Mohd Vasimuddin
@wasim_galaxy
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Parallel Computing, High Performance Computing, Computational Biology, Probabilistic Graphical Models, @Intel Labs (My views only)
Bangalore
Joined September 2010
Thrilled to share new version of Open Omics Acceleration Framework. Open Omics is envisioned as our performant and productive platform for digital biology including genomics, transcriptomics, proteomics, molecular docking, simulation, etc. https://t.co/bgAB3TxrUZ 1/n
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Thoroughly enjoyable collaboration with the brilliant scientist and long time collaborator @chirgjain #genomics
New method speeds up genome alignment of complete and near-complete genome assemblies in minimap2. Can also be useful for faster read mapping Github: https://t.co/odCWHHIDHI DOI: https://t.co/Rm1Xa4PPHE Led by @GhanshyamChand5, collab with @sanchit_misra @wasim_galaxy @intel
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Hey @Flipkart, what happened! can't even install one AC. It's been 5 days since the product arrived, but your people are fooling around and not helping with the installation.
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Happy to report new version of our LISA paper that uses learned-indexes to accelerate DNA sequence search on CPU. Key addition is speedup of seeding phase of BWA-MEM2 by up to 4.7x. 1/n https://t.co/fJaTR15tva…
@Saurabh_Kalikar @wasim_galaxy @tatbul @tim_kraska @lh3lh3 #genomics
biorxiv.org
Next Generation Sequencing (NGS) is transforming fields like genomics, transcriptomics, and epigenetics with rapidly increasing throughput at reduced cost. This also demands overcoming performance...
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It gives me great pleasure to announce that we have released 2.0 version of Open Omics Acceleration Framework with best-in-class performance/cost for 4 pipelines. Open Omics Acceleration Framework is our open sourced data science & AI framework for accelerating digital biology.
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Super excited to report that our accelerated version of AlphaFold2 inference based end-to-end pipeline for protein folding delivers industry-leading performance, folding a set of 77 proteins (<1K in length) in less than 200mins on a dual socket CPU platform.
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I am elated to share that our accelerated version of Google’s DeepVariant based short read germline variant calling pipeline achieves leadership performance, processing the standard HG001 WGX 30x dataset in just 15 mins using 8 CPU sockets and just 3 mins using 64 CPU sockets.
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Happy to announce this event! Join us to hear latest research trends on various topics of computational and systems biology
Symposium on Big Data Algorithms for Biology (BDBIO-2023) will be held in @cdsiisc @iiscbangalore on June 2nd and 3rd Interested participants should register using the link https://t.co/x4nURYPwiR
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1980's construction worker Albert Stalk didn't mess about.. 😮 WOW
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Excited to release mm2-fast-v1.0, the first production ready version compatible with latest minimap2 v2.24 https://t.co/3vOAiTbjxE
@sanchit_misra @wasim_galaxy @lh3lh3 @chirgjain #minimap2 #longreads #HPC #genomics
github.com
This release of mm2-fast is compatible with and achieves the same accuracy as minimap2 v2.24. Moreover, the performance improvement vs minimap2 v2.24 is similar to what mm2-fast-v1.0pre1 gets vs. m...
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Excited to share DistGNN-MB - our work on distributed large-scale mini-batch based GNN training on x86.
DistGNN-MB: novel compute-communication overlap algorithm improves TTT for GraphSAGE on a 3rd gen Intel Xeon cluster by >5x over the widely used DistDGL. Stay tuned for optimization for our next-gen Xeon! https://t.co/uWioKIfbBd
@BharatBKaul @sanchit_misra
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mm2-fast: accelerated version of minimap2 that is up to 1.8x faster. #minimap2 #Genomics #longreads #HPC #iamintel @lh3lh3 @chirgjain @wasim_galaxy @Saurabh_Kalikar
Excited to share a blog summarizing our work on mm2-fast - our accelerated version of minimap2 that is up to 1.8x faster: https://t.co/cLypctu56F. This work also got published at "Nature Computational Science" earlier this year. Code availability https://t.co/LXWKHBJPEM
#Minimap2
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bwa-mem2 seeding accelerated using machine learning.
I am excited to announce that we have further accelerated seeding phase of bwa-mem2 using learned (machine learning based) indexes by up to 4.5x while maintaining identical output https://t.co/iXN8xOy2RW.
@sanchit_misra @wasim_galaxy @lh3lh3 @tim_kraska #genomics #bwamem
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Accelerating Genomics Pipelines Using Intel’s Open Omics Acceleration Framework on AWS https://t.co/wJqiB7QxIp via @awscloud
aws.amazon.com
In this blog, we showcase the first version of Open Omics and benchmark three applications that are used in processing NGS data – sequence alignment tools BWA-MEM, minimap2, and single cell ATAC-Seq...
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Pre-release of mm2-fast - our accelerated version of minimap2 - is out! Compatible with minimap2 v2.22. Working on another release that would be compatible with latest minimap2 version (v2.24). #genomics #longreads #Minimap2 #HPC @Saurabh_Kalikar @chirgjain @wasim_galaxy @lh3lh3
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We are hiring motivated researchers at our India branch of Parallel Computing Labs, Intel, for our digital biology research program. DM or email me if interested. #HPC #Digitalbiology #ComputationalBiology #MachineLearning #ParallelComputing #DataManagement #IAmIntel #Intel
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WooHoooo !!! Congratulations @sanchit_misra @chirgjain @wasim_galaxy @lh3lh3; And this is just a start to our journey of bringing power of Intel Xeon & computing to usher in an era of Digital Biology and enrich billions of lives #iamIntel
Our paper on acceleration of minimap2 is published at "Nature Computational Science"! Woohoo! Here is the link to access full text: https://t.co/maIapELM5x. Latest code: https://t.co/dvBXCNu923
#genomics #longreads #Minimap2 #HPC
@Saurabh_Kalikar @chirgjain @wasim_galaxy @lh3lh3
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Super excited to share that we have accelerated SCANPY based single cell genomics workflow for analyzing 1.3 M mouse brain cells by ~50x on a single Sapphire Rapids CPU to finish in ~6 mins (~2x faster than a single A100 GPU) #IAmIntel
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Graph Neural Networks power inference on data described by graph structures. Check out our lab showing the impressive GNN training performance on Intel Xeon: https://t.co/SENv0w3eet Sasi Avnacha, @sanchit_misra @wasim_galaxy @RamanarayanM @IntelAIResearch @DubeyPradeepK
linkedin.com
Challenge of Sparse Irregular Compute: Xeon accelerates Graph Neural Networks #iamintel, #gnn, #intellabs, Great collaboration with my Intel Labs team mates: Sanchit Misra, Md Vasimuddin, Ramanarayan...
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I am thrilled to present mm2-fast: an accelerated version of Minimap2 that achieves up to 3.5x speedup on CPUs while maintaining identical output. Code: https://t.co/yjjNhF41EK
#genomics #longreads #Minimap2 #HPC @Saurabh_Kalikar @chirgjain @wasim_galaxy @lh3lh3
Accelerating long-read analysis on modern CPUs https://t.co/0ZNrYUssm7
#bioRxiv
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