Curated papers with reproducible code and real impact
Auto-updated from arXiv & bioRxiv · Last sync: 4/1/2026
Guangli Li, Canbiao Wu, Na Tian, Li Zhang, Zhen Liang
arXiv:2603.26713v1 Announce Type: new Abstract: Electroencephalography (EEG)-based emotion recognition suffers from severe performance degradation when models are transferred across heterogeneous d...
Guojie Li, Liu Hong
arXiv:2603.26803v1 Announce Type: new Abstract: Physics-informed neural networks (PINNs) offer a unified framework for solving both forward and inverse problems of differential equations, yet their...
Mitra Nasr Azadani, Syed Usama Imtiaz, Nasrin Alamdari
arXiv:2603.26816v1 Announce Type: new Abstract: High-dimensional low-sample-size (HDLSS) datasets constrain reliable environmental model development, where labeled data remain sparse. Reinforcement...
Yaoyu Fang, Jiahe Qian, Xinkun Wang, Lee A. Cooper, Bo Zhou
arXiv:2603.26827v1 Announce Type: new Abstract: Spatial Transcriptomics (ST) provides spatially resolved gene expression profiles within intact tissue architecture, enabling molecular analysis in h...
Alexander Arjun Lobo, Urvi Awasthi, Leonid Zhukov
arXiv:2603.26889v1 Announce Type: new Abstract: Molecular discovery is increasingly framed as an inverse design problem: identifying molecular structures that satisfy desired property profiles unde...
Bryan Shaddy, Haitong Qin, Brianna Binder, James Haley, Riya Duddalwar, Kyle Hilburn, Assad Oberai
arXiv:2603.26975v1 Announce Type: new Abstract: This study presents a probabilistic surrogate model for localized wildfire spread based on a conditional flow matching algorithm. The approach models...
Marco Garcia Noceda, Matthew T Noakes, Andrew FigPope, Daniel E Mattox, Bryan Howie, Harlan Robins
arXiv:2603.26994v1 Announce Type: new Abstract: T cells are a critical component of the adaptive immune system, playing a role in infectious disease, autoimmunity, and cancer. T cell function is me...
Urvi Awasthi, Alexander Arjun Lobo, Leonid Zhukov
arXiv:2603.27113v1 Announce Type: new Abstract: Generating chemically valid 3D molecules is hindered by discrete bond topology: small local bond errors can cause global failures (valence violations...
Yuying Lu, Wenbo Fei, Yuanjia Wang, Molei Liu
arXiv:2603.27114v1 Announce Type: new Abstract: Precision mental health requires treatment decisions that account for heterogeneous symptoms reflecting multiple clinical domains. However, existing ...
Mirko Degli Esposti
arXiv:2603.27312v1 Announce Type: new Abstract: Maximum entropy (MaxEnt) modelling provides a principled framework for generating synthetic populations from aggregate census data, without access to...
Shafayeth Jamil, Rehan Kapadia
arXiv:2603.27442v1 Announce Type: new Abstract: When the system is linear, why should learning be nonlinear? Linear dynamical systems, the analytical backbone of control theory, signal processing a...
Truong-Son Hy
arXiv:2603.27526v1 Announce Type: new Abstract: Protein fitness optimization is inherently a discrete combinatorial problem, yet most learning-based approaches rely on continuous representations an...
Sahil Shrivastava
arXiv:2603.27589v1 Announce Type: new Abstract: Diabetes mellitus affects over 537 million adults worldwide. Insulin-dependent patients require continuous glucose monitoring and precise dose calcul...
Jnaneshwar Das
arXiv:2603.27880v1 Announce Type: new Abstract: We propose a variational framework in which the kernel function k : X x X -> R, interpreted as the foundational object encoding what distinctions an ...
Christopher Cruz
arXiv:2603.27905v1 Announce Type: new Abstract: We present ATLAS-RTC, a runtime control system for autoregressive language models that enforces structured output during decoding. ATLAS-RTC monitors...
Ehsan Zeraatkar, Rodion Podorozhny, Jelena Te\v{s}i\'c
arXiv:2603.27929v1 Announce Type: new Abstract: Reconstructing continuous physical fields from sparse, irregular observations is a central challenge in scientific machine learning, particularly for...
Kieran Didi, Zuobai Zhang, Guoqing Zhou, Danny Reidenbach, Zhonglin Cao, Sooyoung Cha, Tomas Geffner, Christian Dallago, Jian Tang, Michael M. Bronstein, Martin Steinegger, Emine Kucukbenli, Arash Vahdat, Karsten Kreis
arXiv:2603.27950v1 Announce Type: new Abstract: Protein interaction modeling is central to protein design, which has been transformed by machine learning with applications in drug discovery and bey...
Angelo Rajendram, Xieting Chu, Vijay Ganesh, Max Fieg, Aishik Ghosh
arXiv:2603.27955v1 Announce Type: new Abstract: We introduce AI-Kolmogorov, a novel framework for Symbolic Density Estimation (SymDE). Symbolic regression (SR) has been effectively used to produce ...
Yakov Pyotr Shkolnikov
arXiv:2603.28040v1 Announce Type: new Abstract: Deep learning training is non-deterministic: identical code with different random seeds produces models that agree on aggregate metrics but disagree ...
Pulock Das, Al Amin, Kamrul Hasan, Rohan Thompson, Azubike D. Okpalaeze, Liang Hong
arXiv:2603.28057v1 Announce Type: new Abstract: Deep learning (DL) models have achieved strong performance in an intelligence healthcare setting, yet most existing approaches operate as black boxes...
Siyuan Du, Siyi Li, Shuwei Bai, Ang Li, Haolin Li, Mingqing Xiao, Yang Pan, Dongsheng Li, Weidi Xie, Yanfeng Wang, Ya Zhang, Chencheng Zhang, Jiangchao Yao
arXiv:2603.29176v1 Announce Type: new Abstract: Parkinson's disease (PD) affects over ten million people worldwide. Although temporal interference (TI) and deep brain stimulation (DBS) are promisin...
Claus Metzner, Achim Schilling, Andreas Maier, Thomas Kinfe, Patrick Krauss
arXiv:2603.29597v1 Announce Type: new Abstract: Reservoirs, typically implemented as recurrent neural networks with fixed random connection weights, can be combined with a simple trained readout la...
Pegah Ramezani, Thomas Kinfe, Andreas Maier, Achim Schilling, Patrick Krauss
arXiv:2603.29617v1 Announce Type: new Abstract: Understanding how the brain processes linguistic constructions is a central challenge in cognitive neuroscience and linguistics. Recent computational...
L. Ghiringhelli, A. Zambon, G. Tiana
arXiv:2603.29529v1 Announce Type: cross Abstract: We investigate the parameter space of transformer models trained on protein sequence data using a statistical mechanics framework, sampling the los...
Franco Rugolon, Korbinian Randl, Braslav Jovanovic, Ioanna Miliou, Panagiotis Papapetrou
arXiv:2603.29793v1 Announce Type: cross Abstract: Multimodal Machine Learning offers a holistic view of a patient's status, integrating structured and unstructured data from electronic health recor...
Iain Swift, JingHua Ye, Ruairi O'Reilly
arXiv:2603.29977v1 Announce Type: cross Abstract: Multimodal deep learning for cancer prognosis is commonly assumed to benefit from synergistic cross-modal interactions, yet this assumption has not...
Zofia Rudnicka, Janusz Szczepanski, Agnieszka Pregowska
arXiv:2508.20125v2 Announce Type: replace-cross Abstract: Purpose: Spiking neural networks (SNNs) have recently gained attention as energy-efficient, biologically plausible alternatives to conventi...
Hongqian Niu, Jordan Bryan, Jacob Williams, Hufeng Zhou, Haoyu Zhang, Xihao Li, Didong Li
arXiv:2509.20702v2 Announce Type: replace-cross Abstract: Recent advances in large language model (LLM) embeddings have enabled powerful representations for biological data, but most applications t...
Ahmed A. Elhag, Arun Raja, Alex Morehead, Samuel M. Blau, Hongtao Zhao, Christian Tyrchan, Eva Nittinger, Garrett M. Morris, Michael M. Bronstein
arXiv:2510.00027v3 Announce Type: replace-cross Abstract: Accurate and scalable machine-learned inter-atomic potentials (MLIPs) are essential for molecular simulations ranging from drug discovery t...
Wanying Qu, Jianxiong Gao, Wei Wang, Yanwei Fu
arXiv:2603.24176v2 Announce Type: replace-cross Abstract: Capturing dynamic spatiotemporal neural activity is essential for understanding large-scale brain mechanisms. Functional magnetic resonance...
Zambaldi et al.
AlphaProteo generates novel protein binders with state-of-the-art binding affinities across diverse targets.
Hayes et al.
A multimodal generative language model that reasons over the sequence, structure, and function of proteins.
Abramson et al.
AlphaFold 3 can predict the joint structure of complexes including proteins, nucleic acids, small molecules, ions, and modified residues.
Watson et al.
A structure denoising diffusion probabilistic model for protein backbone generation.
Corso et al.
A diffusion generative model over the non-Euclidean manifold of ligand poses for molecular docking.
Frost, H. R.
We describe an approach for analyzing biological networks using rows of the Krylov subspace of the adjacency matrix. Specifically, we explore the scenario where the Krylov subspace matrix is comput...
Joshi, S., Sowdhamini, R.
Motivation: Characterizing atomic-level stability and cooperative interaction networks is essential for understanding protein function and evolution. However, existing tools often lack the precisio...
Garcia, J. J., Yu, K. M., Freudenreich, C. H., Cowen, L.
In Baker's yeast, there exists a comprehensive collection of pairwise epistasis experiments that, for nearly every pair of non-essential genes, measures the growth of the double-knockout strain as ...
Zhang, H., Jiang, X., Yu, X., Wang, H., Lu, P., Hou, J., Guo, Q., Xiao, T., Wu, S., Yin, H., Geng, P. X., Guo, J., Jousset, A., Wei, Z., Xiao, Y., Zhu, H.
Amplicon sequencing protocol targeting the 16S rRNA gene is a widely used, cost-effective method for exploring bacterial communities. However, its performance is often limited by primer bias arisin...
Bishop, H. V., Prendergast, P. J., Herbold, C. W., Ogilvie, O. J., Dobson, R. C. J.
Celiac disease is an autoimmune condition where the gut microbiome is increasingly recognised as a key environmental factor. While high-throughput sequencing has led to a surge in celiac-related gu...
Chen, Y., Qi, C., Fang, H., Luan, F., Zhang, Z., Arya, S., Wei, Z.
Intercellular communication is a fundamental driver of cellular identity and tissue homeostasis, yet current single-cell representation learning frameworks predominantly model cell state as a funct...
Rios, E., Jin, S., Zhang, C., Neuhaus, F., He, X., Weissenberger, S., Schirmer, M.
The human gut microbiome has been linked to inflammatory bowel disease (IBD) and colorectal cancer (CRC), yet identifying disease-associated microbial genes across diverse human cohort studies rema...
Lin, R., Ahnert, S. E.
Protein function is fundamentally driven by structural dynamics, yet the majority of structural bioinformatics treats proteins as static rigid bodies. While Molecular Dynamics (MD) simulations atte...
He, J., Peng, C., Zhang, Y., Wang, Z., Zhang, H., Fang, L., Zhao, P.
Transposable elements (TEs) are pivotal drivers of eukaryotic genome evolution and phenotypic diversity. However, their functional contributions to complex traits remain largely obscured by express...
Hoyt, S. H., Reddy, T. E., Gordan, R., Allen, A. S., Majoros, W. H.
Interpreting the effects of novel mutations on phenotypic traits remains challenging, particularly for cis-regulatory variants. For rare variants, individuals typically possess at most one affected...
Harviainen, J., Sena, F., Moumard, C., Politov, A., Schmidt, S., Tomescu, A. I.
Motivation: Pangenome graphs are increasingly used in bioinformatics, ranging from environmental surveillance and crop improvement to the construction of population-scale human pangenomes. As these...
Khan, M. S. A., Kabir, M. H., Faisal, M. M.
Single-cell RNA sequencing (scRNA-seq) enables characterization of cellular heterogeneity but clustering remains challenging due to high dimensionality, dropout induced sparsity, and technical nois...
Do, V. H., Tran, T. P. L., Canzar, S.
Spatial transcriptomics (ST) technologies enable measurement of gene expression with spatial context, offering unprecedented insight into tissue architecture and cellular microenvironments. A funda...
Kirshenboim, O., Kabya, A., Yehezkel-Imra, R., Tshuva, Y., Maiers, M., Gragert, L., Bashyal, P., Israeli, S., Louzoun, Y.
Background: The success of hematopoietic stem cell transplantation (HSCT) depends critically on human leukocyte antigen (HLA) matching between donor and recipient. While traditional matching focuse...
Bret, H., Andre, I.
The genetic code is highly redundant, with many synonymous codons encoding the same amino acid. Codon usage influences RNA structure, signaling, and translation rates. Differences in tRNA availabil...
Yadalam, P. K.
Chronic periodontitis is a prevalent inflammatory condition characterized by progressive tissue destruction; however, the molecular determinants that distinguish reversible inflammation from irreve...
Wen, B., Paez, J. S., Hsu, C., Canzani, D., Chang, A. T., Shulman, N., MacLean, B. X., Berg, M. D., Villen, J., Fondrie, W., Pino, L., MacCoss, M. J., Noble, W. S.
Data-independent acquisition (DIA) proteomics enables reproducible and systematic peptide detection and quantification, and trapped ion mobility spectrometry (TIMS) on the timsTOF platform further ...
Pan, X., Shrawat, A., Raghavan, S., Dong, C., Yang, Y., Li, Z., Zheng, W. J., Eckhardt, S. G., Wu, E., Fuxman Bass, J. I., Jarosz, D. F., Chen, S., McGrail, D. J., Sheynkman, G. M., Huang, J. H., Sahni, N., Yi, S. S.
Most proteins exert their functions in complex with other interactors. Single mutations can exhibit a profound impact on perturbing protein interactions, leading to human disease. However, predicti...
Bombina, P., McGee, R. L., Reed, J., Abrams, Z., Abruzzo, L. V., Coombes, K. R.
Understanding biological pathways requires more than static diagrams. We present WayFindR, an R package that converts pathway data from WikiPathways and KEGG into graph structures using igraph, ena...
Fu, Z.
Characterising cellular differentiation from single-cell RNA sequencing (scRNA-seq) requires representations that capture both discrete cell-type identity and continuous developmental trajectories....