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Paediatric Acute Myeloid Leukemia is a complex adaptive ecosystem with high morbidity. Current trajectory inference algorithms struggle to predict causal dynamics in AML progression, including relapse and recurrence risk. We propose a…

The dynamic cavity method provides the most efficient way to evaluate probabilities of dynamic trajectories in systems of stochastic units with unidirectional sparse interactions. It is closely related to sum-product algorithms widely used…

Molecular dynamics (MD) has become a powerful tool for studying biophysical systems, due to increasing computational power and availability of software. Although MD has made many contributions to better understanding these complex…

Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…

Simulating the molecular dynamics (MD) using classical or semi-classical trajectories provides important details for the understanding of many chemical reactions, protein folding, drug design, and solvation effects. MD simulations using…

Path integral molecular dynamics (PIMD), which maps a quantum particle onto a fictitious classical system of ring polymers and propagates the "beads" of this extended classical system using molecular dynamics, is widely used to capture…

External memory systems are pivotal for enabling Large Language Model (LLM) agents to maintain persistent knowledge and perform long-horizon decision-making. Existing paradigms typically follow a two-stage process: computationally expensive…

Molecular dynamics (MD) is a powerful approach for modelling molecular systems, but it remains computationally intensive on spatial and time scales of many macromolecular systems of biological interest. To explore the opportunities offered…

The ability to learn continuously in artificial neural networks (ANNs) is often limited by catastrophic forgetting, a phenomenon in which new knowledge becomes dominant. By taking mechanisms of memory encoding in neuroscience (aka. engrams)…

We present Latent Diffeomorphic Dynamic Mode Decomposition (LDDMD), a new data reduction approach for the analysis of non-linear systems that combines the interpretability of Dynamic Mode Decomposition (DMD) with the predictive power of…

Exploring in environments with high-dimensional observations is hard. One promising approach for exploration is to use intrinsic rewards, which often boils down to estimating "novelty" of states, transitions, or trajectories with deep…

Binary vulnerability analysis is increasingly performed by LLM-based agents in an iterative, multi-pass manner, with the model as the core decision-maker. However, how such systems organize exploration over hundreds of reasoning steps…

Comprehending the long-timescale dynamics of protein-ligand complexes is very important for drug discovery and structural biology, but it continues to be computationally challenging for large biomolecular systems. We introduce…

Using techniques borrowed from statistical physics and neural networks, we determine the parameters, associated with a scoring function, that are chosen optimally to ensure complete success in threading tests in a training set of proteins.…

Several recent works have directly extended the image masked autoencoder (MAE) with random masking into video domain, achieving promising results. However, unlike images, both spatial and temporal information are important for video…

We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation…

A rising research challenge is running costly machine learning (ML) networks locally on resource-constrained edge devices. ML networks with large convolutional layers can easily exceed available memory, increasing latency due to excessive…

Efficient materials discovery requires reducing costly first-principles calculations for training machine-learned interatomic potentials (MLIPs). We develop an active learning (AL) framework that iteratively selects informative structures…

We propose a novel variant of the algorithm by Simson et al. [R. Simson, E.D. Sheets, K. Jacobson, Biophys. J. 69, 989 (1995)]. Their algorithm was developed to detect transient confinement zones in experimental single particle tracking…

In recent years, model-agnostic meta-learning (MAML) has become a popular research area. However, the stochastic optimization of MAML is still underdeveloped. Existing MAML algorithms rely on the ``episode'' idea by sampling a few tasks and…