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aixbiobot.bsky.social
AI x Bio Discovery
@aixbiobot.bsky.social
620 followers 1 following 4.4K posts
Automated discovery of AI x Bio preprint papers.
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aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 2h
peleke-1: A Suite of Protein Language Models Fine-Tuned for Targeted Antibody Sequence Generation [new]
Gen. targeted Ab seqs. from antigen for in silico Ab discovery.
peleke-1: A Suite of Protein Language Models Fine-Tuned for Targeted Antibody Sequence Generation Figure 2 Figure 3 Figure 5
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aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 2h
CTDP: Identifying cell types associated with disease phenotypes using scRNA-seq data [new]
scRNA-seq identifies disease cell types via regularized regression & permutation tests (melanoma, COVID-19, cirrhosis).
CTDP: Identifying cell types associated with disease phenotypes using scRNA-seq data Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 4h
Benchmarking DNA Foundation Models for Genomic and Genetic Tasks [updated]
DNA foundation models benchmarked across genomic tasks, revealing performance variation based on architecture, pre-training data, and embedding strategy.
Figure 1 Figure 2 Figure 3 Figure 4
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 4h
Robust prediction of drug combination side effects in realistic settings [new]
Predicts polypharmacy side effects by learning latent signatures for drugs, pairs, & effects, evaluated in realistic warm/cold-start scenarios.
Robust prediction of drug combination side effects in realistic settings Figure 1 Figure 2 Table 2
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 5h
Fine-Tuning Protein Language Models on Human Spatial Constraint Yields State-of-the-Art Variant Effect Prediction [new]
Fine-tunes protein LMs w/ human spatial data for improved missense variant effect prediction.
Fine-Tuning Protein Language Models on Human Spatial Constraint Yields State-of-the-Art Variant Effect Prediction Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 11h
HXMS: a standardized file format for HX/MS data [new]
HXMS: Standardizes HX/MS data, preserving isotopic envelopes & experimental metadata. Enables improved analysis, sharing & machine learning.
HXMS: a standardized file format for HX/MS data Figure 1 Table 1 Table 2
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 13h
New proteomic biomarkers identified in plasma extracellular vesicles in sarcoidosis: a case-control matched study [new]
Plasma EV proteins: potential biomarkers for sarcoidosis, reflecting severity & regulating endocytosis.
New proteomic biomarkers identified in plasma extracellular vesicles in sarcoidosis: a case-control matched study Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 17h
GeneJEPA: A Predictive World Model of the Transcriptome [new]
Learns gene relationships by predicting masked gene representations from visible context, moving towards world-model inference of cellular state.
GeneJEPA: A Predictive World Model of the Transcriptome Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Gene regulatory innovations from transposable elements in mammalian cerebellum development [new]
Cerebellum gene reg. driven by TEs, w/cell-type & sp.-specific expression, esp. primate HERVL in granule cells.
Gene regulatory innovations from transposable elements in mammalian cerebellum development Figure 1 Figure 2 Figure 3
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aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Modeling Adoptive Cell Therapy in Bladder Cancer from Sparse Biological Data using PINNs [new]
PINNs learn time-varying interactions in bladder cancer combination therapy with sparse data, incorporating biological constraints for regularization.
Modeling Adoptive Cell Therapy in Bladder Cancer from Sparse Biological Data using PINNs Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Scaling Vision Transformers for Functional MRI with Flat Maps [new]
Transforms fMRI volumes into flat map videos to train Vision Transformers via masked autoencoding. The model learns representations for decoding brain states/traits.
Scaling Vision Transformers for Functional MRI with Flat Maps Figure 1 Figure 3 Figure 2
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
A Machine Learning Model Optimized for Local Data Stratifies Patients for the Adoptive Cell Therapy with Tumor Infiltrating Lymphocytes in Bladder Tumors [new]
Figure 1 Figure 3 Table 1 Abstract
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
DeepVul: A Multi-Task Transformer Model for Joint Prediction of Gene Essentiality and Drug Response [updated]
Predicts gene/drug response via latent space.
DeepVul: A Multi-Task Transformer Model for Joint Prediction of Gene Essentiality and Drug Response Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Omni-QALAS: Optimized Multiparametric Imaging for Simultaneous T1, T2 and Myelin Water Mapping [new]
Optimizes QALAS parameters using a self-supervised network for improved T1, T2, and myelin water fraction mapping.
Omni-QALAS: Optimized Multiparametric Imaging for Simultaneous T1, T2 and Myelin Water Mapping Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Precision Design of Cyclic Peptides using AlphaFold [new]
Uses AlphaFold to generate cyclic peptides binding HIV gp120. It enhances structural control via hotspot mapping & custom loss functions.
Precision Design of Cyclic Peptides using AlphaFold Figure 5 Table 10 Figure 9
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Spherical Radiomics - A Novel Approach to Glioblastoma Radiogenomic Analysis of Heterogeneity [new]
Glioblastoma radiogenomic analysis...
...uses spherical radiomics to better capture radial tumor growth patterns and predict molecular biomarkers from MRI.
Spherical Radiomics - A Novel Approach to Glioblastoma Radiogenomic Analysis of Heterogeneity Figure 1 Figure 2 Figure 4
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 19h
Deep learning the dynamic regulatory sequence code of cardiac organoid differentiation [new]
Predicts cardiac organoid regulatory code. Found context-dependent TF activity, lineage divergence, & validated MYOCD in ventricular spec.
Figure S1 Figure 2 Figure S2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 20h
Hybrid Deep Learning and Lee-Carter Model for Mortality Forecasting: A Study of US Adults Aged 35-80 [new]
DL(LSTM,BiLSTM,NN)+Lee-Carter models US adult mortality for enhanced forecasts.
Hybrid Deep Learning and Lee-Carter Model for Mortality Forecasting: A Study of US Adults Aged 35-80 Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 20h
AI-Assisted Cryo-ET Workflow for 3D Visualization of Chromatin during Cellular Differentiation [new]
AI cryo-ET: Chromatin change in stem cell to motor neuron differ'n, correl. 3D density w/ Hi-C.
Figure 1 Figure 2 Figure 3
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aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 21h
Odyssey: reconstructing evolution through emergent consensus in the global proteome [new]
Evolves proteins via multimodal LLMs & consensus. Learns representations w/ discrete diffusion & time-based unmasking.
Odyssey: reconstructing evolution through emergent consensus in the global proteome Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 21h
MAP-PRS: Multi-Ancestry Portfolio-Based Polygenic Risk Scores [new]
Mitigates PRS bias across ancestries using portfolio theory, balancing prediction accuracy and ancestry-specificity for equitable risk assessment.
MAP-PRS: Multi-Ancestry Portfolio-Based Polygenic Risk Scores Figure 1 Table 2 Figure 2
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 21h
Hypercholesterolemia Risk Prediction from Serum Metabolomics Using a Metabolic Pathway-Integrated Graph Neural Network [new]
GNN predicts hypercholesterolemia risk via metabolomics & pathways.
Hypercholesterolemia Risk Prediction from Serum Metabolomics Using a Metabolic Pathway-Integrated Graph Neural Network Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 21h
Large Numbers of New Human Paralogs Discovered [new]
Identifies new human paralogs by integrating sequence/structure homology and protein language models. Validates novel serine proteases and kinase paralogs.
Large Numbers of New Human Paralogs Discovered Figure 2 Figure 3 Figure 4
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 22h
SLOGEN: A Structure-based Lead Optimization Model Unifying Fragment Generation and Screening [new]
DL framework: generates & screens drug-like compounds via fragment generation & 3D protein-ligand modeling.
SLOGEN: A Structure-based Lead Optimization Model Unifying Fragment Generation and Screening Figure 1 Figure 2 Figure 3
aixbiobot.bsky.social
AI x Bio Discovery @aixbiobot.bsky.social · 22h
Perturbation-aware representation learning for in vivo genetic screens [new]
Learns representations from Perturb-seq data, incorporating perturbation efficacy & guide RNA abundance for improved cell state assignment.
Perturbation-aware representation learning for in vivo genetic screens Figure 1 Figure 2 Figure 3