Merge pull request #15 from mims-harvard/quick_fixes

publications consolidate publications to new backend and add moml, neurips, western publications
mims-harvard · Dec 21, 2024 · c29516e · c29516e
2 parents a2cf11b + 915109c
commit c29516e
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Showing 11 changed files with 161 additions and 4 deletions.
diff --git a/app.py b/app.py
@@ -1,5 +1,6 @@
 # from data.single_pred_tasks.tasks import _TASKS
-import task_datasets as data
+import backend.task_datasets as data
+from backend.metadata.publications import _PUBLICATIONS as publications
 import benchmark.groups as benchmark_groups
 import benchmark.leaderboards as benchmark_leaderboards
 
@@ -9,7 +10,11 @@
 
 @app.route('/')
 def index():
-    return render_template('index.html')
+    publications.sort(key=lambda x: (-x["year"], -x["month"]))
+    args = {
+        "publications": publications
+    }
+    return render_template('index.html', **args)
 
 @app.route('/start', strict_slashes=False)
 def start():

diff --git a/backend/metadata/publications.py b/backend/metadata/publications.py
@@ -0,0 +1,140 @@
+from ..model.homepage_publication import HomepagePublication
+
+_PUBLICATIONS = [
+    HomepagePublication(
+        "Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics",
+        "(Spotlight) NeurIPS 2024 Workshop on AI for New Drug Modalities",
+        2024,
+        12,
+        {
+            "Paper": "https://openreview.net/pdf?id=kL8dlYp6IM",
+            "Poster": "https://drive.google.com/file/d/1plypydZCaegbgxyCl-xehFxSgwX6e8So/view?usp=sharing"
+        }
+    ),
+    HomepagePublication(
+        "(Seminar) Signals in the Cells: Multimodal and Contextualized Machine Learning Foundations for Therapeutics",
+        "Western Bioinformatics Seminar Series: Alejandro Velez-Arce",
+        2024,
+        11,
+        {
+            "Event": "https://www.events.westernu.ca/events/schulich-medicine-dentistry/2024-11/western-bioinformatics-nov14.html",
+        }
+    ),
+    HomepagePublication(
+        "TDC-2: Multimodal Foundation for Therapeutic Science",
+        "Molecular Machine Learning Conference (MoML2024). Hosted at Mila Agora on June 19th",
+        2024,
+        6,
+        {
+            "Paper": "https://www.biorxiv.org/content/10.1101/2024.06.12.598655v2",
+            "Conference": "https://portal.ml4dd.com/moml-2024",
+            "Poster and Tweet": "https://x.com/ProjectTDC/status/1803581129376629234"
+        }
+    ),
+    HomepagePublication(
+        "Zero-shot Prediction of Therapeutic Use with Geometric Deep Learning and Clinician Centered Design",
+        "Nature Medicine, 2024",
+        2024,
+        3,
+        {
+            "Paper": "https://www.nature.com/articles/s41591-024-03233-x",
+            "TxGNN Explorer": "http://txgnn.org/"
+        }
+    ),
+    HomepagePublication(
+        "Artificial Intelligence Foundation for Therapeutic Science",
+        "Nature Chemical Biology, 2022",
+        2022,
+        3,
+        {
+            "Paper": "https://www.nature.com/articles/s41589-022-01131-2"
+        }
+    ),
+    HomepagePublication(
+        "Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development",
+        "NeurIPS, 2021",
+        2021,
+        11,
+        {
+            "Paper": "https://datasets-benchmarks-proceedings.neurips.cc/paper/2021/hash/4c56ff4ce4aaf9573aa5dff913df997a-Abstract-round1.html",
+            "Poster": "https://drive.google.com/file/d/1LfF8mfPLUqAVEzH3KPBxDO_VF7nLFtiJ/view?usp=sharing"
+        }
+    ),
+    HomepagePublication(
+        "Benchmarking Molecular Machine Learning in Therapeutics Data Commons",
+        "ELLIS ML4Molecules, 2021",
+        2021,
+        8,
+        {
+            "Paper": "https://cloud.ml.jku.at/s/54pB5Eqf6ftX7qA",
+            "Slides": "https://drive.google.com/file/d/1iOSW_5eruca4vdygDxS1H64c49oQuH40/view?usp=sharing"
+        }
+    ),
+    HomepagePublication(
+        "Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development",
+        "Baylearn, 2021",
+        2021,
+        6,
+        {
+            "Slides": "https://drive.google.com/file/d/1BNpk3dOdqE3ksgyVV-V3xySdBMq-8cXL/view?usp=sharing",
+            "Poster": "https://drive.google.com/file/d/1LfF8mfPLUqAVEzH3KPBxDO_VF7nLFtiJ/view?usp=sharing"
+        }
+    ),
+    HomepagePublication(
+        "Therapeutics Data Commons",
+        "NSF-Harvard Symposium on Drugs for Future Pandemics, 2020",
+        2020,
+        12,
+        {
+            "Slides": "https://drive.google.com/file/d/11eTrh_lsqPcwu3RZRYjJGNpJ3s18YlBS/view",
+            "Video": "https://harvard.zoom.us/rec/share/HO0TjRPs56YG-Fu3i033izaTwebB4KwUhPeNURkWSI-anrH9su03lCtUlHeZG-WP.67ZJmAIHsD7Q_2GQ",
+            "#futuretx20": "https://www.drugsymposium.org/"
+        }
+    ),
+    HomepagePublication(
+        "Machine Learning to Translate the Cancer Genome and Epigenome Session",
+        "AACR Annual Meeting",
+        2022,
+        2,
+        {
+            "Meeting": "https://www.aacr.org/meeting/aacr-annual-meeting-2022/"
+        }
+
+    ),
+    HomepagePublication(
+        "Few-Shot Learning for Network Biology",
+        "KDD Workshop on Data Mining in Bioinformatics",
+        2021,
+        1,
+        {
+            "keynote": "https://biokdd.org/biokdd21/keynote.html"
+        }
+    ),
+    HomepagePublication(
+        "Actionable machine learning for drug discovery and development",
+        "Broad Institute, Models, Inference & Algorithms Seminar",
+        2021,
+        0,
+        {
+            "Talk": "https://www.broadinstitute.org/talks/actionable-machine-learning-drug-discovery-and-development"
+        }
+    ),
+    HomepagePublication(
+        "Graph Neural Networks for Biomedical Data",
+        "Machine Learning in Computational Biology",
+        2020,
+        2,
+        {
+            "Schedule": "https://sites.google.com/cs.washington.edu/mlcb2020/schedule?authuser=0"
+        }
+    ),
+    HomepagePublication(
+        "Graph Neural Networks for Identifying COVID-19 Drug Repurposing Opportunities",
+        "MIT AI Cures",
+        2020,
+        1,
+        {
+            "Webpage": "https://www.aicures.mit.edu/drugdiscoveryconference"
+        }
+    )
+]
diff --git a/backend/model/homepage_publication.py b/backend/model/homepage_publication.py
@@ -0,0 +1,9 @@
+
+class HomepagePublication(dict):
+
+    def __init__(self, name, venue, year, month, links = {}):
+        self["name"] = name
+        self["venue"] = venue
+        self["year"] = year
+        self["month"] = month
+        self["links"] = links
diff --git a/task_datasets/__init__.py → backend/task_datasets/__init__.py b/task_datasets/__init__.py → backend/task_datasets/__init__.py
diff --git a/task_datasets/multi_pred_tasks/__init__.py → ...ask_datasets/multi_pred_tasks/__init__.py b/task_datasets/multi_pred_tasks/__init__.py → ...ask_datasets/multi_pred_tasks/__init__.py
diff --git a/task_datasets/multi_pred_tasks/datasets.py → ...ask_datasets/multi_pred_tasks/datasets.py b/task_datasets/multi_pred_tasks/datasets.py → ...ask_datasets/multi_pred_tasks/datasets.py
diff --git a/task_datasets/multi_pred_tasks/tasks.py → ...d/task_datasets/multi_pred_tasks/tasks.py b/task_datasets/multi_pred_tasks/tasks.py → ...d/task_datasets/multi_pred_tasks/tasks.py
diff --git a/task_datasets/single_pred_tasks/__init__.py → ...sk_datasets/single_pred_tasks/__init__.py b/task_datasets/single_pred_tasks/__init__.py → ...sk_datasets/single_pred_tasks/__init__.py
diff --git a/task_datasets/single_pred_tasks/datasets.py → ...sk_datasets/single_pred_tasks/datasets.py b/task_datasets/single_pred_tasks/datasets.py → ...sk_datasets/single_pred_tasks/datasets.py
diff --git a/task_datasets/single_pred_tasks/tasks.py → .../task_datasets/single_pred_tasks/tasks.py b/task_datasets/single_pred_tasks/tasks.py → .../task_datasets/single_pred_tasks/tasks.py
diff --git a/templates/index.html b/templates/index.html
@@ -275,7 +275,10 @@
                     <div class="column is-12 is-size-5">
                         <div class="box has-background-white">
                             <ul>
-                                <li><b>TDC-2: Multimodal Foundation for Therapeutic Science</b> bioRxiv, 2024 <a href="https://www.biorxiv.org/content/10.1101/2024.06.12.598655v2">[Paper]</a></li>
+                                {% for pub in publications %}
+                                <li><b>{{ pub.name }}.</b> {{ pub.venue }} {% for key, url in pub.links.items() %} <a href="{{ url }}">[{{ key }}] </a> {% endfor %}</li>
+                                {% endfor %}
+                                <!-- <li><b>TDC-2: Multimodal Foundation for Therapeutic Science</b> bioRxiv, 2024 <a href="https://www.biorxiv.org/content/10.1101/2024.06.12.598655v2">[Paper]</a></li>
                                 <li><b>Zero-shot Prediction of Therapeutic Use with Geometric Deep Learning and Clinician Centered Design,</b> MedRxiv, 2023 <a href="https://www.medrxiv.org/content/10.1101/2023.03.19.23287458">[Paper]</a> <a href="http://txgnn.org/">[TxGNN Explorer]</a></li>
 
                                 <li><b>Artificial Intelligence Foundation for Therapeutic Science,</b> Nature Chemical Biology, 2022 <a href="https://www.nature.com/articles/s41589-022-01131-2">[Paper]</a> </li>
@@ -298,7 +301,7 @@
 
                                 <li><b>Graph Neural Networks for Biomedical Data</b>, <a href="https://sites.google.com/cs.washington.edu/mlcb2020/schedule?authuser=0">Machine Learning in Computational Biology</a>, 2020</li>
 
-                                <li><b>Graph Neural Networks for Identifying COVID-19 Drug Repurposing Opportunities</b>, <a href="https://www.aicures.mit.edu/drugdiscoveryconference">MIT AI Cures</a>, 2020</li>
+                                <li><b>Graph Neural Networks for Identifying COVID-19 Drug Repurposing Opportunities</b>, <a href="https://www.aicures.mit.edu/drugdiscoveryconference">MIT AI Cures</a>, 2020</li> -->
                             </ul>
                         </div>
                     </div>