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Bruce A. Bassett

Publications and source records attributed to Bruce A. Bassett.

At least 19 recordsLinked to original sources

Can LLMs Accurately Score Medical Diagnoses and Clinical Reasoning?

Evaluating medical AI systems using expert clinician panels is costly and slow, motivating the use of large language models (LLMs) as alternative adjudicators. Here, we evaluate an LLM Jury, composed of three frontier AI models, for scoring 3334 diagnoses on 300 real-world low- and middle-income country (LMIC) hospital cases. Both LLM- and clinician-generated diagnoses are scored against expert panel diagnoses across four dimensions: diagnosis, differential diagnosis, clinical reasoning, and negative treatment risk. The LLM Jury scores are compared with expert and independent re-scoring panel scores to assess error metrics, inter-rater agreement, severe-risk errors, and the effect of post hoc calibration using isotonic regression. In our data, we find that: (i) the uncalibrated LLM Jury scores preserve ordinal agreement with the expert clinician panel scores, but are systematically lower; (ii) the probability of severe-risk errors is lower for the LLM Jury than the human expert re-score panels; (iii) the LLM Jury combined with LLM diagnoses can be used to identify diagnoses at high risk of error, enabling targeted expert review and improved panel efficiency; (iv) the calibrated LLM Jury scores and rankings of diagnosing agents show excellent agreement with those of the primary expert panels; (v) LLM Jury models show no self-preference bias, they did not score diagnoses generated by their own underlying model or models from the same vendor more (or less) favourably than those generated by other models. Together, these results provide evidence that a calibrated LLM Jury is a trustworthy and reliable proxy for expert clinician evaluation in medical AI benchmarking. Confirming these findings in other clinical settings is an important direction for future work.

cs.LG↗

TABASCAL: Removing multi-satellite interference from radio interferometry observations

In the first trajectory-based radio frequency interference (RFI) subtraction and calibration (TABASCAL) paper, we showed how to calibrate radio interferometers in the presence of RFI sources by simultaneously isolating the trajectories and signals of the RFI sources. In this paper, we show that we can accurately remove RFI (i.e. recover the astronomical signal) from simulated MeerKAT radio interferometry target data. We are able to do so for a single frequency channel, corrupted by up to nine simultaneous satellites, with average RFI amplitudes varying from weak to very strong (1-1000 Jy). Additionally, TABASCAL also manages to leverage the signal-to-noise ratio (S/N) of the RFI to phase-calibrate the astronomical signal. TABASCAL, effectively performs a suitably phased up fringe filter for each RFI source, which essentially allows for an ideal removal of RFI across all RFI strengths. As a result, TABASCAL is able to reach image noises equivalent to the uncorrupted, no-RFI, case. For larger RFI amplitudes, the resulting image noise is 10x - 100x smaller than those from traditional RFI flagging methods such as AOFLAGGER. As a specific application, we show that point-source science with TABASCAL almost matches the no-RFI case with near perfect completeness for all RFI amplitudes. In contrast, the completeness of AOFLAGGER and idealised $3σ$ flagging drops below 40% for strong RFI amplitudes, where recovered flux errors are approximately 10x - 100x worse than those from TABASCAL. Finally, we note that TABASCAL works for astronomical sources with both static and varying fluxes.

astro-ph.IM↗

Artificial Intelligence Can Match Domain Experts in Evidence Extraction and Critical Appraisal of Microbial Oncogenesis Research Publications

Confirmed oncogenic microbes contribute significantly to cancer burden. Identifying novel microbial oncogenicity could yield strategies that will reduce disease burdens. However, relevant evidence is dispersed and infeasible for humans to comprehensively synthesize. LLMs may enable scalable, expert-level systematic evidence synthesis to identify microbe-cancer pairs; however, such capabilities have not yet been demonstrated. Domain experts were recruited to create a dataset to benchmark LLM performance (Gemini 2.5 Pro, Gemini 2.5 Flash, GPT-5, GPT-5 Nano) on 24 research papers using MMTV-LV and breast cancer as a case study. We devised a structured template for evidence extraction and appraisal, consisting of MCQ, Likert-scale, multi-select, and free-text question types (77 items across 24 papers). Agreement between (1) experts and (2) experts and each LLM was determined per question instance using novel metrics. LLMs were assessed by comparing inter-expert and expert-LLM agreement distributions to determine whether LLMs behaved as additional experts by increasing or maintaining inter-expert agreement. Free-text responses were further evaluated qualitatively. Across all question types, LLM responses aligned closely with experts, with GPT-5 and GPT-5 Nano achieving score distributions indistinguishable from experts. Gemini models behaved similarly but were significantly more lenient in applying microbial oncogenesis criteria. Hallucinations were rare. Methodological appraisal and identification of contradictions within full-texts were the most persistent LLM vulnerabilities. GPT-5 and GPT-5 Nano were indistinguishable from experts on structured domain research paper evaluation tasks. This supports use of LLMs for automated systematic evidence synthesis. However, methodological appraisal tasks and contradiction identification in full-texts remain weaknesses requiring strengthening.

q-bio.QM↗

Interoceptive Attention as Dynamic Homeostatic Prioritization in a Foraging Agent

Biological systems must regulate competing needs under limited perceptual bandwidth, where sharpening one estimate costs the capacity to sharpen the others. Any fixed-budget system therefore has to decide where to allocate its perceptual precision. We study this in a foraging agent that must keep several bodily needs satisfied to survive, modelled with active inference. At each step it reads its own body-state beliefs, identifies the most-needed channel, and reallocates a fixed budget of interoceptive precision toward it, so that the same precision-shaped likelihood feeds both belief update and planning. In AffectWorld, a four-channel foraging gridworld, this selective allocation more than doubles learning-phase survival at matched budget against a uniform-precision agent ($0.414$ vs $0.199$ across 11 layouts, $n{=}32$ seeds each, paired cluster-bootstrap $p \leq 10^{-4}$). Two further results sharpen the mechanism. The benefit runs through planning as well as perception, since denying the shaped likelihood to the planner alone removes about half of it. It is also need-aligned, since aiming precision at the least-needed channel does worse than spreading it evenly. The attended channel additionally learns its own dynamics about twice as fast, and stays ahead even at matched observation count, a behavioural trace of the same precision routing, visible in learning speed, not survival.

cs.AI↗

"Perfect" spectra for ESO's HARPS spectrograph

HARPERFECT is the first application of "spectral perfectionism" to a high-resolution echelle spectrograph, reconstructing 1D spectra from 2D detector data via a forward model built on a calibration matrix consisting of point-spread function (PSF) shape, wavelength, and order trace, which were built entirely from laser frequency comb (LFC) observations. HARPS cannot resolve individual LFC lines, so each of 21 148 identified lines directly samples the PSF. We modelled these with a bivariate Gaussian, determining the PSF shape on the detector, calibrating wavelength, and tracing orders more accurately than the standard HARPS pipeline. Applied to 52.5 hours of HARPS data on quasar HE0515-4414, HARPERFECT gives S/N comparable to, though slightly lower than, the standard pipeline. Its value lies in an exact resolution matrix and independent samples, properties standard extraction cannot guarantee for a non-separable PSF - a step toward better measurements of fundamental constants and exoplanet atmospheres.

astro-ph.IM↗

Evaluating Multimodal LLMs for Inpatient Diagnosis: Real-World Performance, Safety, and Cost Across Ten Frontier Models

Background: Large language models (LLMs) are increasingly proposed for diagnostic support, but few evaluations use real-world multimodal inpatient data, particularly in low and middle-income country (LMIC) public hospitals. Methods: We conducted VALID, a retrospective evaluation of 539 multimodal inpatient cases from a tertiary public hospital in South Africa. Inputs included radiology imaging (CT, MRI, CXR) and reports, laboratory results, clinical notes, and vital signs. Expert panels adjudicated 300 cases (balanced and discordant subsets) to establish ground truth diagnoses, differentials, and reasoning. Ten multimodal LLMs generated zero-shot outputs. A calibrated three-model LLM Jury scored all outputs and routine ward diagnoses across diagnostic accuracy, differential quality, reasoning, and patient safety (>10,000 evaluations). Primary outcomes were composite scores ($S_3$, $S_4$) and win rates. Results: (i) LLM performance was tightly clustered (<15% variation) despite large cost differences; low-cost models performed comparably to top models. (ii) All LLMs significantly outperformed routine ward diagnoses on average diagnostic and safety scores. (iii) Top performance was achieved by GPT-5.1, followed by Gemini models. (vi) Adding radiology reports improved performance by 6%. (v) Diagnostic and reasoning scores were highly correlated ($ρ= 0.85$). (vi) Output rates varied (65-100%) due to input constraints. Results were robust across subsets and evaluation design. Conclusions: Across a real-world LMIC dataset, multimodal LLMs showed similar diagnostic performance despite large cost differences and outperformed routine care on average safety metrics. Affordability, robustness, and deployment constraints may outweigh marginal performance differences in LMIC settings.

cs.LG↗

From Handwriting to Structured Data: Benchmarking AI Digitisation of Handwritten Forms

Manual digitisation of structured handwritten documents is slow and costly. We benchmark 17 leading frontier multi-modal large language models and open-source models against a very challenging real-world medical form that mixes dates; structured, printed text; hand-written responses and significant variability challenges. None of the smaller or older models perform well but the latest Google and OpenAI models reach accuracies around $85\%$ with weighted F1 scores $\simeq 90\%$ across the discrete or predefined fields despite the very challenging nature of the responses. Clear task specific strengths emerge: GPT 5.4 excels in noisy date extraction as well as reliability with the lowest hallucination rate ($6\%$). Claude Sonnet 4.6 had the best average performance across formatted fields (dates and numerical values), while Gemini 3.1 delivered the best overall performance, with the lowest free text error rates (WER = $0.50$ and CER = $0.31$) and the strongest results across discrete classification metrics. We further show that prompt optimisation dramatically improves macro precision, recall and F1 by over $60\%$, but has little impact on weighted metrics (only $\sim2-5\%$ improvement). These results provide evidence that the rapid improvements of multimodal large language models offer a compelling pathway toward fully automated digitisation of complex handwritten workflows that is particularly relevant in low- and middle-income countries.

cs.CV↗

Calibrating Beyond English: Language Diversity for Better Quantized Multilingual LLM

Quantization is an effective technique for reducing the storage footprint and computational costs of Large Language Models (LLMs), but it often results in performance degradation. Existing post-training quantization methods typically use small, English-only calibration sets; however, their impact on multilingual models remains underexplored. We systematically evaluate eight calibration settings (five single-language and three multilingual mixes) on two quantizers (GPTQ, AWQ) on data from 10 languages. Our findings reveal a consistent trend: non-English and multilingual calibration sets significantly improve perplexity compared to English-only baselines. Specifically, we observe notable average perplexity gains across both quantizers on Llama3.1 8B and Qwen2.5 7B, with multilingual mixes achieving the largest overall reductions of up to 3.52 points in perplexity. Furthermore, our analysis indicates that tailoring calibration sets to the evaluation language yields the largest improvements for individual languages, underscoring the importance of linguistic alignment. We also identify specific failure cases where certain language-quantizer combinations degrade performance, which we trace to differences in activation range distributions across languages. These results highlight that static one-size-fits-all calibration is suboptimal and that tailoring calibration data, both in language and diversity, plays a crucial role in robustly quantizing multilingual LLMs.

cs.CL↗

Small Language Models Can Use Nuanced Reasoning For Health Science Research Classification: A Microbial-Oncogenesis Case Study

Artificially intelligent (AI) co-scientists must be able to sift through research literature cost-efficiently while applying nuanced scientific reasoning. We evaluate Small Language Models (SLMs, <= 8B parameters) for classifying medical research papers. Using literature on the oncogenic potential of HMTV/MMTV-like viruses in breast cancer as a case study, we assess model performance with both zero-shot and in-context learning (ICL; few-shot prompting) strategies against frontier proprietary Large Language Models (LLMs). Llama 3 and Qwen2.5 outperform GPT-5 (API, low/high effort), Gemini 3 Pro Preview, and Meerkat in zero-shot settings, though trailing Gemini 2.5 Pro. ICL leads to improved performance on a case-by-case basis, allowing Llama 3 and Qwen2.5 to match Gemini 2.5 Pro in binary classification. Systematic lexical-ablation experiments show that SLM decisions are often grounded in valid scientific cues but can be influenced by spurious textual artifacts, underscoring need for interpretability in high-stakes pipelines. Our results reveal both promise and limitations of modern SLMs for scientific triage; pairing SLMs with simple but principled prompting strategies can approach performance of the strongest LLMs for targeted literature filtering in co-scientist pipelines.

cs.CE↗

Critical Learning Periods: Leveraging Early Training Dynamics for Efficient Data Pruning

Neural Machine Translation models are extremely data and compute-hungry. However, not all data points contribute equally to model training and generalization. Data pruning to remove the low-value data points has the benefit of drastically reducing the compute budget without significant drop in model performance. In this paper, we propose a new data pruning technique: Checkpoints Across Time (CAT), that leverages early model training dynamics to identify the most relevant data points for model performance. We benchmark CAT against several data pruning techniques including COMET-QE, LASER and LaBSE. We find that CAT outperforms the benchmarks on Indo-European languages on multiple test sets. When applied to English-German, English-French and English-Swahili translation tasks, CAT achieves comparable performance to using the full dataset, while pruning up to 50% of training data. We inspect the data points that CAT selects and find that it tends to favour longer sentences and sentences with unique or rare words.

cs.CL↗

Trajectory Based RFI Subtraction and Calibration for Radio Interferometry

Radio interferometry calibration and Radio Frequency Interference (RFI) removal are usually done separately. Here we show that jointly modelling the antenna gains and RFI has significant benefits when the RFI follows precise trajectories, such as for satellites. One surprising benefit is improved calibration solutions, by leveraging the RFI signal itself. We present tabascal (TrAjectory BAsed RFI Subtraction and CALibration), a new algorithm that jointly models the RFI and calibration parameters in visibilities. We test tabascal on simulated MeerKAT calibration observations contaminated by satellite-based RFI. We obtain gain estimates that are both unbiased and up to an order of magnitude better constrained compared to uncontaminated data. When combined with an ad hoc RFI subtraction scheme, tabascal solutions can be further applied to an adjacent target observation: 5 minutes of calibration data results in an image with about a third the noise achieved when using flagging alone. The recovered flux distribution of RFI subtracted data was on par with uncontaminated data. In contrast, RFI flagging alone resulted in a higher detection threshold and consistent underestimation of source fluxes. For a mean RFI amplitude of 17 Jy, using RFI subtraction leads to less than 1% loss of data compared to 75% data loss from an ideal $3σ$ flagging algorithm, a very significant increase in data available for science analysis. Although we have examined the case of satellite RFI, tabascal should work for any RFI moving on parameterizable trajectories, relative to the phase centre, such as planes and/or objects fixed to the ground.

astro-ph.IM↗

Towards hate speech detection in low-resource languages: Comparing ASR to acoustic word embeddings on Wolof and Swahili

We consider hate speech detection through keyword spotting on radio broadcasts. One approach is to build an automatic speech recognition (ASR) system for the target low-resource language. We compare this to using acoustic word embedding (AWE) models that map speech segments to a space where matching words have similar vectors. We specifically use a multilingual AWE model trained on labelled data from well-resourced languages to spot keywords in data in the unseen target language. In contrast to ASR, the AWE approach only requires a few keyword exemplars. In controlled experiments on Wolof and Swahili where training and test data are from the same domain, an ASR model trained on just five minutes of data outperforms the AWE approach. But in an in-the-wild test on Swahili radio broadcasts with actual hate speech keywords, the AWE model (using one minute of template data) is more robust, giving similar performance to an ASR system trained on 30 hours of labelled data.

cs.CL↗

Very Low Resource Sentence Alignment: Luhya and Swahili

Language-agnostic sentence embeddings generated by pre-trained models such as LASER and LaBSE are attractive options for mining large datasets to produce parallel corpora for low-resource machine translation. We test LASER and LaBSE in extracting bitext for two related low-resource African languages: Luhya and Swahili. For this work, we created a new parallel set of nearly 8000 Luhya-English sentences which allows a new zero-shot test of LASER and LaBSE. We find that LaBSE significantly outperforms LASER on both languages. Both LASER and LaBSE however perform poorly at zero-shot alignment on Luhya, achieving just 1.5% and 22.0% successful alignments respectively (P@1 score). We fine-tune the embeddings on a small set of parallel Luhya sentences and show significant gains, improving the LaBSE alignment accuracy to 53.3%. Further, restricting the dataset to sentence embedding pairs with cosine similarity above 0.7 yielded alignments with over 85% accuracy.

cs.CL↗

Learning to Detect Interesting Anomalies

Anomaly detection algorithms are typically applied to static, unchanging, data features hand-crafted by the user. But how does a user systematically craft good features for anomalies that have never been seen? Here we couple deep learning with active learning -- in which an Oracle iteratively labels small amounts of data selected algorithmically over a series of rounds -- to automatically and dynamically improve the data features for efficient outlier detection. This approach, AHUNT, shows excellent performance on MNIST, CIFAR10, and Galaxy-DESI data, significantly outperforming both standard anomaly detection and active learning algorithms with static feature spaces. Beyond improved performance, AHUNT also allows the number of anomaly classes to grow organically in response to Oracle's evaluations. Extensive ablation studies explore the impact of Oracle question selection strategy and loss function on performance. We illustrate how the dynamic anomaly class taxonomy represents another step towards fully personalized rankings of different anomaly classes that reflect a user's interests, allowing the algorithm to learn to ignore statistically significant but uninteresting outliers (e.g., noise). This should prove useful in the era of massive astronomical datasets serving diverse sets of users who can only review a tiny subset of the incoming data.

cs.LG↗

COMET-QE and Active Learning for Low-Resource Machine Translation

Active learning aims to deliver maximum benefit when resources are scarce. We use COMET-QE, a reference-free evaluation metric, to select sentences for low-resource neural machine translation. Using Swahili, Kinyarwanda and Spanish for our experiments, we show that COMET-QE significantly outperforms two variants of Round Trip Translation Likelihood (RTTL) and random sentence selection by up to 5 BLEU points for 20k sentences selected by Active Learning on a 30k baseline. This suggests that COMET-QE is a powerful tool for sentence selection in the very low-resource limit.

cs.CL↗

A Hitchhiker's Guide to Anomaly Detection with Astronomaly

The next generation of telescopes such as the SKA and the Rubin Observatory will produce enormous data sets, requiring automated anomaly detection to enable scientific discovery. Here, we present an overview and friendly user guide to the Astronomaly framework for active anomaly detection in astronomical data. Astronomaly uses active learning to combine the raw processing power of machine learning with the intuition and experience of a human user, enabling personalised recommendations of interesting anomalies. It makes use of a Python backend to perform data processing, feature extraction and machine learning to detect anomalous objects; and a JavaScript frontend to allow interaction with the data, labelling of interesting anomalous and active learning. Astronomaly is designed to be modular, extendable and run on almost any type of astronomical data. In this paper, we detail the structure of the Astronomaly code and provide guidelines for basic usage.

astro-ph.IM↗

The Hydrogen Intensity and Real-time Analysis eXperiment: 256-Element Array Status and Overview

The Hydrogen Intensity and Real-time Analysis eXperiment (HIRAX) is a radio interferometer array currently in development, with an initial 256-element array to be deployed at the South African Radio Astronomy Observatory (SARAO) Square Kilometer Array (SKA) site in South Africa. Each of the 6m, $f/0.23$ dishes will be instrumented with dual-polarisation feeds operating over a frequency range of 400-800 MHz. Through intensity mapping of the 21 cm emission line of neutral hydrogen, HIRAX will provide a cosmological survey of the distribution of large-scale structure over the redshift range of $0.775 < z < 2.55$ over $\sim$15,000 square degrees of the southern sky. The statistical power of such a survey is sufficient to produce $\sim$7 percent constraints on the dark energy equation of state parameter when combined with measurements from the Planck satellite. Additionally, HIRAX will provide a highly competitive platform for radio transient and HI absorber science while enabling a multitude of cross-correlation studies. In this paper, we describe the science goals of the experiment, overview of the design and status of the sub-components of the telescope system, and describe the expected performance of the initial 256-element array as well as the planned future expansion to the final, 1024-element array.

astro-ph.IM↗

Astronomaly: Personalised Active Anomaly Detection in Astronomical Data

Survey telescopes such as the Vera C. Rubin Observatory and the Square Kilometre Array will discover billions of static and dynamic astronomical sources. Properly mined, these enormous datasets will likely be wellsprings of rare or unknown astrophysical phenomena. The challenge is that the datasets are so large that most data will never be seen by human eyes; currently the most robust instrument we have to detect relevant anomalies. Machine learning is a useful tool for anomaly detection in this regime. However, it struggles to distinguish between interesting anomalies and irrelevant data such as instrumental artefacts or rare astronomical sources that are simply not of interest to a particular scientist. Active learning combines the flexibility and intuition of the human brain with the raw processing power of machine learning. By strategically choosing specific objects for expert labelling, it minimises the amount of data that scientists have to look through while maximising potential scientific return. Here we introduce Astronomaly: a general anomaly detection framework with a novel active learning approach designed to provide personalised recommendations. Astronomaly can operate on most types of astronomical data, including images, light curves and spectra. We use the Galaxy Zoo dataset to demonstrate the effectiveness of Astronomaly, as well as simulated data to thoroughly test our new active learning approach. We find that for both datasets, Astronomaly roughly doubles the number of interesting anomalies found in the first 100 objects viewed by the user. Astronomaly is easily extendable to include new feature extraction techniques, anomaly detection algorithms and even different active learning approaches. The code is publicly available at https://github.com/MichelleLochner/astronomaly.

astro-ph.IM↗