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adr_llama3

Finetuning Llama3 8B instruction for ADR

allennlp

An open-source NLP research library, built on PyTorch.

alphafold

Open source code for AlphaFold.

assemblies-of-putative-sars-cov2-spike-encoding-mrna-sequences-for-vaccines-bnt-162b2-and-mrna-1273

RNA vaccines have become a key tool in moving forward through the challenges raised both in the current pandemic and in numerous other public health and medical challenges. With the rollout of vaccines for COVID-19, these synthetic mRNAs have become broadly distributed RNA species in numerous human populations. Despite their ubiquity, sequences are not always available for such RNAs. Standard methods facilitate such sequencing. In this note, we provide experimental sequence information for the RNA components of the initial Moderna (https://pubmed.ncbi.nlm.nih.gov/32756549/) and Pfizer/BioNTech (https://pubmed.ncbi.nlm.nih.gov/33301246/) COVID-19 vaccines, allowing a working assembly of the former and a confirmation of previously reported sequence information for the latter RNA. Sharing of sequence information for broadly used therapeutics has the benefit of allowing any researchers or clinicians using sequencing approaches to rapidly identify such sequences as therapeutic-derived rather than host or infectious in origin. For this work, RNAs were obtained as discards from the small portions of vaccine doses that remained in vials after immunization; such portions would have been required to be otherwise discarded and were analyzed under FDA authorization for research use. To obtain the small amounts of RNA needed for characterization, vaccine remnants were phenol-chloroform extracted using TRIzol Reagent (Invitrogen), with intactness assessed by Agilent 2100 Bioanalyzer before and after extraction. Although our analysis mainly focused on RNAs obtained as soon as possible following discard, we also analyzed samples which had been refrigerated (~4 ℃) for up to 42 days with and without the addition of EDTA. Interestingly a substantial fraction of the RNA remained intact in these preparations. We note that the formulation of the vaccines includes numerous key chemical components which are quite possibly unstable under these conditions-- so these data certainly do not suggest that the vaccine as a biological agent is stable. But it is of interest that chemical stability of RNA itself is not sufficient to preclude eventual development of vaccines with a much less involved cold-chain storage and transportation. For further analysis, the initial RNAs were fragmented by heating to 94℃, primed with a random hexamer-tailed adaptor, amplified through a template-switch protocol (Takara SMARTerer Stranded RNA-seq kit), and sequenced using a MiSeq instrument (Illumina) with paired end 78-per end sequencing. As a reference material in specific assays, we included RNA of known concentration and sequence (from bacteriophage MS2). From these data, we obtained partial information on strandedness and a set of segments that could be used for assembly. This was particularly useful for the Moderna vaccine, for which the original vaccine RNA sequence was not available at the time our study was carried out. Contigs encoding full-length spikes were assembled from the Moderna and Pfizer datasets. The Pfizer/BioNTech data [Figure 1] verified the reported sequence for that vaccine (https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/), while the Moderna sequence [Figure 2] could not be checked against a published reference. RNA preparations lacking dsRNA are desirable in generating vaccine formulations as these will minimize an otherwise dramatic biological (and nonspecific) response that vertebrates have to double stranded character in RNA (https://www.nature.com/articles/nrd.2017.243). In the sequence data that we analyzed, we found that the vast majority of reads were from the expected sense strand. In addition, the minority of antisense reads appeared different from sense reads in lacking the characteristic extensions expected from the template switching protocol. Examining only the reads with an evident template switch (as an indicator for strand-of-origin), we observed that both vaccines overwhelmingly yielded sense reads (>99.99%). Independent sequencing assays and other experimental measurements are ongoing and will be needed to determine whether this template-switched sense read fraction in the SmarterSeq protocol indeed represents the actual dsRNA content in the original material. This work provides an initial assessment of two RNAs that are now a part of the human ecosystem and that are likely to appear in numerous other high throughput RNA-seq studies in which a fraction of the individuals may have previously been vaccinated. ProtoAcknowledgements: Thanks to our colleagues for help and suggestions (Nimit Jain, Emily Greenwald, Lamia Wahba, William Wang, Amisha Kumar, Sameer Sundrani, David Lipman, Bijoyita Roy). Figure 1: Spike-encoding contig assembled from BioNTech/Pfizer BNT-162b2 vaccine. Although the full coding region is included, the nature of the methodology used for sequencing and assembly is such that the assembled contig could lack some sequence from the ends of the RNA. Within the assembled sequence, this hypothetical sequence shows a perfect match to the corresponding sequence from documents available online derived from manufacturer communications with the World Health Organization [as reported by https://berthub.eu/articles/posts/reverse-engineering-source-code-of-the-biontech-pfizer-vaccine/]. The 5’ end for the assembly matches the start site noted in these documents, while the read-based assembly lacks an interrupted polyA tail (A30(GCATATGACT)A70) that is expected to be present in the mRNA.

biobert-pretrained

BioBERT: a pre-trained biomedical language representation model for biomedical text mining

copula4retirement

coyd-iot

darknet-events

Go-based Darknet parser to extract Darknet events such as scanning and backscatter

darts

A python library for user-friendly forecasting and anomaly detection on time series.

docker-aws-graph-notebook

Dockerized AWS Graph Notebook

drwh

Dr Warehouse - document oriented biomedical data warehouse

fingpt

Data-Centric FinGPT. Open-source for open finance! Revolutionize 🔥 We release the trained model on HuggingFace.

gemini-chatbot-interface-with-streamlit

This project is a Streamlit-based chat application that interacts with the Gemini AI model, allowing users to engage in conversations with an artificial intelligence assistant. The application stores chat history, allowing users to revisit and continue previous conversations.

gpt-3

GPT-3: Language Models are Few-Shot Learners

gym

A toolkit for developing and comparing reinforcement learning algorithms.

gym-anytrading

The most simple, flexible, and comprehensive OpenAI Gym trading environment (Approved by OpenAI Gym)

hanlp

Natural Language Processing for the next decade. Tokenization, Part-of-Speech Tagging, Named Entity Recognition, Syntactic & Semantic Dependency Parsing, Document Classification

huggingface_notebook

Notebooks using the Hugging Face libraries 🤗

kaggle-web-traffic

1st place solution

kubernetes

Production-Grade Container Scheduling and Management

llama-2-onnx

llama-dl

High-speed download of LLaMA, Facebook's 65B parameter GPT model

llm_guardrail

LLM-based Guardrail Model for Secure GenAI System Resistant to Prompt Injection Attacks and Jailbreaking

lstm-fcn

Codebase for the paper LSTM Fully Convolutional Networks for Time Series Classification

ma-nlp

machine-learning-articles

🧠💬 Articles I wrote about machine learning, archived from MachineCurve.com.

mesh

Mesh TensorFlow: Model Parallelism Made Easier

mirai-source-code

Leaked Mirai Source Code for Research/IoC Development Purposes

mlflow

Open source platform for the machine learning lifecycle

nvflare

NVIDIA Federated Learning Application Runtime Environment