing the class imbalance problem, however, they are not effective when there is label dependency besides class imbalance because they result in oversampling of common labels. Here, we introduce the application of balancing loss functions for multi-label text classification. We perform experiments on a general domain dataset with 90 labels (Reuters-21578) and a domain-specific dataset from PubMed with 18211 labels. We find that a distribution-balanced loss function, which inherently addresses both the class imbalance and label linkage problems, outperforms commonly used loss functions. Distribution balancing methods have been successfully used in the image recognition field. Here, we show their effectiveness in natural language processing. Source code is available at https://github.com/Roche/BalancedLossNLP.

cs.CL↗

arXiv2021

Cluster-based Mention Typing for Named Entity Disambiguation

An entity mention in text such as "Washington" may correspond to many different named entities such as the city "Washington D.C." or the newspaper "Washington Post." The goal of named entity disambiguation is to identify the mentioned named entity correctly among all possible candidates. If the type (e.g. location or person) of a mentioned entity can be correctly predicted from the context, it may increase the chance of selecting the right candidate by assigning low probability to the unlikely ones. This paper proposes cluster-based mention typing for named entity disambiguation. The aim of mention typing is to predict the type of a given mention based on its context. Generally, manually curated type taxonomies such as Wikipedia categories are used. We introduce cluster-based mention typing, where named entities are clustered based on their contextual similarities and the cluster ids are assigned as types. The hyperlinked mentions and their context in Wikipedia are used in order to obtain these cluster-based types. Then, mention typing models are trained on these mentions, which have been labeled with their cluster-based types through distant supervision. At the named entity disambiguation phase, first the cluster-based types of a given mention are predicted and then, these types are used as features in a ranking model to select the best entity among the candidates. We represent entities at multiple contextual levels and obtain different clusterings (and thus typing models) based on each level. As each clustering breaks the entity space differently, mention typing based on each clustering discriminates the mention differently. When predictions from all typing models are used together, our system achieves better or comparable results based on randomization tests with respect to the state-of-the-art levels on four defacto test sets.

cs.CL↗

arXiv2021

Resources for Turkish Dependency Parsing: Introducing the BOUN Treebank and the BoAT Annotation Tool

In this paper, we introduce the resources that we developed for Turkish dependency parsing, which include a novel manually annotated treebank (BOUN Treebank), along with the guidelines we adopted, and a new annotation tool (BoAT). The manual annotation process we employed was shaped and implemented by a team of four linguists and five Natural Language Processing (NLP) specialists. Decisions regarding the annotation of the BOUN Treebank were made in line with the Universal Dependencies (UD) framework as well as our recent efforts for unifying the Turkish UD treebanks through manual re-annotation. To the best of our knowledge, BOUN Treebank is the largest Turkish treebank. It contains a total of 9,761 sentences from various topics including biographical texts, national newspapers, instructional texts, popular culture articles, and essays. In addition, we report the parsing results of a state-of-the-art dependency parser obtained over the BOUN Treebank as well as two other treebanks in Turkish. Our results demonstrate that the unification of the Turkish annotation scheme and the introduction of a more comprehensive treebank lead to improved performance with regard to dependency parsing.

cs.CL↗

arXiv2020

ChemBoost: A chemical language based approach for protein-ligand binding affinity prediction

Identification of high affinity drug-target interactions is a major research question in drug discovery. Proteins are generally represented by their structures or sequences. However, structures are available only for a small subset of biomolecules and sequence similarity is not always correlated with functional similarity. We propose ChemBoost, a chemical language based approach for affinity prediction using SMILES syntax. We hypothesize that SMILES is a codified language and ligands are documents composed of chemical words. These documents can be used to learn chemical word vectors that represent words in similar contexts with similar vectors. In ChemBoost, the ligands are represented via chemical word embeddings, while the proteins are represented through sequence-based features and/or chemical words of their ligands. Our aim is to process the patterns in SMILES as a language to predict protein-ligand affinity, even when we cannot infer the function from the sequence. We used eXtreme Gradient Boosting to predict protein-ligand affinities in KIBA and BindingDB data sets. ChemBoost was able to predict drug-target binding affinity as well as or better than state-of-the-art machine learning systems. When powered with ligand-centric representations, ChemBoost was more robust to the changes in protein sequence similarity and successfully captured the interactions between a protein and a ligand, even if the protein has low sequence similarity to the known targets of the ligand.

cs.LG↗