Receive a weekly summary and discussion of the top papers of the week by leading researchers in the field.

General General

Toward autonomous robotic prostate biopsy: a pilot study.

In International journal of computer assisted radiology and surgery

PURPOSE : We present the validation of PROST, a robotic device for prostate biopsy. PROST is designed to minimize human error by introducing some autonomy in the execution of the key steps of the procedure, i.e., target selection, image fusion and needle positioning. The robot allows executing a targeted biopsy through ultrasound (US) guidance and fusion with magnetic resonance (MR) images, where the target was defined.

METHODS : PROST is a parallel robot with 4 degrees of freedom (DOF) to orient the needle and 1 DOF to rotate the US probe. We reached a calibration error of less than 2 mm, computed as the difference between the needle positioning in robot coordinates and in the US image. The autonomy of the robot is given by the image analysis software, which employs deep learning techniques, the integrated image fusion algorithms and automatic computation of the needle trajectory. For safety reasons, the insertion of the needle is assigned to the doctor.

RESULTS : System performance was evaluated in terms of positioning accuracy. Tests were performed on a 3D printed object with nine 2-mm spherical targets and on an anatomical commercial phantom that simulates human prostate with three lesions and the surrounding structures. The average accuracy reached in the laboratory experiments was [Formula: see text] in the first test and [Formula: see text] in the second test.

CONCLUSIONS : We introduced a first prototype of a prostate biopsy robot that has the potential to increase the detection of clinically significant prostate cancer and, by including some level of autonomy, to simplify the procedure, to reduce human errors and shorten training time. The use of a robot for the biopsy of the prostate will create the possibility to include also a treatment, such as focal ablation, to be delivered through the same system.

Maris Bogdan, Tenga Chiara, Vicario Rudy, Palladino Luigi, Murr Noe, De Piccoli Michela, Calanca Andrea, Puliatti Stefano, Micali Salvatore, Tafuri Alessandro, Fiorini Paolo

2021-Jul-05

Automatic segmentation, Image fusion, Medical robotics, Prostate biopsy, Robot-assisted biopsy

oncology Oncology

Prediction of pathologic complete response to neoadjuvant chemotherapy using machine learning models in patients with breast cancer.

In Breast cancer research and treatment

BACKGROUND : The aim of this study was to develop a machine learning (ML) based model to accurately predict pathologic complete response (pCR) to neoadjuvant chemotherapy (NAC) using pretreatment clinical and pathological characteristics of electronic medical record (EMR) data in breast cancer (BC).

METHODS : The EMR data from patients diagnosed with early and locally advanced BC and who received NAC followed by curative surgery were reviewed. A total of 16 clinical and pathological characteristics was selected to develop ML model. We practiced six ML models using default settings for multivariate analysis with extracted variables.

RESULTS : In total, 2065 patients were included in this analysis. Overall, 30.6% (n = 632) of patients achieved pCR. Among six ML models, the LightGBM had the highest area under the curve (AUC) for pCR prediction. After hyper-parameter tuning with Bayesian optimization, AUC was 0.810. Performance of pCR prediction models in different histology-based subtypes was compared. The AUC was highest in HR+HER2- subgroup and lowest in HR-/HER2- subgroup (HR+/HER2- 0.841, HR+/HER2+ 0.716, HR-/HER2 0.753, HR-/HER2- 0.653).

CONCLUSIONS : A ML based pCR prediction model using pre-treatment clinical and pathological characteristics provided useful information to predict pCR during NAC. This prediction model would help to determine treatment strategy in patients with BC planned NAC.

Kim Ji-Yeon, Jeon Eunjoo, Kwon Soonhwan, Jung Hyungsik, Joo Sunghoon, Park Youngmin, Lee Se Kyung, Lee Jeong Eon, Nam Seok Jin, Cho Eun Yoon, Park Yeon Hee, Ahn Jin Seok, Im Young-Hyuck

2021-Jul-05

Breast cancer, Machine learning, Neoadjuvant chemotherapy, Pathologic complete response

Public Health Public Health

Prediction of blood lactate values in critically ill patients: a retrospective multi-center cohort study.

In Journal of clinical monitoring and computing

Elevations in initially obtained serum lactate levels are strong predictors of mortality in critically ill patients. Identifying patients whose serum lactate levels are more likely to increase can alert physicians to intensify care and guide them in the frequency of tending the blood test. We investigate whether machine learning models can predict subsequent serum lactate changes. We investigated serum lactate change prediction using the MIMIC-III and eICU-CRD datasets in internal as well as external validation of the eICU cohort on the MIMIC-III cohort. Three subgroups were defined based on the initial lactate levels: (i) normal group (< 2 mmol/L), (ii) mild group (2-4 mmol/L), and (iii) severe group (> 4 mmol/L). Outcomes were defined based on increase or decrease of serum lactate levels between the groups. We also performed sensitivity analysis by defining the outcome as lactate change of > 10% and furthermore investigated the influence of the time interval between subsequent lactate measurements on predictive performance. The LSTM models were able to predict deterioration of serum lactate values of MIMIC-III patients with an AUC of 0.77 (95% CI 0.762-0.771) for the normal group, 0.77 (95% CI 0.768-0.772) for the mild group, and 0.85 (95% CI 0.840-0.851) for the severe group, with only a slightly lower performance in the external validation. The LSTM demonstrated good discrimination of patients who had deterioration in serum lactate levels. Clinical studies are needed to evaluate whether utilization of a clinical decision support tool based on these results could positively impact decision-making and patient outcomes.

Mamandipoor Behrooz, Yeung Wesley, Agha-Mir-Salim Louis, Stone David J, Osmani Venet, Celi Leo Anthony

2021-Jul-05

Critical illness, Deep learning, Lactate, Resuscitation, Time series

General General

An Explainable AI System for the Diagnosis of High Dimensional Biomedical Data

ArXiv Preprint

Typical state of the art flow cytometry data samples consists of measures of more than 100.000 cells in 10 or more features. AI systems are able to diagnose such data with almost the same accuracy as human experts. However, there is one central challenge in such systems: their decisions have far-reaching consequences for the health and life of people, and therefore, the decisions of AI systems need to be understandable and justifiable by humans. In this work, we present a novel explainable AI method, called ALPODS, which is able to classify (diagnose) cases based on clusters, i.e., subpopulations, in the high-dimensional data. ALPODS is able to explain its decisions in a form that is understandable for human experts. For the identified subpopulations, fuzzy reasoning rules expressed in the typical language of domain experts are generated. A visualization method based on these rules allows human experts to understand the reasoning used by the AI system. A comparison to a selection of state of the art explainable AI systems shows that ALPODS operates efficiently on known benchmark data and also on everyday routine case data.

Alfred Ultsch, Jörg Hoffmann, Maximilian Röhnert, Malte Von Bonin, Uta Oelschlägel, Cornelia Brendel, Michael C. Thrun

2021-07-05

Radiology Radiology

RATCHET: Medical Transformer for Chest X-ray Diagnosis and Reporting

ArXiv Preprint

Chest radiographs are one of the most common diagnostic modalities in clinical routine. It can be done cheaply, requires minimal equipment, and the image can be diagnosed by every radiologists. However, the number of chest radiographs obtained on a daily basis can easily overwhelm the available clinical capacities. We propose RATCHET: RAdiological Text Captioning for Human Examined Thoraces. RATCHET is a CNN-RNN-based medical transformer that is trained end-to-end. It is capable of extracting image features from chest radiographs, and generates medically accurate text reports that fit seamlessly into clinical work flows. The model is evaluated for its natural language generation ability using common metrics from NLP literature, as well as its medically accuracy through a surrogate report classification task. The model is available for download at: http://www.github.com/farrell236/RATCHET.

Benjamin Hou, Georgios Kaissis, Ronald Summers, Bernhard Kainz

2021-07-05

General General

An empirical investigation of deviations from the Beer-Lambert law in optical estimation of lactate.

In Scientific reports ; h5-index 158.0

The linear relationship between optical absorbance and the concentration of analytes-as postulated by the Beer-Lambert law-is one of the fundamental assumptions that much of the optical spectroscopy literature is explicitly or implicitly based upon. The common use of linear regression models such as principal component regression and partial least squares exemplifies how the linearity assumption is upheld in practical applications. However, the literature also establishes that deviations from the Beer-Lambert law can be expected when (a) the light source is far from monochromatic, (b) the concentrations of analytes are very high and (c) the medium is highly scattering. The lack of a quantitative understanding of when such nonlinearities can become predominant, along with the mainstream use of nonlinear machine learning models in different fields, have given rise to the use of methods such as random forests, support vector regression, and neural networks in spectroscopic applications. This raises the question that, given the small number of samples and the high number of variables in many spectroscopic datasets, are nonlinear effects significant enough to justify the additional model complexity? In the present study, we empirically investigate this question in relation to lactate, an important biomarker. Particularly, to analyze the effects of scattering matrices, three datasets were generated by varying the concentration of lactate in phosphate buffer solution, human serum, and sheep blood. Additionally, the fourth dataset pertained to invivo, transcutaneous spectra obtained from healthy volunteers in an exercise study. Linear and nonlinear models were fitted to each dataset and measures of model performance were compared to attest the assumption of linearity. To isolate the effects of high concentrations, the phosphate buffer solution dataset was augmented with six samples with very high concentrations of lactate between (100-600 mmol/L). Subsequently, three partly overlapping datasets were extracted with lactate concentrations varying between 0-11, 0-20 and 0-600 mmol/L. Similarly, the performance of linear and nonlinear models were compared in each dataset. This analysis did not provide any evidence of substantial nonlinearities due high concentrations. However, the results suggest that nonlinearities may be present in scattering media, justifying the use of complex, nonlinear models.

Mamouei M, Budidha K, Baishya N, Qassem M, Kyriacou P A

2021-Jul-02