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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.

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., Comment: 43 pages, 14 figures

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., Comment: 16 pages, 11 figures, new computational analysis and extended case studies

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, Comment: 12 pages, to appear in Bioinformatics

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., Comment: This is a peer reviewed article that has been presented in The International Conference on Agglutinative Language Technologies as a challenge of Natural Language Processing (ALTNLP) 2022

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., Comment: 24 pages, 11 figures, 7 tables

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.

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., Comment: 46 pages, 11 figures, 14 tables

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., Comment: EMNLP 2021

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.

Relation classification is one of the key topics in information extraction, which can be used to construct knowledge bases or to provide useful information for question answering. Current approaches for relation classification are mainly focused on the English language and require lots of training data with human annotations. Creating and annotating a large amount of training data for low-resource languages is impractical and expensive. To overcome this issue, we propose two cross-lingual relation classification models: a baseline model based on Multilingual BERT and a new multilingual pretraining setup, which significantly improves the baseline with distant supervision. For evaluation, we introduce a new public benchmark dataset for cross-lingual relation classification in English, French, German, Spanish, and Turkish, called RELX. We also provide the RELX-Distant dataset, which includes hundreds of thousands of sentences with relations from Wikipedia and Wikidata collected by distant supervision for these languages. Our code and data are available at: https://github.com/boun-tabi/RELX, Comment: Findings of EMNLP 2020

Coronavirus Disease of 2019 (COVID-19) created dire consequences globally and triggered an intense scientific effort from different domains. The resulting publications created a huge text collection in which finding the studies related to a biomolecule of interest is challenging for general purpose search engines because the publications are rich in domain specific terminology. Here, we present Vapur: an online COVID-19 search engine specifically designed to find related protein - chemical pairs. Vapur is empowered with a relation-oriented inverted index that is able to retrieve and group studies for a query biomolecule with respect to its related entities. The inverted index of Vapur is automatically created with a BioNLP pipeline and integrated with an online user interface. The online interface is designed for the smooth traversal of the current literature by domain researchers and is publicly available at https://tabilab.cmpe.boun.edu.tr/vapur/ ., Comment: EMNLP 2020 - COVID-19 Workshop

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., Comment: Language Resource and Evaluation

Fully data-driven, deep learning-based models are usually designed as language-independent and have been shown to be successful for many natural language processing tasks. However, when the studied language is low-resourced and the amount of training data is insufficient, these models can benefit from the integration of natural language grammar-based information. We propose two approaches to dependency parsing especially for languages with restricted amount of training data. Our first approach combines a state-of-the-art deep learning-based parser with a rule-based approach and the second one incorporates morphological information into the parser. In the rule-based approach, the parsing decisions made by the rules are encoded and concatenated with the vector representations of the input words as additional information to the deep network. The morphology-based approach proposes different methods to include the morphological structure of words into the parser network. Experiments are conducted on the IMST-UD Treebank and the results suggest that integration of explicit knowledge about the target language to a neural parser through a rule-based parsing system and morphological analysis leads to more accurate annotations and hence, increases the parsing performance in terms of attachment scores. The proposed methods are developed for Turkish, but can be adapted to other languages as well., Comment: 25 pages, 7 figures

Text-based representations of chemicals and proteins can be thought of as unstructured languages codified by humans to describe domain-specific knowledge. Advances in natural language processing (NLP) methodologies in the processing of spoken languages accelerated the application of NLP to elucidate hidden knowledge in textual representations of these biochemical entities and then use it to construct models to predict molecular properties or to design novel molecules. This review outlines the impact made by these advances on drug discovery and aims to further the dialogue between medicinal chemists and computer scientists.

Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence information to predict binding affinity. Results: WideDTA uses four text-based information sources, namely the protein sequence, ligand SMILES, protein domains and motifs, and maximum common substructure words to predict binding affinity. WideDTA outperformed one of the state of the art deep learning methods for drug-target binding affinity prediction, DeepDTA on the KIBA dataset with a statistical significance. This indicates that the word-based sequence representation adapted by WideDTA is a promising alternative to the character-based sequence representation approach in deep learning models for binding affinity prediction, such as the one used in DeepDTA. In addition, the results showed that, given the protein sequence and ligand SMILES, the inclusion of protein domain and motif information as well as ligand maximum common substructure words do not provide additional useful information for the deep learning model. Interestingly, however, using only domain and motif information to represent proteins achieved similar performance to using the full protein sequence, suggesting that important binding relevant information is contained within the protein motifs and domains.

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., Comment: Molecular Informatics

Recently, due to the increasing popularity of social media, the necessity for extracting information from informal text types, such as microblog texts, has gained significant attention. In this study, we focused on the Named Entity Recognition (NER) problem on informal text types for Turkish. We utilized a semi-supervised learning approach based on neural networks. We applied a fast unsupervised method for learning continuous representations of words in vector space. We made use of these obtained word embeddings, together with language independent features that are engineered to work better on informal text types, for generating a Turkish NER system on microblog texts. We evaluated our Turkish NER system on Twitter messages and achieved better F-score performances than the published results of previously proposed NER systems on Turkish tweets. Since we did not employ any language dependent features, we believe that our method can be easily adapted to microblog texts in other morphologically rich languages., Comment: Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016)

The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand based approach can be utilized in protein representation. In this study, we propose SMILESVec, a SMILES-based method to represent ligands and a novel method to compute similarity of proteins by describing them based on their ligands. The proteins are defined utilizing the word-embeddings of the SMILES strings of their ligands. The performance of the proposed protein description method is evaluated in protein clustering task using TransClust and MCL algorithms. Two other protein representation methods that utilize protein sequence, BLAST and ProtVec, and two compound fingerprint based protein representation methods are compared. We showed that ligand-based protein representation, which uses only SMILES strings of the ligands that proteins bind to, performs as well as protein-sequence based representation methods in protein clustering. The results suggest that ligand-based protein description can be an alternative to the traditional sequence or structure based representation of proteins and this novel approach can be applied to different bioinformatics problems such as prediction of new protein-ligand interactions and protein function annotation.

The identification of novel drug-target (DT) interactions is a substantial part of the drug discovery process. Most of the computational methods that have been proposed to predict DT interactions have focused on binary classification, where the goal is to determine whether a DT pair interacts or not. However, protein-ligand interactions assume a continuum of binding strength values, also called binding affinity and predicting this value still remains a challenge. The increase in the affinity data available in DT knowledge-bases allows the use of advanced learning techniques such as deep learning architectures in the prediction of binding affinities. In this study, we propose a deep-learning based model that uses only sequence information of both targets and drugs to predict DT interaction binding affinities. The few studies that focus on DT binding affinity prediction use either 3D structures of protein-ligand complexes or 2D features of compounds. One novel approach used in this work is the modeling of protein sequences and compound 1D representations with convolutional neural networks (CNNs). The results show that the proposed deep learning based model that uses the 1D representations of targets and drugs is an effective approach for drug target binding affinity prediction. The model in which high-level representations of a drug and a target are constructed via CNNs achieved the best Concordance Index (CI) performance in one of our larger benchmark data sets, outperforming the KronRLS algorithm and SimBoost, a state-of-the-art method for DT binding affinity prediction., Comment: extended version