Biology subjects

Clifton, D. A.

Publications and source records attributed to Clifton, D. A..

3 recordsLinked to original sources

bioRxiv2026

MedMisBench: Measuring Epistemic Resilience of LLMs Under Misleading Medical Context

Large language models (LLMs) now reach expert-level scores on medical licensing exams, encouraging the assumption that high scores imply safe medical judgment while patients increasingly use them for health advice. We show this assumption is fragile: when misleading context is injected into questions that LLMs originally answer correctly, they abandon the correct answer. We call the ability to maintain correct judgment under adversarial context epistemic resilience, and introduce MedMisBench to measure it. MedMisBench contains 10,932 medical question items and 48,889 misleading context-option pairs spanning medical reasoning, agentic capability, and patient-journey evaluation. Across 11 model configurations, mean accuracy falls from 71.1% on original questions to 38.0% under focused misleading context, with 51.5% attack success. The most damaging injections are formal, rule-like fabrications: authority-framed falsehoods reach 69.5% attack success and exception-poisoning claims reach 64.1%. A 14-member clinical panel from 7 countries identified serious potential harm in 38.2% of reviewed cases. MedMisBench exposes a structural blind spot in LLM evaluation in medical settings: existing benchmarks measure what models know, but not whether they preserve correct medical judgment under misleading context.1

bioengineering↗

bioRxiv2022

ProSelfLC: Progressive Self Label Correction Towards A Low-Temperature Entropy State

To train robust deep neural networks (DNNs), we systematically study several target modification approaches, which include output regularisation, self and non-self label correction (LC). Three key issues are discovered: (1) Self LC is the most appealing as it exploits its own knowledge and requires no extra models. However, how to automatically decide the trust degree of a learner as training goes is not well answered in the literature. (2) Some methods penalise while the others reward low-entropy predictions, prompting us to ask which one is better. (3) Using the standard training setting, a trained network is of low confidence when severe noise exists, making it hard to leverage its high-entropy self knowledge. To resolve the issue (1), taking two well-accepted propositions-deep neural networks learn meaningful patterns before fitting noise and minimum entropy regularisation principle-we propose a novel end-to-end method named ProSelfLC, which is designed according to learning time and entropy. Specifically, given a data point, we progressively increase trust in its predicted label distribution versus its annotated one if a model has been trained for enough time and the prediction is of low entropy (high confidence). For the issue (2), according to ProSelfLC, we empirically prove that it is better to redefine a meaningful low-entropy status and optimise the learner toward it. This serves as a defence of entropy minimisation. To address the issue (3), we decrease the entropy of self knowledge using a low temperature before exploiting it to correct labels, so that the revised labels redefine a low-entropy target state. We demonstrate the effectiveness of ProSelfLC through extensive experiments in both clean and noisy settings, and on both image and protein datasets. Furthermore, our source code is available at https://github.com/XinshaoAmosWang/ProSelfLC-AT.

bioinformatics↗

bioRxiv2021

Machine learning to predict the source of campylobacteriosis using whole genome data

Campylobacteriosis is among the worlds most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using machine learning. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential. Author summaryC. jejuni are the most common cause of food-borne bacterial gastroenteritis but the relative contribution of different sources are incompletely understood. We traced the origin of human C. jejuni infections using machine learning algorithms that compare the DNA sequences of bacteria sampled from infected people, contaminated chickens, cattle, sheep, wild birds and the environment. This approach achieved improvement in accuracy of source attribution by 33% over existing methods that use only a subset of genes within the genome and provided evidence for the relative contribution of different infection sources. Sometimes even very similar bacteria showed differences, demonstrating the value of basing analyses on the entire genome when developing this algorithm that can be used for understanding the global epidemiology and other important bacterial infections.

bioinformatics↗