Iterated cross validation method for prediction of survival in diffuse large B-cell lymphoma for small size dataset

Differential gene expression analysis pipelines and bioinformatic tools for the identification of specific biomarkers: A review

In recent years, the role of bioinformatics and computational biology together with omics techniques and transcriptomics has gained tremendous importance in biomedicine and healthcare, particularly for the identification of biomarkers for precision medicine and drug discovery. Differential gene expression (DGE) analysis is one of the most used techniques for RNA-sequencing (RNA-seq) data analysis. This tool, which is typically used in various RNA-seq data processing applications, allows the identification of differentially expressed genes across two or more sample sets. Functional enrichment analyses can then be performed to annotate and contextualize the resulting gene lists. These studies provide valuable information about disease-causing biological processes and can help in identifying molecular targets for novel therapies. This review focuses on differential gene expression (DGE) analysis pipelines and bioinformatic techniques commonly used to identify specific biomarkers and discuss the advantages and disadvantages of these techniques.

Enhancing Lymphoma Diagnosis, Treatment, and Follow-Up Using 18F-FDG PET/CT Imaging: Contribution of Artificial Intelligence and Radiomics Analysis

Lymphoma, encompassing a wide spectrum of immune system malignancies, presents significant complexities in its early detection, management, and prognosis assessment since it can mimic post-infectious/inflammatory diseases. The heterogeneous nature of lymphoma makes it challenging to definitively pinpoint valuable biomarkers for predicting tumor biology and selecting the most effective treatment strategies. Although molecular imaging modalities, such as positron emission tomography/computed tomography (PET/CT), specifically 18F-FDG PET/CT, hold significant importance in the diagnosis of lymphoma, prognostication, and assessment of treatment response, they still face significant challenges. Over the past few years, radiomics and artificial intelligence (AI) have surfaced as valuable tools for detecting subtle features within medical images that may not be easily discerned by visual assessment. The rapid expansion of AI and its application in medicine/radiomics is opening up new opportunities in the nuclear medicine field. Radiomics and AI capabilities seem to hold promise across various clinical scenarios related to lymphoma. Nevertheless, the need for more extensive prospective trials is evident to substantiate their reliability and standardize their applications. This review aims to provide a comprehensive perspective on the current literature regarding the application of AI and radiomics applied/extracted on/from 18F-FDG PET/CT in the management of lymphoma patients.

Prognosis Prediction of Diffuse Large B-Cell Lymphoma in 18F-FDG PET Images Based on Multi-Deep-Learning Models

Diffuse large B-cell lymphoma (DLBCL), a cancer of B cells, has been one of the most challenging and complicated diseases because of its considerable variation in clinical behavior, response to therapy, and prognosis. Radiomic features from medical images, such as PET images, have become one of the most valuable features for disease classification or prognosis prediction using learning-based methods. In this paper, a new flexible ensemble deep learning model is proposed for the prognosis prediction of the DLBCL in 18F-FDG PET images. This study proposes the multi-R-signature construction through selected pre-trained deep learning models for predicting progression-free survival (PFS) and overall survival (OS). The proposed method is trained and validated on two datasets from different imaging centers. Through analyzing and comparing the results, the prediction models, including Age, Ann abor stage, Bulky disease, SUVmax, TMTV, and multi-R-signature, achieve the almost best PFS prediction performance (C-index: 0.770, 95% CI: 0.705-0.834, with feature adding fusion method and C-index: 0.764, 95% CI: 0.695-0.832, with feature concatenate fusion method) and OS prediction (C-index: 0.770 (0.692-0.848) and 0.771 (0.694-0.849)) on the validation dataset. The developed multiparametric model could achieve accurate survival risk stratification of DLBCL patients. The outcomes of this study will be helpful for the early identification of high-risk DLBCL patients with refractory relapses and for guiding individualized treatment strategies.

Segmentation of patients with small cell lung cancer into responders and non-responders using the optimal cross-validation technique

BACKGROUND

The timing of treating cancer patients is an essential factor in the efficacy of treatment. So, patients who will not respond to current therapy should receive a different treatment as early as possible. Machine learning models can be built to classify responders and nonresponders. Such classification models predict the probability of a patient being a responder. Most methods use a probability threshold of 0.5 to convert the probabilities into binary group membership. However, the cutoff of 0.5 is not always the optimal choice.

METHODS

In this study, we propose a novel data-driven approach to select a better cutoff value based on the optimal cross-validation technique. To illustrate our novel method, we applied it to three clinical trial datasets of small-cell lung cancer patients. We used two different datasets to build a scoring system to segment patients. Then the models were applied to segment patients into the test data.

RESULTS

We found that, in test data, the predicted responders and non-responders had significantly different long-term survival outcomes. Our proposed novel method segments patients better than the standard approach using a cutoff of 0.5. Comparing clinical outcomes of responders versus non-responders, our novel method had a p-value of 0.009 with a hazard ratio of 0.668 for grouping patients using the Cox proportion hazard model and a p-value of 0.011 using the accelerated failure time model which approved a significant difference between responders and non-responders. In contrast, the standard approach had a p-value of 0.194 with a hazard ratio of 0.823 using the Cox proportion hazard model and a p-value of 0.240 using the accelerated failure time model indicating the responders and non-responders do not differ significantly in survival.

CONCLUSION

In summary, our novel prediction method can successfully segment new patients into responders and non-responders. Clinicians can use our prediction to decide if a patient should receive a different treatment or stay with the current treatment.

Methodological evaluation of original articles on radiomics and machine learning for outcome prediction based on positron emission tomography (PET)

AIM

Despite a vast number of articles on radiomics and machine learning in positron emission tomography (PET) imaging, clinical applicability remains limited, partly owing to poor methodological quality. We therefore systematically investigated the methodology described in publications on radiomics and machine learning for PET-based outcome prediction.

METHODS

A systematic search for original articles was run on PubMed. All articles were rated according to 17 criteria proposed by the authors. Criteria with >2 rating categories were binarized into "adequate" or "inadequate". The association between the number of "adequate" criteria per article and the date of publication was examined.

RESULTS

One hundred articles were identified (published between 07/2017 and 09/2023). The median proportion of articles per criterion that were rated "adequate" was 65% (range: 23-98%). Nineteen articles (19%) mentioned neither a test cohort nor cross-validation to separate training from testing. The median number of criteria with an "adequate" rating per article was 12.5 out of 17 (range, 4-17), and this did not increase with later dates of publication (Spearman's rho, 0.094; p = 0.35). In 22 articles (22%), less than half of the items were rated "adequate". Only 8% of articles published the source code, and 10% made the dataset openly available.

CONCLUSION

Among the articles investigated, methodological weaknesses have been identified, and the degree of compliance with recommendations on methodological quality and reporting shows potential for improvement. Better adherence to established guidelines could increase the clinical significance of radiomics and machine learning for PET-based outcome prediction and finally lead to the widespread use in routine clinical practice.

Robust deep learning-based PET prognostic imaging biomarker for DLBCL patients: a multicenter study

OBJECTIVE

To develop and independently externally validate robust prognostic imaging biomarkers distilled from PET images using deep learning techniques for precise survival prediction in patients with diffuse large B cell lymphoma (DLBCL).

METHODS

A total of 684 DLBCL patients from three independent medical centers were included in this retrospective study. Deep learning scores (DLS) were generated from PET images using deep convolutional neural network architecture known as VGG19 and DenseNet121. These DLSs were utilized to predict progression-free survival (PFS) and overall survival (OS). Furthermore, multiparametric models were designed based on results from the Cox proportional hazards model and assessed through calibration curves, concordance index (C-index), and decision curve analysis (DCA) in the training and validation cohorts.

RESULTS

The DLSPFS and DLSOS exhibited significant associations with PFS and OS, respectively (P<0.05) in the training and validation cohorts. The multiparametric models that incorporated DLSs demonstrated superior efficacy in predicting PFS (C-index: 0.866) and OS (C-index: 0.835) compared to competing models in training cohorts. In external validation cohorts, the C-indices for PFS and OS were 0.760 and. 0.770 and 0.748 and 0.766, respectively, indicating the reliable validity of the multiparametric models. The calibration curves displayed good consistency, and the decision curve analysis (DCA) confirmed that the multiparametric models offered more net clinical benefits.

CONCLUSIONS

The DLSs were identified as robust prognostic imaging biomarkers for survival in DLBCL patients. Moreover, the multiparametric models developed in this study exhibited promising potential in accurately stratifying patients based on their survival risk.

Application of Deep Learning in Cancer Prognosis Prediction Model

As an important branch of artificial intelligence and machine learning, deep learning (DL) has been widely used in various aspects of cancer auxiliary diagnosis, among which cancer prognosis is the most important part. High-accuracy cancer prognosis is beneficial to the clinical management of patients with cancer. Compared with other methods, DL models can significantly improve the accuracy of prediction. Therefore, this article is a systematic review of the latest research on DL in cancer prognosis prediction. First, the data type, construction process, and performance evaluation index of the DL model are introduced in detail. Then, the current mainstream baseline DL cancer prognosis prediction models, namely, deep neural networks, convolutional neural networks, deep belief networks, deep residual networks, and vision transformers, including network architectures, the latest application in cancer prognosis, and their respective characteristics, are discussed. Next, some key factors that affect the predictive performance of the model and common performance enhancement techniques are listed. Finally, the limitations of the DL cancer prognosis prediction model in clinical practice are summarized, and the future research direction is prospected. This article could provide relevant researchers with a comprehensive understanding of DL cancer prognostic models and is expected to promote the research progress of cancer prognosis prediction.