Rising — Salient

RECON infers regions of interest from H&E images and reconstructs whole-slide molecular profiles at single-cell resolution

1d · Yang, X., Hao, N., Zhao, R., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Spatial Transcriptomics As Rasterized Image Tensors (STARIT) characterizes cell states with subcellular molecular heterogeneity

1d · Velazquez, D., Hallinan, C., An, R., et al. · biorxiv

method development top 10% novel

Surfaced because: matches the platform's topic region.

Data-driven spectroscopic dictionaries and detector-calibrated inference for photon-limited Raman hyperspectral imaging of living cells

1d · Yagi, S., Sagami, N., Eshima, I., et al. · biorxiv

method development top 1% novel

Surfaced because: matches the platform's topic region.

The first OpenBind release: An open experimental structure-affinity dataset and benchmark for structure-based AI

1d · Nelen, J., Khan, O., Adams, E., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

HESTIA: Scalable Multimodal Integration of Histology and High-Resolution Spatial Transcriptomics for Robust Spatial Domain Identification

2d · Zhong, Z., Zhu, X., Guo, J., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

A self-supervised DNA foundation model with collapse-resistant multimodal fusion

2d · Chen, Y. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

GNMCADS: Sampling For Protein Conformation Diversity With Gaussian Network Model Guided Condition Annealed Diffusion Sampler

1d · Uzum, A. S., Haliloglu, T. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

TomatoPGFM: A graph-conditioned foundation model for tomato pangenomes

1d · Han, J., yushan, t., Wang, J., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Accurate and efficient prediction of protein conformations with ProtMonomer

2d · Si, Y., Zhang, S., Chen, L. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Topologically-based parameter inference for agent-based model selection from spatiotemporal cellular data

4d · Wenzel, A. R., Haughey, P. M., Nguyen, K. C., et al. · biorxiv

method development code benchmarked top 10% noveltop 1% open

Surfaced because: open code, benchmarked against baselines.

Scaling recipes for single-cell RNA sequencing foundation models: when do scaling laws hold?

1d · Borra, F., Ciro', G., Castellini, A., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Calibration-free compression brings Evo 2 to its full million-token context on a single GPU

1d · Patsakis, M., Tzanakakis, A., Georgakopoulos-Soares, I. · biorxiv

method development

Surfaced because: matches the platform's topic region.

XpBrew and PanXpresso - automatic RNA-seq processing workflow and comprehensive collection of gene expression data

1d · Natarajan, S., Sterling, C., Choudhary, N., et al. · biorxiv

method development code top 2% open

Surfaced because: open code.

PhageTransformer - scalable and accurate host assignments for bacteriophages

3d · Siemers, M., Lopez, J. L., Dutilh, B. E. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

nf_xpatial: A Reproducible Framework for Standardized Preprocessing and Clustering of Xenium Data

4d · Potter, L. A., Trull, A., Kumar, N., et al. · biorxiv

method development top 3% novel

Surfaced because: matches the platform's topic region.

Using sequence-to-function models to interpret archaic hominin introgression

1d · Comerford, M., Alvim, I., Johanson, T. M., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

Vipsania: Unsupervised Deep Gene Finding

3d · Krieg, R., Becker, F., Saenko, S., et al. · biorxiv

method development code top 2% open

Surfaced because: open code.

PMPNN-DDG: an accurate machine learning-based {triangleup}{triangleup}G prediction pipeline trained on a novel interpretable feature set extracted from ProteinMPNN

6d · Jani, R., Ahmed, S. · biorxiv

method development code benchmarked top 1% open

Surfaced because: open code, benchmarked against baselines.

Chemi-Proteome Language Attention Network Empowers Fragment-Based Ligand Interactome and Binding Sites Discovery with Evidence

3d · Liao, B., He, J., zhao, M., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

RegimeFormer: A Large Protein Model of Global Perturbation Regimes

3d · Ma, S., Chai, Y., Wu, Y., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Universal physical principles of protein structural genesis emerge in language-model representation space

2d · Chuanyang, L., Liu, J., Qiu, X., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

BatchRefiner: fast, significant improvement in batch integration of single-cell embeddings with ensemble refinement

7d · Schäffer, D. E., Kang, H., Aksu, E. D., et al. · biorxiv

method development benchmarked top 1% noveltop 2% open

Surfaced because: benchmarked against baselines.

OmicsFM brings proteomics into the foundation model era

5d · Heyndrickx, S., Gabriels, R., Ramadasan, H., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

SPC-Clean: A napari Plugin for Reducing Speckle and Isolated Pixel Noise in Fluorescence Microscopy Images

6d · Alirezazadeh, P., Kirsch, E. M., Tian, Y., et al. · biorxiv

method development top 2% novel

Surfaced because: matches the platform's topic region.

scDisent: regulatory-aware disentangled representation learning for multi-omic single-cell analysis

7d · Xi, G. · biorxiv

method development code benchmarked top 1% open

Surfaced because: open code, benchmarked against baselines.

A pretrained unified model enables cellular functional profile prediction and multi-objective virtual drug screening

5d · Chen, R., Huang, L., Qiao, Y., et al. · biorxiv

method development

Surfaced because: matches the platform's topic region.

OmniScore: Universal Scoring of Diverse Biomolecular Complexes via Equivariant Geometry-Aware Discrete Representation Learning

4d · Bui, T.-C., Lee, J., Ko, J. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Gene expression inference from cell-free DNA using uncertainty-aware deep learning

5d · Patton, R. D., McDeed, A. P., Netzley, A., et al. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

Evaluating the performance of splicing predictors on thousands of synthetic gene variants

6d · Bellido Molias, F., Kudla, G. · biorxiv

method development benchmarked top 2% open

Surfaced because: benchmarked against baselines.

A multimodal perturbation atlas defines the phenotypic resolution of cellular morphology.

8d · Liu, C., Hillsley, A., Sekhar, M., et al. · biorxiv

method development top 3% novel

Surfaced because: matches the platform's topic region.