18 papers · ranked by Valyu relevance
Carl Kingsford, Rob Patro
Motivation: Storing, transmitting and archiving data produced by next-generation sequencing is a significant computational burden. New compression techniques tailored to short-read sequence data are needed. Results: We present here an approach to compression that reduces the difficulty of managing large-scale…
Adiseshu Hari, Urs Niesen, Gordon Wilfong
Packet networks need to maintain state in the form of forwarding tables at each switch. The cost of this state increases as networks support ever more sophisticated per-flow routing, traffic engineering, and service chaining. Perflow or per-path state at the switches can be eliminated by encoding each packet's desired…
Carl Kingsford, Rob Patro
Storing, transmitting, and archiving the amount of data produced by next generation sequencing is becoming a significant computational burden. For example, large-scale RNA-seq meta-analyses may now routinely process tens of terabytes of sequence. We present here an approach to biological sequence compression that…
Lei Yang, En Cheng, Z Meral Özsoyoğlu
A pedigree is a diagram of family relationships, and it is often used to determine the mode of inheritance (dominant, recessive, etc.) of genetic diseases. Along with rapidly growing knowledge of genetics and accumulation of genealogy information, pedigree data is becoming increasingly important. In large pedigree…
Li Huang, Hongkyun Kim, Jacob Furst, Daniela Raicu
The nematode Caenorhabditis elegans explores the environment using a combination of different movement patterns, which include straight movement, reversal, and turns. We propose to quantify C. elegans movement behavior using a computer vision approach based on run-length encoding of step-length data. In this approach…
Rich Pang, Stefano Recanatesi
Hebbian plasticity has long dominated neurobiological models of memory formation. Yet plasticity rules operating on one-shot episodic memory timescales rarely depend on both pre- and postsynaptic spiking, challenging Hebbian theory in this crucial regime. To address this, we present an episodic memory model governed by…
Serhat Nazim Avci, Ender Ayanoğlu
—Link failures in wide area networks are common and cause significant data losses. Mesh-based protection schemes offer high capacity efficiency but they are slow and require complex signaling. Additionally, real-time reconfigurations of crossconnects threaten their transmission integrity. On the other hand, there are…
Bomin Liu, Linjun He, Yan Zhu, Anil Yaman
Vision Transformers have demonstrated remarkable performance in image classification and structural modeling; however, fixed patch partitioning and static positional encoding often disrupt spatial continuity, thereby limiting their ability to represent rotated structures and irregular boundary regions. To address these…
S. K. Harootonian, R. C. Wilson, L. Hejtmánek, E. M. Ziskin + 1 more
Path integration is thought to rely on vestibular and proprioceptive cues yet most studies in humans involve primarily visual input, providing limited insight into their contributions. We developed a paradigm involving walking in an omnidirectional treadmill in which participants were guided on two legs of a triangle…
Tianhao Chu, Yuling Wu, Neil Burgess, Zilong Ji + 1 more
Path integration is essential for spatial navigation. Experimental studies have identified neural correlates for path integration, but exactly how the neural system accomplishes this computation remains unresolved. Here, we adopt recurrent neural networks (RNNs) trained to perform a path integration task to explore…
Lifu Song, Feng Geng, Ziyi Gong, Bingzhi Li + 1 more
High density and long-term features make DNA data storage a potential media. However, DNA data channel is a unique channel with unavoidable ‘data reputations’ in the forms of multiple error-rich strand copies. This multi-copy feature cannot be well harnessed by available codec systems optimized for single-copy media.…
Chen Fu, Heming Sun, Zhiqiang Zhang, Jinjia Zhou + 1 more
Recently, specifically designed video codecs have been preferred due to the expansion of video data in Internet of Things (IoT) devices. Context Adaptive Binary Arithmetic Coding (CABAC) is the entropy coding module widely used in recent video coding standards such as HEVC/H.265 and VVC/H.266. CABAC is a well known…
Mohsen Moradi
—Despite the extreme error-correction performance, the amount of computation of sequential decoding of the polarization-adjusted convolutional (PAC) codes is random. In sequential decoding of convolutional codes, the computational cutoff rate denotes the region between rates whose average computational complexity of…
Shinichi Yamagiwa, Yuma Ichinomiya, Stefania Perri
Video applications have become one of the major services in the engineering field, which are implemented by server-client systems connected via the Internet, broadcasting services for mobile devices such as smartphones and surveillance cameras for security. Recently, the majority of video encoding mechanisms to reduce…
Mohsen Moradi, Amir Mozammel
—Sorting operation is one of the main bottlenecks for the successive-cancellation list (SCL) decoding. This paper introduces an improvement to the SCL decoding for polar and pre-transformed polar codes that reduces the number of sorting operations without degrading the code's error-correction performance. In an SCL…
Ian Holmes
We describe a strategy for constructing codes for DNA-based information storage by serial composition of weighted finite-state transducers. The resulting state machines can integrate correction of substitution errors; synchronization by interleaving watermark and periodic marker signals; conversion from binary to…
Jordi Poater, Diego M. Andrada, Miquel Sola, Cina Foroutan-Nejad
Here, we provide evidence of the path-dependency of the energy components of the energy decomposition analysis scheme, EDA, by studying a set of thirty-one closed-shell model systems with D2h symmetry point group. For each system, we computed EDA components from nine different pathways and numerically showed that the…
Shin-ichi Koda, Shinji Saito
Rapid generation of a plausible reaction path connecting a given reactant and product in advance is crucial for the efficient computation of precise reaction paths or transition states. We propose a computationally efficient potential energy based on molecular structure to generate such paths. This potential energy has…