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Molecular electronics and other technologies whose components comprise individual molecules have been pursued for half a century because the molecular scale represents the limit of miniaturisation of objects whose structure is tuneable for…
We propose an assembly algorithm {\sc Barnacle} for sequences generated by the clone-based approach. We illustrate our approach by assembling the human genome. Our novel method abandons the original physical-mapping-first framework. As we…
DNA-coated particles are promising as building blocks for functional and finite-sized assemblies because they can be programmed with orthogonal interactions owing to the sequence-specific hybridization of DNA strands. To fully exploit this…
Functions of chemical composition are complex and discrete in nature making it impossible to optimize them with gradient methods. Genetic algorithms, which do not use derivative information, are used to maximize the thermal conductivity of…
Large language models (LLMs) excel at implementing code from functionality descriptions but struggle with algorithmic problems that require not only implementation but also identification of the suitable algorithm. Moreover, LLM-generated…
Long-range and highly accurate de novo assembly from short-read data is one of the most pressing challenges in genomics. Recently, it has been shown that read pairs generated by proximity ligation of DNA in chromatin of living tissue can…
Large language models (LLMs) have the potential to revolutionize how we design and implement compilers and code translation tools. However, existing LLMs struggle to handle long and complex programs. We introduce LEGO-Compiler, a novel…
With the advent of Genome Sequencing, the field of Personalized Medicine has been revolutionized. From drug testing and studying diseases and mutations to clan genomics, studying the genome is required. However, genome sequence assembly is…
It is common practice for methods that use galaxy clustering to constrain the galaxy-halo relationship, such as the halo occupation distribution (HOD) and/or conditional luminosity function (CLF), to assume that halo mass alone suffices to…
Combinatorial assembly uses standardized unit primitives to build objects that satisfy user specifications. This paper studies assembly sequence planning (ASP) for physical combinatorial assembly. Given the shape of the desired object, the…
De novo whole genome assembly reconstructs genomic sequence from short, overlapping, and potentially erroneous DNA segments and is one of the most important computations in modern genomics. This work presents HipMER, a high-quality…
Compound AI applications chain together subcomponents such as generative language models, document retrievers, and embedding models. Applying traditional systems optimizations such as parallelism and pipelining in compound AI systems is…
In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
Metagenome assembly is the process of transforming a set of short, overlapping, and potentially erroneous DNA segments from environmental samples into the accurate representation of the underlying microbiomes's genomes. State-of-the-art…
3D printing enables the fabrication of complex architectures by automating long sequences of additive steps. The increasing sophistication of printers, materials, and generative design promises to make geometric complexity a non-issue in…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
Programmable arrays of optical traps enable the assembly of configurations of single atoms to perform controlled experiments on quantum many-body systems. Finding the sequence of control operations to transform an arbitrary configuration of…
Genome assembly is a fundamental problem in Bioinformatics, requiring to reconstruct a source genome from an assembly graph built from a set of reads (short strings sequenced from the genome). A notion of genome assembly solution is that of…
Gel electrophoresis, a widely used technique to separate DNA according to their size and weight, generates images that can be analyzed automatically. Manual or semiautomatic image processing presents a bottleneck for further development and…