Search arXiv⌕ Search
Home/Archive/arXiv

arXiv · 2208.10228

Review of Natural Language Processing in Pharmacology

Dimitar Trajanov·Vangel Trajkovski·Makedonka Dimitrieva·Jovana Dobreva·Milos Jovanovik·Matej Klemen·Aleš Žagar·Marko Robnik-Šikonja
View original source ↗Read source document ↗Export metadata ↓

Abstract

Natural language processing (NLP) is an area of artificial intelligence that applies information technologies to process the human language, understand it to a certain degree, and use it in various applications. This area has rapidly developed in the last few years and now employs modern variants of deep neural networks to extract relevant patterns from large text corpora. The main objective of this work is to survey the recent use of NLP in the field of pharmacology. As our work shows, NLP is a highly relevant information extraction and processing approach for pharmacology. It has been used extensively, from intelligent searches through thousands of medical documents to finding traces of adversarial drug interactions in social media. We split our coverage into five categories to survey modern NLP methodology, commonly addressed tasks, relevant textual data, knowledge bases, and useful programming libraries. We split each of the five categories into appropriate subcategories, describe their main properties and ideas, and summarize them in a tabular form. The resulting survey presents a comprehensive overview of the area, useful to practitioners and interested observers.

Explore related subjects

cs.CLcs.LGq-bio.BM

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Dimitar Trajanov, Vangel Trajkovski, Makedonka Dimitrieva, Jovana Dobreva, Milos Jovanovik, Matej Klemen, Aleš Žagar, Marko Robnik-Šikonja. 2023-01-26. Review of Natural Language Processing in Pharmacology. https://doi.org/10.1124/pharmrev.122.000715

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related papers

arXiv2026

Hierarchical attention interpretation: an interpretable speech-level transformer for bi-modal depression detection

Depression is a common mental disorder. Automatic depression detection tools using speech, enabled by machine learning, help early screening of depression. This paper addresses two limitations that may hinder the clinical implementations of such tools: noise resulting from segment-level labelling and a lack of model interpretability. We propose a bi-modal speech-level transformer to avoid segment-level labelling and introduce a hierarchical interpretation approach to provide both speech-level and sentence-level interpretations, based on gradient-weighted attention maps derived from all attention layers to track interactions between input features. We show that the proposed model outperforms a model that learns at a segment level ($p$=0.854, $r$=0.947, $F1$=0.897 compared to $p$=0.732, $r$=0.808, $F1$=0.768). For model interpretation, using one true positive sample, we show which sentences within a given speech are most relevant to depression detection; and which text tokens and Mel-spectrogram regions within these sentences are most relevant to depression detection. These interpretations allow clinicians to verify the validity of predictions made by depression detection tools, promoting their clinical implementations.

cs.CL↗
arXiv2026

Cultural Alignment in Large Language Models Using Soft Prompt Tuning

Large Language Model (LLM) alignment is commonly achieved through supervised fine-tuning or reinforcement learning, both of which require labeled or preference data and update model weights. Without targeted cultural adaptation, however, deployed LLMs often exhibit culturally homogeneous behavior that fails to reflect diverse local values. Aligning models to cultural value frameworks such as Hofstede's Value Survey Module (VSM13) presents a distinct challenge: alignment signals are available only as aggregated survey-level scores computed after generating responses to an entire survey, providing no per-token gradient and requiring no preference data by construction. This makes standard gradient-based alignment methods ill-suited to the task. We propose a deployment-friendly approach that encodes cultural behavior in short, tunable soft prompts optimized with Differential Evolution (DE), while keeping model weights frozen and requiring no preference data. At inference, the system inserts the appropriate cultural-specific prompt to adapt model responses for different cultures. Experiments across four countries and four instruction-tuned models show that DE-optimized prompts generally reduce discrepancy with VSM13 reference profiles, improve rank agreement with the World Values Survey (WVS), an independent framework not seen during optimization, and are preferred in blinded pairwise evaluations using majority voting across three LLM judges.

cs.CL↗
arXiv2026

VQ-Logits: Compressing the Output Bottleneck of Large Language Models via Vector Quantized Logits

Large Language Models (LLMs) have achieved remarkable success but face significant computational and memory challenges, particularly due to their extensive output vocabularies. The final linear projection layer, mapping hidden states to vocabulary-sized logits, often constitutes a substantial portion of the model's parameters and computational cost during inference. Existing methods like adaptive softmax or hierarchical softmax introduce structural complexities. In this paper, we propose VQ-Logits, a novel approach that leverages Vector Quantization (VQ) to drastically reduce the parameter count and computational load of the LLM output layer. VQ-Logits replaces the large V * dmodel output embedding matrix with a small, shared codebook of K embedding vectors (K << V ). Each token in the vocabulary is mapped to one of these K codebook vectors. The LLM predicts logits over this compact codebook, which are then efficiently "scattered" to the full vocabulary space using the learned or preassigned mapping. We demonstrate through extensive experiments on standard language modeling benchmarks (e.g., WikiText-103, C4) that VQ-Logits can achieve up to 99% parameter reduction in the output layer and 6x speedup in logit computation, with only a marginal 4% increase in perplexity compared to full softmax baselines. We further provide detailed ablation studies on codebook size, initialization, and learning strategies, showcasing the robustness and effectiveness of our approach.

cs.CL↗