25 papers · ranked by Valyu relevance
Liran Ringel, Yaniv Romano
Speculative decoding accelerates autoregressive language models by using a lightweight drafter to propose multiple future tokens, which the target model then verifies in parallel. DFlash shows that a block diffusion drafter can generate an entire draft block in a single forward pass and achieve state-of-the-art…
Shuai Zhang, Huachuan Qiu, Hongliang He, Yong Dai
Speculative decoding accelerates inference by having a lightweight drafter propose tokens verified in parallel by the target language model. Block diffusion drafters such as DFlash generate an entire draft block in one pass, yielding per-position marginals; DDTree uses these to build a candidate tree that maximizes…
Fuliang Liu, Xue Lian Li, Ketai Zhao, Yinxi Gao + 6 more
Speculative decoding is an effective and lossless approach for accelerating LLM inference. However, existing widely adopted model-based draft designs, such as EAGLE3, improve accuracy at the cost of multi-step autoregressive inference, resulting in high drafting latency and ultimately rendering the drafting stage…
Stephen A. Smith, Karen A. Cranston, James F. Allman, Joseph W. Brown + 18 more
Reconstructing the phylogenetic relationships that unite all biological lineages (the tree of life) is a grand challenge of biology. However, the paucity of readily available homologous character data across disparately related lineages renders direct phylogenetic inference currently untenable. Our best recourse…
Yuhao Shen, Tianyu Liu, Xinyi Hu, Quan Kong + 8 more
Speculative decoding (SD) accelerates large language model inference by leveraging a draft-then-verify paradigm. To maximize the acceptance rate, recent methods construct expansive draft trees, which unfortunately incur severe VRAM bandwidth and computational overheads that bottleneck end-to-end speedups. While…
Zhuoyu Wang, Junnan Huang, Xinyu Chen
Using a diffusion model for parallel drafting is a promising approach for speculative decoding. By predicting tokens at multiple future positions in a single forward pass, diffusion drafters substantially reduce drafting latency. However, this shifts the bottleneck to verification: verifying a single sequence limits…
Sangup PARK, Doohyuk Jang, Sung-Yub Kim, Souvik Kundu + 1 more
Drafting for Visual Auto-regressive Models Authors: ['Sangup PARK' 'Doohyuk Jang' 'Sung-Yub Kim' 'Souvik Kundu' 'Eunho Yang'] Speculative decoding has been widely used to accelerate autoregressive (AR) text generation. However, its effectiveness in visual AR models remains limited due to token selection ambiguity…
Yuhui Li, Fangyun Wei, Chao Zhang, Hongyang Zhang
Inference with modern Large Language Models (LLMs) is expensive and time-consuming, and speculative sampling has proven to be an effective solution. Most speculative sampling methods such as EAGLE use a static draft tree, implicitly assuming that the acceptance rate of draft tokens depends only on their position.…
Yunkui Xiong, Ruoyu Zhang, Yanzeng Li, Tianhao Wu + 1 more
While speculative decoding has recently appeared as a promising direction for accelerating the inference of large language models (LLMs), the speedup and scalability are strongly bounded by the token acceptance rate. Prevalent methods usually organize predicted tokens as independent chains or fixed token trees, which…
Ivica Letunic, Peer Bork
The Interactive Tree Of Life ([https://itol.embl.de]()) is an online tool for the display, manipulation and annotation of phylogenetic and other trees. It is freely available and open to everyone. iTOL version 5 introduces a completely new tree display engine, together with numerous new features. For example, a new…
Julia Voelker, Mervyn Shepherd, Ramil Mauleon
The economically important Melaleuca alternifolia (tea tree) is the source of a terpene-rich essential oil with therapeutic and cosmetic uses around the world. Tea tree has been cultivated and bred in Australia since the 1990s. It has been extensively studied for the genetics and biochemistry of terpene biosynthesis.…
G Achaz, E Schertzer
Neutral theory assumes that in a population of size N, diversity results from an equilibrium between new mutations arising at rate μ and genetic drift that purge them at rate 1/N, predicting an equilibrium value proportional to Nμ. The difference between this expectation and the much lower observed molecular diversity…
Caner Bagci, David Bryant, Banu Cetinkaya, Daniel H. Huson
Microbial studies typically involve the sequencing and assembly of draft genomes for individual microbes or whole microbiomes. Given a draft genome, one first task is to determine its phylogenetic context, that is, to place it relative to the set of related reference genomes. We provide a new interactive graphical tool…
Remco R. Bouckaert, Joseph Heled
Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip on a distributions over trees. Visualisation tools like DensiTree can give good intuition on tree distributions. It works by drawing all trees in the…
Mohan Krishnamoorthy, Pragneshkumar Patel, Mira Dimitrijevic, Jonathan Dietrich + 2 more
'Jonathan Dietrich' 'Margaret Green' 'Catherine Macken'] Background Large databases of genetic data are often biased in their representation. Thus, selection of genetic data with desired properties, such as evolutionary representation or shared genotypes, is problematic. Selection on the basis of epidemiological…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
Authors not listed
We present a simple yet efficient random (brute-force) algorithm for constructing solvated molecular systems. By placing solvent molecules at random positions and orientations within a simulation box, we circumvent the complexities typically associated with more sophisticated packing algorithms. The main computational…
Lars Berling, Jonathan Klawitter, Remco Bouckaert, Dong Xie + 2 more
Bayesian phylogenetic analysis with MCMC algorithms generates an estimate of the posterior distribution of phylogenetic trees in the form of a sample of phylogenetic trees and related parameters. The high dimensionality and non-Euclidean nature of tree space complicates summarizing the central tendency and variance of…
Ramith Hettiarachchi, Avi Swartz, Sergey Ovchinnikov
Inferring the most probable evolutionary tree given leaf nodes is an important problem in computational biology that reveals the evolutionary relationships between species. Due to the exponential growth of possible tree topologies, finding the best tree in polynomial time becomes computationally infeasible. In this…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev, Dmitriy Slutskiy
In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretraining of JT VAE on a large dataset and further optimization with a regression model led to a latent space that can…
Thomas Grubinger, Conrad Kobel, Karl-Peter Pfeiffer
Background DRG-systems are used to allocate resources fairly to hospitals based on their performance. Statistically, this allocation is based on simple rules that can be modeled with regression trees. However, the resulting models often have to be adjusted manually to be medically reasonable and ethical. Methods…
Jill L. Wegrzyn, Jennifer M. Lee, Brandon R. Tearse, David B. Neale
The Dendrome Project and associated TreeGenes database serve the forest genetics research community through a curated and integrated web-based relational database. The research community is composed of approximately 2 000 members representing over 730 organizations worldwide. The database itself is composed of a wide…
Jaime Sebastian‐Azcona, Eduardo P. Cappa, Letitia Da Ros, Blaise Ratcliffe + 7 more
'Blaise Ratcliffe' 'Charles Chen' 'Xiaojing Wei' 'Yang Liu' 'Shawn D. Mansfield' 'Andreas Hamann' 'Yousry A. El‐Kassaby' 'Barb R. Thomas'] Title: ABSTRACT Drought tolerance of tree species is a concern in the context of climate change, and tree ring analyses can be used to assess past growth response(s), to drought…
Mateusz Korbik, Tatiana Swoczyna, Piotr Latocha, Frank M. Thomas
Trees in urban conditions struggle with many factors that reduce their growth. In many cases, newly planted trees do not survive to maturity. The trees are produced using various methods, the most popular of which are balled and burlapped (B&B) and container production. Different production methods have their cons, but…