Related papers: PLUMED 2: New feathers for an old bird

C++QED is a framework for simulating open quantum dynamics in general. Historically, it has in the first place been developed for problems in moving-particle cavity QED, but since then has been applied in other fields as well. It is known…

Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…

Recent advances in Large Language Models (LLMs) have introduced a new paradigm for software development, where source code is generated from natural language prompts. While this paradigm significantly boosts development productivity,…

LIBS2ML is a library based on scalable second order learning algorithms for solving large-scale problems, i.e., big data problems in machine learning. LIBS2ML has been developed using MEX files, i.e., C++ with MATLAB/Octave interface to…

There is a pressing need for better development methods and tools to keep up with the growing demand and increasing complexity of new software systems. New types of user interfaces, the need for intelligent components, sustainability…

This proposal discusses the growing challenges in reverse engineering modern software binaries, particularly those compiled from newer system programming languages such as Rust, Go, and Mojo. Traditional reverse engineering techniques,…

PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is…

Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the gap between electronic-structure theory and continuum…

This paper introduces LLM-Streamline, a pioneer work on layer pruning for large language models (LLMs). It is based on the observation that different layers have varying impacts on hidden states, enabling the identification of less…

Recent increases in supercomputing power, driven by the multi-core revolution and accelerators such as the IBM Cell processor, graphics processing units (GPUs) and Intel's Many Integrated Core (MIC) technology have enabled kinetic…

The emergence of Multimodal Large Language Models ((M)LLMs) has ushered in new avenues in artificial intelligence, particularly for autonomous driving by offering enhanced understanding and reasoning capabilities. This paper introduces…

Deep Learning models are getting more and more popular but constraints on explainability, adversarial robustness and fairness are often major concerns for production deployment. Although the open source ecosystem is abundant on addressing…

In this report, we introduce PLaMo 2, a series of Japanese-focused large language models featuring a hybrid Samba-based architecture that transitions to full attention via continual pre-training to support 32K token contexts. Training…

Code language models (CLMs) play a central role in software engineering across both generation and classification tasks. However, these models still exhibit notable mispredictions in real-world applications, even when trained on up-to-date…

Recent advances in multimodal large language models (MLLMs) have shown impressive reasoning capabilities. However, further enhancing existing MLLMs necessitates high-quality vision-language datasets with carefully curated task complexities,…

Preference learning provides a promising solution to address the limitations of supervised fine-tuning (SFT) for code language models, where the model is not explicitly trained to differentiate between correct and incorrect code. Recent…

The Agent Based Model community has a rich and diverse ecosystem of libraries, platforms, and applications to help modelers develop rigorous simulations. Despite this robust and diverse ecosystem, the complexity of life from microbial…

The C preprocessor (CPP) is a standard tool for introducing variability into source programs and is often applied either implicitly or explicitly for implementing a Software Product Line (SPL). Despite its practical relevance, CPP has many…

Guiding biological systems toward desired states, such as morphogenetic outcomes, remains a fundamental challenge with far-reaching implications for medicine and synthetic biology. While large language models (LLMs) have enabled natural…

We present the PML 2 language, which provides a uniform environment for programming, and for proving properties of programs in an ML-like setting. The language is Curry-style and call-by-value, it provides a control operator (interpreted in…