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The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations result from mechanical perturbations in cells. These different topologies have…
We consider the task of detecting regulatory elements in the human genome directly from raw DNA. Past work has focused on small snippets of DNA, making it difficult to model long-distance dependencies that arise from DNA's 3-dimensional…
Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational…
Scaling Maximum Entropy Reinforcement Learning (RL) to high-dimensional humanoid control remains a fundamental challenge, as the ''curse of dimensionality'' induces severe exploration inefficiency and training instability. Consequently,…
Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…
The comparative genomics revolution of the past decade has enabled the discovery of functional elements in the human genome via sequence comparison. While that is so, an important class of elements, those specific to humans, is entirely…
Grid cells in the entorhinal cortex of mammalian brains exhibit striking hexagon grid firing patterns in their response maps as the animal (e.g., a rat) navigates in a 2D open environment. In this paper, we study the emergence of the…
The addition of deep near infrared images to the database provided by the HDF-S WFPC2 is essential to monitor the SEDs of the objects on a wide baseline and address a number of key issues including the total stellar content of baryonic…
The generation of drug-like molecules is crucial for drug design. Existing reinforcement learning (RL) methods often overlook structural information. However, feature engineering-based methods usually merely focus on binding affinity…
Accurate, fair, and explainable allocation of candidates to roles represents a fundamental challenge across multiple domains including corporate hiring, academic admissions, fellowship awards, and volunteer placement systems. Current…
We consider a model of large regulatory gene expression networks where the thresholds activating the sigmoidal interactions between genes and the signs of these interactions are shuffled randomly. Such an approach allows for a qualitative…
DNA methylation is an epigenetic mechanism that regulates gene expression by adding methyl groups to DNA. Abnormal methylation patterns can disrupt gene expression and have been linked to cancer development. To quantify DNA methylation,…
We investigate node representation learning on text-attributed graphs (TAGs), where nodes are associated with text information. Although recent studies on graph neural networks (GNNs) and pretrained language models (PLMs) have exhibited…
In this work, we describe a computational framework for the genome-wide identification and characterization of mixed transcriptional/post-transcriptional regulatory circuits in humans. We concentrated in particular on feed-forward loops…
Convolutional neural networks (CNNs) have demonstrated strong performance in visual recognition tasks, but their inherent reliance on regular grid structures limits their capacity to model complex topological relationships and non-local…
Models of human motion commonly focus either on trajectory prediction or action classification but rarely both. The marked heterogeneity and intricate compositionality of human motion render each task vulnerable to the data degradation and…
Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key…
The spreading and regulation of epigenetic marks on chromosomes is crucial to establish and maintain cellular identity. Nonetheless, the dynamical mechanism leading to the establishment and maintenance of a given, cell-line specific,…
Autism Spectrum Disorder (ASD) is a neurodevelopmental condition characterized by varied social cognitive challenges and repetitive behavioral patterns. Identifying reliable brain imaging-based biomarkers for ASD has been a persistent…
DNA language models like Evo2 now fit million-token contexts large enough to cover entire TADs, yet whether they learn 3D chromatin structure, a key regulatory layer acting atop primary sequence, remains untested and questionable, given…