Hello everyone!
Recently I have been coming across a lot of Pathology Foundation Models trained on slides, and I was wondering what is the current state and if they are truly used ?
Hello everyone,
I recently got green light from my PI to apply for a PhD in NY, he recommended that I go through an unfunded program as it would be less competitive to get accepted, and he offered that I would be hired as an RA for 50 dollars per hour (limited to 20 hours per week since I am international). however, I still have to pay for the tiution fees and courses at the first two years (around 33k per year), I was wondering if there is any programs that I could apply to get a tuition waivers or a scholarship in the usa ?
Hello everyone,
With recent advancement in open models capabilities driven primarily by Chinese labs, I was wondering what kind of hardware the models are trained on, and if the Huawei chips and ecosystem is mature enough for scaling such models to trillion parameter range !?
Hello, I am trying to calculate the transcriptomic similarity profile between two dataset across defined clusters/cell types, I was wondering what kind of metric is appropiate (e.g. spearman, pearson, cosine...), and should I just calculate for variable genes HVG or across the whole transcriptome, and if there are other considerations ?
Hello everyone,
due to a recent change in my institute policies, I lost access to compute cluster as a volunteer. The group leader suggested we will move to Google Cloud for compute, I was wondering since Google offers both GPU and TPU, is there a cost difference between training a model using a TPU and GPU ? mainly because running ablation using the same set up I was using on HPC, will burn through a lot of money monthly.
Hello, I am trying to distinguish the difference in the context of developmental biology and gene regulatory network.
Hello everyone!
I am trying to train a set of models on pairs of protein sequences and drug smiles, I am trying to create a cold split for both drugs and protein to evaluate the generalizability of the model across sequence similarity, however I am not sure how to proceed, do i cluster the sequences then calculate the similarity between clusters ? do i calculate the similarities from the get go...
I received single cell tracing data using PEtracer, and I am trying to compute and visualize ancestroy linkage using pycea package, what I found confusing is how can two have directionally different diveregence time, diveregence of Cell A to cell B is different from the divergence of Cell B to Cell A
Hello everyone!
I am reading and diving into single cell foundation models, and have struglling to wrap up my head between masked objective and Next Token Objective in single cell foundation.
masked objective are easy to understand, you just mask a percentage of input gene tokens, then you predict them and optimize the loss function which is count based. for Next Token Objective, there isn't an ordered data structure unlike in NLP, this where my confusion steams from.
Hello everyone, I have been using LIANA plus for cell cell communication inference, however i am finding the visualisation toolkit/functions quite lacking, specially for chord circular plots. does anyone have recommendations for packages that can be used for visualisation and intergated with LIANA+ results.
Hello everyone,
I have a multi-ome data, and used scenicplus to identify different TF enrichment in my cell type, and I was wondering if it possibille to check the different enhancers that TF bind to, in the different cell type.
Hello everyone, I’m annotating cells from VisiumHD samples that I recently received. The quality of the samples is quite low in terms of the total number of counts and the number of genes detected by the cells. As a result, I was unable to reliably identify around 30 to 65% of the cells. When I looked closer, I discovered that these cells mostly express unique markers. For instance, one cluster expresses a unique marker of Cell Type A, while another cluster expresses another marker of Cell Type A, even though biologically, these markers should be expressed in the same cells (the differences is driven by noise and low number of UMIs). Additionally, most genes have only around one transcript. I’m wondering if this could be a problem during peer review and if it makes sense to annotate them in this way by just assigning a label regardless of depth if that marker is unique when cross referencing with single cell dataset.