Neural Generative Models and the Parallel Architecture of Language: A Critical Review and Outlook.

According to the parallel architecture, syntactic and semantic information processing are two separate streams that interact selectively during language comprehension. While considerable effort is put into psycho- and neurolinguistics to understand the interchange of processing mechanisms in human comprehension, the nature of this interaction in recent neural Large Language Models remains elusive. In this article, we revisit influential linguistic and behavioral experiments and evaluate the ability of a large language model, GPT-3, to perform these tasks. The model can solve semantic tasks autonomously from syntactic realization in a manner that resembles human behavior. However, the outcomes present a complex and variegated picture, leaving open the question of how Language Models could learn structured conceptual representations.

Event Knowledge in Large Language Models: The Gap Between the Impossible and the Unlikely.

Word co-occurrence patterns in language corpora contain a surprising amount of conceptual knowledge. Large language models (LLMs), trained to predict words in context, leverage these patterns to achieve impressive performance on diverse semantic tasks requiring world knowledge. An important but understudied question about LLMs' semantic abilities is whether they acquire generalized knowledge of common events. Here, we test whether five pretrained LLMs (from 2018's BERT to 2023's MPT) assign a higher likelihood to plausible descriptions of agent-patient interactions than to minimally different implausible versions of the same event. Using three curated sets of minimal sentence pairs (total n = 1215), we found that pretrained LLMs possess substantial event knowledge, outperforming other distributional language models. In particular, they almost always assign a higher likelihood to possible versus impossible events (The teacher bought the laptop vs. The laptop bought the teacher). However, LLMs show less consistent preferences for likely versus unlikely events (The nanny tutored the boy vs. The boy tutored the nanny). In follow-up analyses, we show that (i) LLM scores are driven by both plausibility and surface-level sentence features, (ii) LLM scores generalize well across syntactic variants (active vs. passive constructions) but less well across semantic variants (synonymous sentences), (iii) some LLM errors mirror human judgment ambiguity, and (iv) sentence plausibility serves as an organizing dimension in internal LLM representations. Overall, our results show that important aspects of event knowledge naturally emerge from distributional linguistic patterns, but also highlight a gap between representations of possible/impossible and likely/unlikely events.

Towards AI-driven longevity research: An overview.

While in the past technology has mostly been utilized to store information about the structural configuration of proteins and molecules for research and medical purposes, Artificial Intelligence is nowadays able to learn from the existing data how to predict and model properties and interactions, revealing important knowledge about complex biological processes, such as aging. Modern technologies, moreover, can rely on a broader set of information, including those derived from the next-generation sequencing (e.g., proteomics, lipidomics, and other omics), to understand the interactions between human body and the external environment. This is especially relevant as external factors have been shown to have a key role in aging. As the field of computational systems biology keeps improving and new biomarkers of aging are being developed, artificial intelligence promises to become a major ally of aging research.

A study on surprisal and semantic relatedness for eye-tracking data prediction.

Previous research in computational linguistics dedicated a lot of effort to using language modeling and/or distributional semantic models to predict metrics extracted from eye-tracking data. However, it is not clear whether the two components have a distinct contribution, with recent studies claiming that surprisal scores estimated with large-scale, deep learning-based language models subsume the semantic relatedness component. In our study, we propose a regression experiment for estimating different eye-tracking metrics on two English corpora, contrasting the quality of the predictions with and without the surprisal and the relatedness components. Different types of relatedness scores derived from both static and contextual models have also been tested. Our results suggest that both components play a role in the prediction, with semantic relatedness surprisingly contributing also to the prediction of function words. Moreover, they show that when the metric is computed with the contextual embeddings of the BERT model, it is able to explain a higher amount of variance.

LitCovid ensemble learning for COVID-19 multi-label classification.

The Coronavirus Disease 2019 (COVID-19) pandemic has shifted the focus of research worldwide, and more than 10 000 new articles per month have concentrated on COVID-19-related topics. Considering this rapidly growing literature, the efficient and precise extraction of the main topics of COVID-19-relevant articles is of great importance. The manual curation of this information for biomedical literature is labor-intensive and time-consuming, and as such the procedure is insufficient and difficult to maintain. In response to these complications, the BioCreative VII community has proposed a challenging task, LitCovid Track, calling for a global effort to automatically extract semantic topics for COVID-19 literature. This article describes our work on the BioCreative VII LitCovid Track. We proposed the LitCovid Ensemble Learning (LCEL) method for the tasks and integrated multiple biomedical pretrained models to address the COVID-19 multi-label classification problem. Specifically, seven different transformer-based pretrained models were ensembled for the initialization and fine-tuning processes independently. To enhance the representation abilities of the deep neural models, diverse additional biomedical knowledge was utilized to facilitate the fruitfulness of the semantic expressions. Simple yet effective data augmentation was also leveraged to address the learning deficiency during the training phase. In addition, given the imbalanced label distribution of the challenging task, a novel asymmetric loss function was applied to the LCEL model, which explicitly adjusted the negative-positive importance by assigning different exponential decay factors and helped the model focus on the positive samples. After the training phase, an ensemble bagging strategy was adopted to merge the outputs from each model for final predictions. The experimental results show the effectiveness of our proposed approach, as LCEL obtains the state-of-the-art performance on the LitCovid dataset. Database URL: https://github.com/JHnlp/LCEL.

Increasing adverse drug events extraction robustness on social media: Case study on negation and speculation.

In the last decade, an increasing number of users have started reporting adverse drug events (ADEs) on social media platforms, blogs, and health forums. Given the large volume of reports, pharmacovigilance has focused on ways to use natural language processing (NLP) techniques to rapidly examine these large collections of text, detecting mentions of drug-related adverse reactions to trigger medical investigations. However, despite the growing interest in the task and the advances in NLP, the robustness of these models in face of linguistic phenomena such as negations and speculations is an open research question. Negations and speculations are pervasive phenomena in natural language and can severely hamper the ability of an automated system to discriminate between factual and non-factual statements in text. In this article, we take into consideration four state-of-the-art systems for ADE detection on social media texts. We introduce SNAX, a benchmark to test their performance against samples containing negated and speculated ADEs, showing their fragility against these phenomena. We then introduce two possible strategies to increase the robustness of these models, showing that both of them bring significant increases in performance, lowering the number of spurious entities predicted by the models by 60% for negation and 80% for speculations.

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.

The coronavirus disease 2019 (COVID-19) pandemic has been severely impacting global society since December 2019. The related findings such as vaccine and drug development have been reported in biomedical literature-at a rate of about 10 000 articles on COVID-19 per month. Such rapid growth significantly challenges manual curation and interpretation. For instance, LitCovid is a literature database of COVID-19-related articles in PubMed, which has accumulated more than 200 000 articles with millions of accesses each month by users worldwide. One primary curation task is to assign up to eight topics (e.g. Diagnosis and Treatment) to the articles in LitCovid. The annotated topics have been widely used for navigating the COVID literature, rapidly locating articles of interest and other downstream studies. However, annotating the topics has been the bottleneck of manual curation. Despite the continuing advances in biomedical text-mining methods, few have been dedicated to topic annotations in COVID-19 literature. To close the gap, we organized the BioCreative LitCovid track to call for a community effort to tackle automated topic annotation for COVID-19 literature. The BioCreative LitCovid dataset-consisting of over 30 000 articles with manually reviewed topics-was created for training and testing. It is one of the largest multi-label classification datasets in biomedical scientific literature. Nineteen teams worldwide participated and made 80 submissions in total. Most teams used hybrid systems based on transformers. The highest performing submissions achieved 0.8875, 0.9181 and 0.9394 for macro-F1-score, micro-F1-score and instance-based F1-score, respectively. Notably, these scores are substantially higher (e.g. 12%, higher for macro F1-score) than the corresponding scores of the state-of-art multi-label classification method. The level of participation and results demonstrate a successful track and help close the gap between dataset curation and method development. The dataset is publicly available via https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/ for benchmarking and further development. Database URL https://ftp.ncbi.nlm.nih.gov/pub/lu/LitCovid/biocreative/.

Monitoring User Opinions and Side Effects on COVID-19 Vaccines in the Twittersphere: Infodemiology Study of Tweets.

BACKGROUND: In the current phase of the COVID-19 pandemic, we are witnessing the most massive vaccine rollout in human history. Like any other drug, vaccines may cause unexpected side effects, which need to be investigated in a timely manner to minimize harm in the population. If not properly dealt with, side effects may also impact public trust in the vaccination campaigns carried out by national governments. OBJECTIVE: Monitoring social media for the early identification of side effects, and understanding the public opinion on the vaccines are of paramount importance to ensure a successful and harmless rollout. The objective of this study was to create a web portal to monitor the opinion of social media users on COVID-19 vaccines, which can offer a tool for journalists, scientists, and users alike to visualize how the general public is reacting to the vaccination campaign. METHODS: We developed a tool to analyze the public opinion on COVID-19 vaccines from Twitter, exploiting, among other techniques, a state-of-the-art system for the identification of adverse drug events on social media; natural language processing models for sentiment analysis; statistical tools; and open-source databases to visualize the trending hashtags, news articles, and their factuality. All modules of the system are displayed through an open web portal. RESULTS: A set of 650,000 tweets was collected and analyzed in an ongoing process that was initiated in December 2020. The results of the analysis are made public on a web portal (updated daily), together with the processing tools and data. The data provide insights on public opinion about the vaccines and its change over time. For example, users show a high tendency to only share news from reliable sources when discussing COVID-19 vaccines (98% of the shared URLs). The general sentiment of Twitter users toward the vaccines is negative/neutral; however, the system is able to record fluctuations in the attitude toward specific vaccines in correspondence with specific events (eg, news about new outbreaks). The data also show how news coverage had a high impact on the set of discussed topics. To further investigate this point, we performed a more in-depth analysis of the data regarding the AstraZeneca vaccine. We observed how media coverage of blood clot-related side effects suddenly shifted the topic of public discussions regarding both the AstraZeneca and other vaccines. This became particularly evident when visualizing the most frequently discussed symptoms for the vaccines and comparing them month by month. CONCLUSIONS: We present a tool connected with a web portal to monitor and display some key aspects of the public's reaction to COVID-19 vaccines. The system also provides an overview of the opinions of the Twittersphere through graphic representations, offering a tool for the extraction of suspected adverse events from tweets with a deep learning model.

Artificial Intelligence-Aided Precision Medicine for COVID-19: Strategic Areas of Research and Development.

Artificial intelligence (AI) technologies can play a key role in preventing, detecting, and monitoring epidemics. In this paper, we provide an overview of the recently published literature on the COVID-19 pandemic in four strategic areas: (1) triage, diagnosis, and risk prediction; (2) drug repurposing and development; (3) pharmacogenomics and vaccines; and (4) mining of the medical literature. We highlight how AI-powered health care can enable public health systems to efficiently handle future outbreaks and improve patient outcomes.