Parameter estimation in nonlinear biological dynamical systems is a difficult inverse problem because the governing equations are often stiff or oscillatory, the data are sparse and noisy, and the objective landscape is non-convex. Physics-informed n... read more
Machine-learning surrogate models are positioned to help optimize deep brain stimulation (DBS) usage by predicting neural activation in response to electrical stimulation, while minimizing tradeoffs between computational expense and accuracy. Previou... read more
Developing scientific hypotheses in biology requires integrating heterogeneous evidence across DNA sequence, gene context, protein function, and prior literature. Existing multimodal AI systems expose biological evidence to reasoning models through t... read more
Artificial intelligence has reached a pivotal threshold. Multimodal large models can approach human-level speech comprehension by rapidly transforming sound into meaning. However, whether this process relies on human-like mechanisms remains unknown. ... read more
Recent deep learning models for L1000 chemical perturbation prediction incorporate dedicated drug molecular encoders. We retrained seven such models from scratch with zeroed or shuffled drug inputs, and compared them with a multilayer perceptron that... read more
Sequence-to-Function (S2F) foundation models are revolutionizing genomic research, yet their fragmented ecosystem severely bottlenecks practical application by incompatible inputs, outputs, and runtime environments. General-purpose coding agents lack... read more
Glioblastoma multiforme (GBM) is characterised by profound genomic heterogeneity and heavy-tailed gene-expression distributions that challenge conventional machine-learning methods. We introduce the Tsallis-Gated Autoencoder (Tsallis-GAE), a physics-... read more
Malignant pleural mesothelioma (MPM) is an aggressive asbestos-linked cancer with limited therapeutic options and a dismal 5-year survival rate of ~5%. While aberrant production of reactive oxygen and nitrogen species (ROS/RNS) is a hallmark of MPM, ... read more
Spatial transcriptomics enables investigation of tissue organization while preserving molecular and spatial information within intact tissues. However, existing computational methods primarily focus on clustering and batch integration and provide lim... read more
Humans have a remarkable ability to judge causal relationships from a limited number of unreliable observations. Past work on causal cognition has largely focused on normative accounts of human behavior, leaving unknown how biologically plausible neu... read more
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