Learning to Receive Help: Intervention-Aware Concept Embedding Models

Concept Bottleneck Models (CBMs) tackle the opacity of neural architectures by constructing and explaining their predictions using a set of high-level concepts. A special property of these models is that they permit concept interventions, wherein users can correct mispredicted concepts and thus improve the model's performance. Recent work, however, has shown that intervention efficacy can be highly dependent on the order in which concepts are intervened on and on the model's architecture and training hyperparameters. We argue that this is rooted in a CBM's lack of train-time incentives for the model to be appropriately receptive to concept interventions. To address this, we propose Intervention-aware Concept Embedding models (IntCEMs), a novel CBM-based architecture and training paradigm that improves a model's receptiveness to test-time interventions. Our model learns a concept intervention policy in an end-to-end fashion from where it can sample meaningful intervention trajectories at train-time. This conditions IntCEMs to effectively select and receive concept interventions when deployed at test-time. Our experiments show that IntCEMs significantly outperform state-of-the-art concept-interpretable models when provided with test-time concept interventions, demonstrating the effectiveness of our approach.Comment: Accepted as a spotlight at the Thirty-seventh Conference on Neural Information Processing Systems (NeurIPS 2023

Deduction of physiochemical properties from solubilities: 2,4-dihydroxybenzophenone, biotin, and caprolactam as examples

Article discussing the deduction of physiochemical properties from solubilities and 2,4-dihydroxybenzophenone, biotin, and caprolactam as examples

Psychosocial impact of undergoing prostate cancer screening for men with BRCA1 or BRCA2 mutations.

OBJECTIVES: To report the baseline results of a longitudinal psychosocial study that forms part of the IMPACT study, a multi-national investigation of targeted prostate cancer (PCa) screening among men with a known pathogenic germline mutation in the BRCA1 or BRCA2 genes. PARTICPANTS AND METHODS: Men enrolled in the IMPACT study were invited to complete a questionnaire at collaborating sites prior to each annual screening visit. The questionnaire included sociodemographic characteristics and the following measures: the Hospital Anxiety and Depression Scale (HADS), Impact of Event Scale (IES), 36-item short-form health survey (SF-36), Memorial Anxiety Scale for Prostate Cancer, Cancer Worry Scale-Revised, risk perception and knowledge. The results of the baseline questionnaire are presented. RESULTS: A total of 432 men completed questionnaires: 98 and 160 had mutations in BRCA1 and BRCA2 genes, respectively, and 174 were controls (familial mutation negative). Participants' perception of PCa risk was influenced by genetic status. Knowledge levels were high and unrelated to genetic status. Mean scores for the HADS and SF-36 were within reported general population norms and mean IES scores were within normal range. IES mean intrusion and avoidance scores were significantly higher in BRCA1/BRCA2 carriers than in controls and were higher in men with increased PCa risk perception. At the multivariate level, risk perception contributed more significantly to variance in IES scores than genetic status. CONCLUSION: This is the first study to report the psychosocial profile of men with BRCA1/BRCA2 mutations undergoing PCa screening. No clinically concerning levels of general or cancer-specific distress or poor quality of life were detected in the cohort as a whole. A small subset of participants reported higher levels of distress, suggesting the need for healthcare professionals offering PCa screening to identify these risk factors and offer additional information and support to men seeking PCa screening

Cancer Surveillance Guideline for individuals with PTEN hamartoma tumour syndrome

Abstract: PTEN hamartoma tumour syndrome is a diverse multi-system disorder predisposing to the development of hamartomatous growths, increasing risk of breast, thyroid, renal cancer, and possibly increasing risk of endometrial cancer, colorectal cancer and melanoma. There is no international consensus on cancer surveillance in PHTS and all current guidelines are based on expert opinion. A comprehensive literature review was undertaken and guidelines were developed by clinicians with expertise from clinical genetics, gynaecology, endocrinology, dermatology, radiology, gastroenterology and general surgery, together with affected individuals and their representatives. Recommendations were put forward for surveillance for breast, thyroid and renal cancers. Limited recommendations were developed for other sites including endometrial, colon and skin. The proposed cancer surveillance recommendations for PHTS require a coordinated multidisciplinary approach and significant patient commitment. The evidence base for cancer surveillance in this guideline are limited, emphasising the need for prospective evaluation of the effectiveness of surveillance in the PHTS population

Low rates of rock organic carbon oxidation and anthropogenic cycling of rhenium in a slowly denuding landscape

International audienceThe oxidation of petrogenic organic carbon (OCpetro) is a source of carbon dioxide to the atmosphere over geological timescales. The rates of OCpetro oxidation in locations that experience low rates of denudation remain poorly constrained, despite these landscapes dominating Earth's continental surface area. Here, we track OCpetro oxidation using radiocarbon and the trace element rhenium (Re) in the deep weathering profiles, soils and stream waters of the Susquehanna Shale Hills Critical Zone Observatory (PA, USA). In a ridge-top borehole, radiocarbon measurements reveal the presence of a broad OCpetro weathering front, with a first-order assessment of ~40% loss occurring over ~6 m. However, the low OCpetro concentration ( 80% of Re in the rock is associated with OCpetro, based on Re/Na and Re/S ratios. Using estimates of long-term denudation rates, the observed OCpetro loss and the Re proxy are equivalent to a low OCpetro oxidation yield of < 1.7 × 10−2 tC km−2 yr−1. This is consistent with the low OCpetro concentrations and low denudation rates at this location. In addition, we find the surface cycle of Re is decoupled from that of deep weathering, with an enrichment of Re in surface soils and elevated Re concentrations in stream water, precipitation, and shallow groundwater. A mass balance model shows that this can be explained by a historical anthropogenic contribution of Re through atmospheric deposition. We estimate that the topsoil Re pool could take decades to centuries to deplete and call for a renewed focus on anthropogenic perturbation of the surface Re cycle in low denudation rate settings

Changes in pulmonary artery systolic pressure correlate with radiographic severity and peripheral oxygenation in adults with community-acquired pneumonia

The aim of this prospective observational study was to evaluate the relationship between changes in pulmonary artery systolic pressure (ΔPASP) and both severity of community-acquired pneumonia (CAP) and changes in peripheral blood oxygen partial pressure (PaO2 ). Seventy-five consecutive adult patients hospitalized for treatment of CAP were recruited in this single-center cohort study. Doppler echocardiographic measurement of PASP was performed by 2 staff cardiologists. Follow-up assessment was performed within 2 to 4 weeks of ending antibiotic treatment at radiographic resolution of CAP. Fifteen patients were excluded during follow-up due to confirmation of chronic obstructive pulmonary disease. Pneumonia was unilateral in 40 (66.7%) and bilateral in 20 (33.3%) patients. Radiographic extent of pneumonia involved 2 pulmonary segments in 31 patients (51.7%), 3 to 5 pulmonary segments in 25 (41.7%), and 6 pulmonary segments in 4 patients (6.6%). ΔPASP between hospital admission and follow-up correlated with the number of pulmonary segments involved (Rho = 0.953 ; P < .001) and PaO2 (Rho = -0.667 ; P < .001). The maximum PASP was greater during pneumonia than after resolution (34.82 ± 3.96 vs. 22.67 ± 4.04, P < .001). Changes in PASP strongly correlated with radiological severity of CAP and PaO2 . During pneumonia, PASP appeared increased without significant change in left ventricular filling pressures. This suggests that disease-related changes in lung tissue caused by pneumonia may easily and reproducibly be assessed using conventional noninvasive bedside diagnostics such as echocardiography and arterial blood gas analysis

Low rates of rock organic carbon oxidation and anthropogenic cycling of rhenium in a slowly denuding landscape

The oxidation of petrogenic organic carbon (OCpetro) is a source of carbon dioxide to the atmosphere over geological timescales. The rates of OCpetro oxidation in locations that experience low rates of denudation remain poorly constrained, despite these landscapes dominating Earth’s continental surface area. Here, we track OCpetro oxidation using radiocarbon and the trace element rhenium (Re) in the deep weathering profiles, soils and stream waters of the Susquehanna Shale Hills Critical Zone Observatory (PA, USA). In a ridge-top borehole, radiocarbon measurements reveal the presence of a broad OCpetro weathering front, with a first order assessment of ~40% loss occurring over ~6 m. However, the low OCpetro concentration (80% of Re in the rock is associated with OCpetro, based on Re/Na and Re/S ratios. Using estimates of long-term denudation rates, the observed OCpetro loss and the Re proxy are equivalent to a low OCpetro oxidation yield of <1.7×10-2 tC km-2 yr-1. This is consistent with the low OCpetro concentrations and low denudation rates at this location. In addition, we find the surface cycle of Re is decoupled from that of deep weathering, with an enrichment of Re in surface soils and elevated Re concentrations in stream water, precipitation, and shallow groundwater. A mass balance model shows that this can be explained by a historical anthropogenic contribution of Re through atmospheric deposition. We estimate that the topsoil Re pool could take decades to centuries to deplete and call for a renewed focus on anthropogenic perturbation of the surface Re cycle in low denudation rate settings

Evaluating Language Models for Mathematics through Interactions.

There is much excitement about the opportunity to harness the power of large language models (LLMs) when building problem-solving assistants. However, the standard methodology of evaluating LLMs relies on static pairs of inputs and outputs; this is insufficient for making an informed decision about which LLMs are best to use in an interactive setting, and how that varies by setting. Static assessment therefore limits how we understand language model capabilities. We introduce CheckMate, an adaptable prototype platform for humans to interact with and evaluate LLMs. We conduct a study with CheckMate to evaluate three language models (InstructGPT, ChatGPT, and GPT-4) as assistants in proving undergraduate-level mathematics, with a mixed cohort of participants from undergraduate students to professors of mathematics. We release the resulting interaction and rating dataset, MathConverse. By analysing MathConverse, we derive a taxonomy of human query behaviours and uncover that despite a generally positive correlation, there are notable instances of divergence between correctness and perceived helpfulness in LLM generations, amongst other findings. Further, we garner a more granular understanding of GPT-4 mathematical problem-solving through a series of case studies, contributed by experienced mathematicians. We conclude with actionable takeaways for ML practitioners and mathematicians: models that communicate uncertainty, respond well to user corrections, and can provide a concise rationale for their recommendations, may constitute better assistants. Humans should inspect LLM output carefully given their current shortcomings and potential for surprising fallibility

Reconstructing Prehistoric African Population Structure

We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100–2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations