Boyang Fu, Sameer Gabbita, George Dasoulas, Xiang Lin, Shanghua Gao, Xiaorui Su, Soumya Ghosh, Marinka Zitnik
Prediction of the transcriptional response of a cell to a genetic perturbation is a central problem in the computational modeling of gene regulation. Perturbations of the same gene can produce different transcriptional responses depending on the targeted locus, such as an alternative transcription start site or a distal regulatory element, and gene-level perturbation models represent these distinct interventions with a single gene identifier. We introduce STRAND, a generative model that encodes the regulatory DNA sequence at the perturbation locus and uses this encoding to parameterize a conditional transport process from control to perturbed single-cell states. Sequence conditioning enables zero-shot prediction for perturbation targets absent from training and supports locus-resolved inputs at 128 bp model resolution within a 524 kb sequence window. On CRISPRi screens in K562, Jurkat, and RPE1 cells, STRAND achieves the best average rank on few-shot and unseen-gene benchmarks, with gains of up to 33% in perturbation discrimination, and improves transfer to held-out cell lines by up to 0.12 in $Δ$Pearson. Ablation studies attribute these gains to sequence conditioning and to conditional transport. At the locus level, STRAND distinguishes alternative transcription start sites and validated regulatory elements that gene-identifier models represent as a single perturbation. STRAND is available at https://github.com/mims-harvard/STRAND.
Amir Reza Vazifeh, Christian Zeigler, Sornanathan Meyyappan, Richard Jeske, Jason W. Fleischer
Cell viability assessment is a core requirement in cell culture systems, with critical applications in biopharmaceutical manufacturing and drug development. Conventionally, it is measured by adding membrane-impermeable dyes to a sample (a process called staining), which allows compromised cell membranes to be distinguished from intact ones. However, staining has several limitations: (a) chemical agents can perturb normal cellular processes of the cells being measured, (b) it is often ambiguous to assign viability to individual cells whose membrane integrity is only partially compromised, (c) photobleaching can undermine measurement accuracy over time when using fluorescent stains, and (d) staining cannot be performed in situ or in real time. Here, we show that (1) stained cells captured under brightfield imaging contain sufficient information to distinguish live and dead cells, and (2) cells captured under unstained brightfield imaging exhibit similar image features to their stained counterparts, enabling models trained on stained cells to generalize to unstained ones. We then report the development and validation of ViabiLens, an AI-assisted software tool for label-free cell viability analysis. ViabiLens combines a cell detection model for localizing individual cells with a convolutional neural network (CNN) classifier for live/dead prediction, paired with an interactive UMAP-based viewer for visualizing and exploring individual cells across the sample. Evaluated on Chinese Hamster Ovary (CHO) cells spanning a wide range of viability conditions, ViabiLens achieves a mean absolute error of 2.33\% on unstained samples against fluorescence-based reference measurements. The demo of ViabiLens software is available at https://amirrezavazifeh.github.io/ViabiLens-Project-Page/.