Surface-Enhanced Raman Spectroscopy (SERS) is often used for heavy metal ion detection. However, large variations in signal strength, spectral profile, and nonlinearity of measurements often cause problems that produce varying results. It raises concerns about the reproducibility of the results. Consequently, the manual classification of the SERS spectrum requires carefully controlled experimentation that further hinders the large-scale adaptation. Recent advances in machine learning offer decent opportunities to address these issues. However, well-documented procedures for model development and evaluation, as well as benchmark datasets, are missing. Towards this end, we provide the SERS spectral benchmark dataset of lead(II) nitride (Pb(NO₃)₂) for a heavy metal ion detection task and evaluate the classification performance of several machine learning models. We also perform a comparative study to find the best combination between the preprocessing methods and the machine learning models. The proposed model can successfully identify the Pb(NO₃)₂ molecule from SERS measurements of independent test experiments. In particular, the proposed model shows an $84.6\%$ balanced accuracy for the cross-batch testing task.

Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and biochemical samples compared with the conventional, macroscale instruments. Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes. Since it is believed that the development of synthetic biology can be accelerated through the use of microfluidic technology, in this review work we focus our discussion on the latest microfluidic technologies that can provide unprecedented means in synthetic biology for dynamic profiling of gene expression/regulation with high resolution, highly sensitive on-chip and off-chip detection of metabolites, and whole-cell analysis.

It is of utmost importance to develop a computational method for accurate prediction of antioxidants, as they play a vital role in the prevention of several diseases caused by oxidative stress. In this correspondence, we present an effective computational methodology based on the notion of deep latent space encoding. A deep neural network classifier fused with an auto-encoder learns class labels in a pruned latent space. This strategy has eliminated the need to separately develop classifier and the feature selection model, allowing the standalone model to effectively harness discriminating feature space and perform improved predictions. A thorough analytical study has been presented alongwith the PCA/tSNE visualization and PCA-GCNR scores to show the discriminating power of the proposed method. The proposed method showed a high MCC value of 0.43 and a balanced accuracy of 76.2%, which is superior to the existing models. The model has been evaluated on an independent dataset during which it outperformed the contemporary methods by correctly identifying the novel proteins with an accuracy of 95%.

Neoadjuvant chemotherapy (NAC) response is an important indicator of patient survival in triple negative breast cancer (TNBC), but predicting chemosensitivity remains a challenge in clinical practice. We developed an 86-gene-based random forest (RF) classifier capable of predicting neoadjuvant chemotherapy response (pathological Complete Response (pCR) or Residual Disease (RD)) in TNBC patients. The performance of pCR classification of the proposed model was evaluated by Receiver Operating Characteristic (ROC) curve and Precision Recall (PR) curve. The AUROC and AUPRC of the proposed model on the test set were 0.891 and 0.829, respectively. At a predefined specificity (>90%), the proposed model shows a superior sensitivity compared to the best performing reported NAC response prediction model (69.2% vs. 36.9%). Moreover, the predicted pCR status by the model well explains the distance recurrence free survival (DRFS) of TNBC patients. In addition, the pCR probabilities of the proposed model using the expression profiles of the CCLE TNBC cell lines show a high Spearman rank correlation with cyclophosphamide sensitivity in the TNBC cell lines (SRCC $=0.697$, p-value $=0.031$). Associations between the 86 genes and DNA repair/cell cycle mechanisms were provided through function enrichment analysis. Our study suggests that the random forest-based prediction model provides a reliable prediction of the clinical response to neoadjuvant chemotherapy and may explain chemosensitivity in TNBC.