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Protein evolution through amino acid mutations is a cornerstone of life sciences. Recent advances in protein language models have shown rich evolutionary patterns, offering unprecedented potential for in-silicon directed evolution. However,…
We propose an approach of open-ended evolution via the simulation of swarm dynamics. In nature, swarms possess remarkable properties, which allow many organisms, from swarming bacteria to ants and flocking birds, to form higher-order…
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundreds, or even thousands, of proteins assemble around the…
Disentangling the mechanisms underlying the social network evolution is one of social science's unsolved puzzles. Preferential attachment is a powerful mechanism explaining social network dynamics, yet not able to explain all scaling-laws…
Recent advances in vision-language models (VLMs) trained on web-scale image-text pairs have enabled impressive zero-shot transfer across a diverse range of visual tasks. However, comprehensive and independent evaluation beyond standard…
Large language models (LLMs) have demonstrated exceptional proficiency in understanding and generating human language, but efficient inference on resource-constrained embedded devices remains challenging due to large model sizes and…
The impact of developmental and aging processes on brain connectivity and the connectome has been widely studied. Network theoretical measures and certain topological principles are computed from the entire brain, however there is a need to…
CLIP is a discriminative model trained to align images and text in a shared embedding space. Due to its multimodal structure, it serves as the backbone of many generative pipelines, where a decoder is trained to map from the shared space…
We consider a heteroclinic network in the framework of winnerless competition of species. It consists of two levels of heteroclinic cycles. On the lower level, the heteroclinic cycle connects three saddles, each representing the survival of…
Sensorial language -- the language connected to our senses including vision, sound, touch, taste, smell, and interoception, plays a fundamental role in how we communicate experiences and perceptions. We explore the relationship between…
The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…
Migratory and tissue resident cells exhibit highly branched morphologies to perform their function and to adapt to the microenvironment. Immune cells, for example, display transient branched shapes while exploring the surrounding tissues.…
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local,…
Self-supervised learning (SSL) has produced a diverse landscape of vision transformers (ViTs) whose pretrained representations support a wide range of downstream tasks. Towards a better understanding of these models, a body of work has…
This article reviews and evaluates models of network evolution based on the notion of structural diversity. We show that diversity is an underlying theme of three principles of network evolution: the preferential attachment model,…
In epistatic fitness landscapes, the fitness effect of a mutation depends on the genetic background and may even switch between deleterious and beneficial depending on the presence of another mutation. Epistatic interactions may cause both…
Traffic signal control TSC requires strategies that are both effective and interpretable for deployment, yet reinforcement learning produces opaque neural policies while program synthesis depends on restrictive domain-specific languages. We…
Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…
Recent advances in 3D scene-language understanding have leveraged Large Language Models (LLMs) for 3D reasoning by transferring their general reasoning ability to 3D multi-modal contexts. However, existing methods typically adopt standard…
The ubiquity of integrating detectors in imaging and other applications implies that a variety of real-world data are well modeled as Poisson random variables whose means are in turn proportional to an underlying vector-valued signal of…