app.py

from transformers import AutoTokenizer, AutoModelForSequenceClassification, pipeline
import streamlit as st


@st.cache_data
def prepare_model():
    """
    Prepare the tokenizer and the model for classification.
    """
    tokenizer = AutoTokenizer.from_pretrained("oracat/bert-paper-classifier")
    model = AutoModelForSequenceClassification.from_pretrained(
        "oracat/bert-paper-classifier"
    )
    return (tokenizer, model)


def process(text):
    """
    Translate incoming text to tokens and classify it
    """
    pipe = pipeline("text-classification", model=model, tokenizer=tokenizer)
    result = pipe(text)[0]
    return result["label"]


tokenizer, model = prepare_model()


# State managements
#
# The state in the app is the title and the abstract.
# State management is used here in order to pre-fill
# input fields with values for demos.

if "title" not in st.session_state:
    st.session_state["title"] = ""

if "abstract" not in st.session_state:
    st.session_state["abstract"] = ""

if "output" not in st.session_state:
    st.session_state["output"] = ""


# Simple streamlit interface

st.markdown("### Hello, paper classifier!")


## Demo buttons and their callbacks


def demo_immunology_callback():
    """
    Use https://www.biorxiv.org/content/10.1101/2022.12.01.518788v1 for demo
    """
    paper_title = "Using TCR and BCR sequencing to unravel the role of T and B cells in abdominal aortic aneurysm"
    paper_abstract = "Recent evidence suggests that AAA displays characteristics of an autoimmune disease and it gained increasing prominence that specific antigen-driven T cells in the aortic tissue may contribute to the initial immune response. We found no clonal expansion of TCRs or BCRs in elastase-induced AAA in mice."
    st.session_state["title"] = paper_title
    st.session_state["abstract"] = paper_abstract


def demo_virology_callback():
    """
    Use https://doi.org/10.1016/j.cell.2020.08.001 for demo
    """
    paper_title = "Severe COVID-19 Is Marked by a Dysregulated Myeloid Cell Compartment"
    paper_abstract = "Coronavirus disease 2019 (COVID-19) is a mild to moderate respiratory tract infection, however, a subset of patients progress to severe disease and respiratory failure. The mechanism of protective immunity in mild forms and the pathogenesis of severe COVID-19 associated with increased neutrophil counts and dysregulated immune responses remain unclear. In a dual-center, two-cohort study, we combined single-cell RNA-sequencing and single-cell proteomics of whole-blood and peripheral-blood mononuclear cells to determine changes in immune cell composition and activation in mild versus severe COVID-19 (242 samples from 109 individuals) over time. HLA-DRhiCD11chi inflammatory monocytes with an interferon-stimulated gene signature were elevated in mild COVID-19. Severe COVID-19 was marked by occurrence of neutrophil precursors, as evidence of emergency myelopoiesis, dysfunctional mature neutrophils, and HLA-DRlo monocytes. Our study provides detailed insights into the systemic immune response to SARS-CoV-2 infection and reveals profound alterations in the myeloid cell compartment associated with severe COVID-19."
    st.session_state["title"] = paper_title
    st.session_state["abstract"] = paper_abstract


def clear_callback():
    """
    Clear input fields
    """
    st.session_state["title"] = ""
    st.session_state["abstract"] = ""
    st.session_state["output"] = ""


col1, col2, col3 = st.columns([1, 1, 1])
with col1:
    st.button("Demo: immunology", on_click=demo_immunology_callback)
with col2:
    st.button("Demo: virology", on_click=demo_virology_callback)
with col3:
    st.button("Clear fields", on_click=clear_callback)

## Input fields

placeholder = st.empty()

title = st.text_input("Enter the title:", key="title")
abstract = st.text_area(
    "... and maybe the abstract of the paper you want to classify:", key="abstract"
)

text = "\n".join([title, abstract])

## Output

if len(text.strip()) > 0:
    st.markdown(f"<h4>Predicted class: {process(text)}</h4>", unsafe_allow_html=True)