In recent years, there has been a surge in the publication of clinical trial reports, making it challenging to conduct systematic reviews. Automatically extracting Population, Intervention, Comparator, and Outcome (PICO) from clinical trial studies can alleviate the traditionally time-consuming process of manually scrutinizing systematic reviews. Existing approaches of PICO frame extraction involves supervised approach that relies on the existence of manually annotated data points in the form of BIO label tagging. Recent approaches, such as In-Context Learning (ICL), which has been shown to be effective for a number of downstream NLP tasks, require the use of labeled examples. In this work, we adopt ICL strategy by employing the pretrained knowledge of Large Language Models (LLMs), gathered during the pretraining phase of an LLM, to automatically extract the PICO-related terminologies from clinical trial documents in unsupervised set up to bypass the availability of large number of annotated data instances. Additionally, to showcase the highest effectiveness of LLM in oracle scenario where large number of annotated samples are available, we adopt the instruction tuning strategy by employing Low Rank Adaptation (LORA) to conduct the training of gigantic model in low resource environment for the PICO frame extraction task. Our empirical results show that our proposed ICL-based framework produces comparable results on all the version of EBM-NLP datasets and the proposed instruction tuned version of our framework produces state-of-the-art results on all the different EBM-NLP datasets. Our project is available at \url{https://github.com/shrimonmuke0202/AlpaPICO.git}.
Plain language summarization with LLMs can be useful for improving textual accessibility of technical content. But how factual are these summaries in a high-stakes domain like medicine? This paper presents FactPICO, a factuality benchmark for plain language summarization of medical texts describing randomized controlled trials (RCTs), which are the basis of evidence-based medicine and can directly inform patient treatment. FactPICO consists of 345 plain language summaries of RCT abstracts generated from three LLMs (i.e., GPT-4, Llama-2, and Alpaca), with fine-grained evaluation and natural language rationales from experts. We assess the factuality of critical elements of RCTs in those summaries: Populations, Interventions, Comparators, Outcomes (PICO), as well as the reported findings concerning these. We also evaluate the correctness of the extra information (e.g., explanations) added by LLMs. Using FactPICO, we benchmark a range of existing factuality metrics, including the newly devised ones based on LLMs. We find that plain language summarization of medical evidence is still challenging, especially when balancing between simplicity and factuality, and that existing metrics correlate poorly with expert judgments on the instance level.
Existing large language models (LLMs) evaluation methods typically focus on testing the performance on some closed-environment and domain-specific benchmarks with human annotations. In this paper, we explore a novel unsupervised evaluation direction, utilizing peer-review mechanisms to measure LLMs automatically. In this setting, both open-source and closed-source LLMs lie in the same environment, capable of answering unlabeled questions and evaluating each other, where each LLM's response score is jointly determined by other anonymous ones. To obtain the ability hierarchy among these models, we assign each LLM a learnable capability parameter to adjust the final ranking. We formalize it as a constrained optimization problem, intending to maximize the consistency of each LLM's capabilities and scores. The key assumption behind is that high-level LLM can evaluate others' answers more accurately than low-level ones, while higher-level LLM can also achieve higher response scores. Moreover, we propose three metrics called PEN, CIN, and LIS to evaluate the gap in aligning human rankings. We perform experiments on multiple datasets with these metrics, validating the effectiveness of the proposed approach.
Medical systematic reviews can be very costly and resource intensive. We explore how Large Language Models (LLMs) can support and be trained to perform literature screening when provided with a detailed set of selection criteria. Specifically, we instruction tune LLaMA and Guanaco models to perform abstract screening for medical systematic reviews. Our best model, Bio-SIEVE, outperforms both ChatGPT and trained traditional approaches, and generalises better across medical domains. However, there remains the challenge of adapting the model to safety-first scenarios. We also explore the impact of multi-task training with Bio-SIEVE-Multi, including tasks such as PICO extraction and exclusion reasoning, but find that it is unable to match single-task Bio-SIEVE's performance. We see Bio-SIEVE as an important step towards specialising LLMs for the biomedical systematic review process and explore its future developmental opportunities. We release our models, code and a list of DOIs to reconstruct our dataset for reproducibility.
Under partial-label learning (PLL) where, for each training instance, only a set of ambiguous candidate labels containing the unknown true label is accessible, contrastive learning has recently boosted the performance of PLL on vision tasks, attributed to representations learned by contrasting the same/different classes of entities. Without access to true labels, positive points are predicted using pseudo-labels that are inherently noisy, and negative points often require large batches or momentum encoders, resulting in unreliable similarity information and a high computational overhead. In this paper, we rethink a state-of-the-art contrastive PLL method PiCO[24], inspiring the design of a simple framework termed PaPi (Partial-label learning with a guided Prototypical classifier), which demonstrates significant scope for improvement in representation learning, thus contributing to label disambiguation. PaPi guides the optimization of a prototypical classifier by a linear classifier with which they share the same feature encoder, thus explicitly encouraging the representation to reflect visual similarity between categories. It is also technically appealing, as PaPi requires only a few components in PiCO with the opposite direction of guidance, and directly eliminates the contrastive learning module that would introduce noise and consume computational resources. We empirically demonstrate that PaPi significantly outperforms other PLL methods on various image classification tasks.
Single-Photon Avalanche Detector (SPAD) arrays are a rapidly emerging technology. These multi-pixel sensors have single-photon sensitivities and pico-second temporal resolutions thus they can rapidly generate depth images with millimeter precision. Such sensors are a key enabling technology for future autonomous systems as they provide guidance and situational awareness. However, to fully exploit the capabilities of SPAD array sensors, it is crucial to establish the quality of depth images they are able to generate in a wide range of scenarios. Given a particular optical system and a finite image acquisition time, what is the best-case depth resolution and what are realistic images generated by SPAD arrays? In this work, we establish a robust yet simple numerical procedure that rapidly establishes the fundamental limits to depth imaging with SPAD arrays under real world conditions. Our approach accurately generates realistic depth images in a wide range of scenarios, allowing the performance of an optical depth imaging system to be established without the need for costly and laborious field testing. This procedure has applications in object detection and tracking for autonomous systems and could be easily extended to systems for underwater imaging or for imaging around corners.
Language model (LM) pretraining can learn various knowledge from text corpora, helping downstream tasks. However, existing methods such as BERT model a single document, and do not capture dependencies or knowledge that span across documents. In this work, we propose LinkBERT, an LM pretraining method that leverages links between documents, e.g., hyperlinks. Given a text corpus, we view it as a graph of documents and create LM inputs by placing linked documents in the same context. We then pretrain the LM with two joint self-supervised objectives: masked language modeling and our new proposal, document relation prediction. We show that LinkBERT outperforms BERT on various downstream tasks across two domains: the general domain (pretrained on Wikipedia with hyperlinks) and biomedical domain (pretrained on PubMed with citation links). LinkBERT is especially effective for multi-hop reasoning and few-shot QA (+5% absolute improvement on HotpotQA and TriviaQA), and our biomedical LinkBERT sets new states of the art on various BioNLP tasks (+7% on BioASQ and USMLE). We release our pretrained models, LinkBERT and BioLinkBERT, as well as code and data at https://github.com/michiyasunaga/LinkBERT.
The accuracy of tinyML applications is often affected by various environmental factors, such as noises, location/calibration of sensors, and time-related changes. This article introduces a neural network based on-device learning (ODL) approach to address this issue by retraining in deployed environments. Our approach relies on semi-supervised sequential training of multiple neural networks tailored for low-end edge devices. This article introduces its algorithm and implementation on wireless sensor nodes consisting of a Raspberry Pi Pico and low-power wireless module. Experiments using vibration patterns of rotating machines demonstrate that retraining by ODL improves anomaly detection accuracy compared with a prediction-only deep neural network in a noisy environment. The results also show that the ODL approach can save communication cost and energy consumption for battery-powered Internet of Things devices.
Multi-agent pathfinding (MAPF) has been widely used to solve large-scale real-world problems, e.g., automation warehouses. The learning-based, fully decentralized framework has been introduced to alleviate real-time problems and simultaneously pursue optimal planning policy. However, existing methods might generate significantly more vertex conflicts (or collisions), which lead to a low success rate or more makespan. In this paper, we propose a PrIoritized COmmunication learning method (PICO), which incorporates the \textit{implicit} planning priorities into the communication topology within the decentralized multi-agent reinforcement learning framework. Assembling with the classic coupled planners, the implicit priority learning module can be utilized to form the dynamic communication topology, which also builds an effective collision-avoiding mechanism. PICO performs significantly better in large-scale MAPF tasks in success rates and collision rates than state-of-the-art learning-based planners.
Partial label learning (PLL) is an important problem that allows each training example to be labeled with a coarse candidate set, which well suits many real-world data annotation scenarios with label ambiguity. Despite the promise, the performance of PLL often lags behind the supervised counterpart. In this work, we bridge the gap by addressing two key research challenges in PLL -- representation learning and label disambiguation -- in one coherent framework. Specifically, our proposed framework PiCO consists of a contrastive learning module along with a novel class prototype-based label disambiguation algorithm. PiCO produces closely aligned representations for examples from the same classes and facilitates label disambiguation. Theoretically, we show that these two components are mutually beneficial, and can be rigorously justified from an expectation-maximization (EM) algorithm perspective. Moreover, we study a challenging yet practical noisy partial label learning setup, where the ground-truth may not be included in the candidate set. To remedy this problem, we present an extension PiCO+ that performs distance-based clean sample selection and learns robust classifiers by a semi-supervised contrastive learning algorithm. Extensive experiments demonstrate that our proposed methods significantly outperform the current state-of-the-art approaches in standard and noisy PLL tasks and even achieve comparable results to fully supervised learning.
Annotation quality and quantity positively affect the learning performance of sequence labeling, a vital task in Natural Language Processing. Hiring domain experts to annotate a corpus is very costly in terms of money and time. Crowdsourcing platforms, such as Amazon Mechanical Turk (AMT), have been deployed to assist in this purpose. However, the annotations collected this way are prone to human errors due to the lack of expertise of the crowd workers. Existing literature in annotation aggregation assumes that annotations are independent and thus faces challenges when handling the sequential label aggregation tasks with complex dependencies. To conquer the challenges, we propose an optimization-based method that infers the ground truth labels using annotations provided by workers for sequential labeling tasks. The proposed Aggregation method for Sequential Labels from Crowds ($AggSLC$) jointly considers the characteristics of sequential labeling tasks, workers' reliabilities, and advanced machine learning techniques. Theoretical analysis on the algorithm's convergence further demonstrates that the proposed $AggSLC$ halts after a finite number of iterations. We evaluate $AggSLC$ on different crowdsourced datasets for Named Entity Recognition (NER) tasks and Information Extraction tasks in biomedical (PICO), as well as a simulated dataset. Our results show that the proposed method outperforms the state-of-the-art aggregation methods. To achieve insights into the framework, we study the effectiveness of $AggSLC$'s components through ablation studies.
The rapid growth in published clinical trials makes it difficult to maintain up-to-date systematic reviews, which requires finding all relevant trials. This leads to policy and practice decisions based on out-of-date, incomplete, and biased subsets of available clinical evidence. Extracting and then normalising Population, Intervention, Comparator, and Outcome (PICO) information from clinical trial articles may be an effective way to automatically assign trials to systematic reviews and avoid searching and screening - the two most time-consuming systematic review processes. We propose and test a novel approach to PICO span detection. The major difference between our proposed method and previous approaches comes from detecting spans without needing annotated span data and using only crowdsourced sentence-level annotations. Experiments on two datasets show that PICO span detection results achieve much higher results for recall when compared to fully supervised methods with PICO sentence detection at least as good as human annotations. By removing the reliance on expert annotations for span detection, this work could be used in human-machine pipeline for turning low-quality crowdsourced, and sentence-level PICO annotations into structured information that can be used to quickly assign trials to relevant systematic reviews.
Clinical trials provide essential guidance for practicing Evidence-Based Medicine, though often accompanying with unendurable costs and risks. To optimize the design of clinical trials, we introduce a novel Clinical Trial Result Prediction (CTRP) task. In the CTRP framework, a model takes a PICO-formatted clinical trial proposal with its background as input and predicts the result, i.e. how the Intervention group compares with the Comparison group in terms of the measured Outcome in the studied Population. While structured clinical evidence is prohibitively expensive for manual collection, we exploit large-scale unstructured sentences from medical literature that implicitly contain PICOs and results as evidence. Specifically, we pre-train a model to predict the disentangled results from such implicit evidence and fine-tune the model with limited data on the downstream datasets. Experiments on the benchmark Evidence Integration dataset show that the proposed model outperforms the baselines by large margins, e.g., with a 10.7% relative gain over BioBERT in macro-F1. Moreover, the performance improvement is also validated on another dataset composed of clinical trials related to COVID-19.
This research on data extraction methods applies recent advances in natural language processing to evidence synthesis based on medical texts. Texts of interest include abstracts of clinical trials in English and in multilingual contexts. The main focus is on information characterized via the Population, Intervention, Comparator, and Outcome (PICO) framework, but data extraction is not limited to these fields. Recent neural network architectures based on transformers show capacities for transfer learning and increased performance on downstream natural language processing tasks such as universal reading comprehension, brought forward by this architecture's use of contextualized word embeddings and self-attention mechanisms. This paper contributes to solving problems related to ambiguity in PICO sentence prediction tasks, as well as highlighting how annotations for training named entity recognition systems are used to train a high-performing, but nevertheless flexible architecture for question answering in systematic review automation. Additionally, it demonstrates how the problem of insufficient amounts of training annotations for PICO entity extraction is tackled by augmentation. All models in this paper were created with the aim to support systematic review (semi)automation. They achieve high F1 scores, and demonstrate the feasibility of applying transformer-based classification methods to support data mining in the biomedical literature.
Biomedical text tagging systems are plagued by the dearth of labeled training data. There have been recent attempts at using pre-trained encoders to deal with this issue. Pre-trained encoder provides representation of the input text which is then fed to task-specific layers for classification. The entire network is fine-tuned on the labeled data from the target task. Unfortunately, a low-resource biomedical task often has too few labeled instances for satisfactory fine-tuning. Also, if the label space is large, it contains few or no labeled instances for majority of the labels. Most biomedical tagging systems treat labels as indexes, ignoring the fact that these labels are often concepts expressed in natural language e.g. `Appearance of lesion on brain imaging'. To address these issues, we propose constructing extra labeled instances using label-text (i.e. label's name) as input for the corresponding label-index (i.e. label's index). In fact, we propose a number of strategies for manufacturing multiple artificial labeled instances from a single label. The network is then fine-tuned on a combination of real and these newly constructed artificial labeled instances. We evaluate the proposed approach on an important low-resource biomedical task called \textit{PICO annotation}, which requires tagging raw text describing clinical trials with labels corresponding to different aspects of the trial i.e. PICO (Population, Intervention/Control, Outcome) characteristics of the trial. Our empirical results show that the proposed method achieves a new state-of-the-art performance for PICO annotation with very significant improvements over competitive baselines.
In evidence-based medicine (EBM), defining a clinical question in terms of the specific patient problem aids the physicians to efficiently identify appropriate resources and search for the best available evidence for medical treatment. In order to formulate a well-defined, focused clinical question, a framework called PICO is widely used, which identifies the sentences in a given medical text that belong to the four components typically reported in clinical trials: Participants/Problem (P), Intervention (I), Comparison (C) and Outcome (O). In this work, we propose a novel deep learning model for recognizing PICO elements in biomedical abstracts. Based on the previous state-of-the-art bidirectional long-short term memory (biLSTM) plus conditional random field (CRF) architecture, we add another layer of biLSTM upon the sentence representation vectors so that the contextual information from surrounding sentences can be gathered to help infer the interpretation of the current one. In addition, we propose two methods to further generalize and improve the model: adversarial training and unsupervised pre-training over large corpora. We tested our proposed approach over two benchmark datasets. One is the PubMed-PICO dataset, where our best results outperform the previous best by 5.5%, 7.9%, and 5.8% for P, I, and O elements in terms of F1 score, respectively. And for the other dataset named NICTA-PIBOSO, the improvements for P/I/O elements are 2.4%, 13.6%, and 1.0% in F1 score, respectively. Overall, our proposed deep learning model can obtain unprecedented PICO element detection accuracy while avoiding the need for any manual feature selection.
We describe a method for visual object detection based on an ensemble of optimized decision trees organized in a cascade of rejectors. The trees use pixel intensity comparisons in their internal nodes and this makes them able to process image regions very fast. Experimental analysis is provided through a face detection problem. The obtained results are encouraging and demonstrate that the method has practical value. Additionally, we analyse its sensitivity to noise and show how to perform fast rotation invariant object detection. Complete source code is provided at https://github.com/nenadmarkus/pico.
We propose a method for downlink coordinated multipoint (DL CoMP) in heterogeneous fifth generation New Radio (NR) networks. The primary contribution of our paper is an algorithm to enhance the trigger of DL CoMP using online machine learning. We use support vector machine (SVM) classifiers to enhance the user downlink throughput in a realistic frequency division duplex network environment. Our simulation results show improvement in both the macro and pico base station downlink throughputs due to the informed triggering of the multiple radio streams as learned by the SVM classifier.