Publicaciones

@article{KjelgaardMikkelsen2023,

title = {Newton’s method revisited: How accurate do we have to be?},

author = {Carl Christian Kjelgaard Mikkelsen and Lorién López‐Villellas and Pablo García‐Risueño},

url = {http://dx.doi.org/10.1002/cpe.7853},

doi = {10.1002/cpe.7853},

issn = {1532-0634},

year  = {2023},

date = {2023-07-01},

journal = {Concurrency and Computation: Practice and Experience},

volume = {36},

number = {10},

publisher = {Wiley},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{navarro2023balancer,

title = {BALANCER: bandwidth allocation and cache partitioning for multicore processors},

author = {Agustín Navarro-Torres and Jesús Alastruey-Benedé and Pablo Ibáñez and Víctor Viñals-Yúfera},

url = {https://doi.org/10.1007/s11227-023-05070-0},

doi = {10.1007/s11227-023-05070-0},

year  = {2023},

date = {2023-01-01},

urldate = {2023-01-01},

journal = {The Journal of Supercomputing},

pages = {1--25},

publisher = {Springer},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{LOPEZVILLELLAS2023108742,

title = {Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code},

author = {Lorién López-Villellas and Carl Christian Kjelgaard Mikkelsen and Juan José Galano-Frutos and Santiago Marco-Sola and Jesús Alastruey-Benedé and Pablo Ibáñez and Miquel Moretó and Javier Sancho and Pablo García-Risueño},

url = {https://www.sciencedirect.com/science/article/pii/S0010465523000875},

doi = {https://doi.org/10.1016/j.cpc.2023.108742},

issn = {0010-4655},

year  = {2023},

date = {2023-01-01},

journal = {Computer Physics Communications},

volume = {288},

pages = {108742},

abstract = {In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton's method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{10093071,

title = {Porting and Optimizing BWA-MEM2 Using the Fujitsu A64FX Processor},

author = {Rubén Langarita and Adrià Armejach and Pablo Ibáñez and Jesús Alastruey-Benedé and Miquel Moretó},

doi = {10.1109/TCBB.2023.3264514},

year  = {2023},

date = {2023-01-01},

journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics},

volume = {20},

number = {5},

pages = {3139-3153},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{escuin2023l2c2,

title = {L2C2: Last-level compressed-contents non-volatile cache and a procedure to forecast performance and lifetime},

author = {Carlos Escuin and Pablo Ibáñez and Denis Navarro and Teresa Monreal and José M Llabería and Víctor Viñals},

year  = {2023},

date = {2023-01-01},

journal = {Plos one},

volume = {18},

number = {2},

pages = {e0278346},

publisher = {Public Library of Science San Francisco, CA USA},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{nano13172392,

title = {Isotope Dilution Analysis for Particle Mass Determination Using Single-Particle Inductively Coupled Plasma Time-of-Flight Mass Spectrometry: Application to Size Determination of Silver Nanoparticles},

author = {Maite Aramendía and Diego Leite and Javier Resano and Martín Resano and Kharmen Billimoria and Heidi Goenaga-Infante},

url = {https://www.mdpi.com/2079-4991/13/17/2392},

doi = {10.3390/nano13172392},

issn = {2079-4991},

year  = {2023},

date = {2023-01-01},

journal = {Nanomaterials},

volume = {13},

number = {17},

abstract = {This paper describes methodology based on the application of isotope dilution (ID) in single-particle inductively coupled plasma time-of-flight mass spectrometry (spICP-ToFMS) mode for the mass determination (and sizing) of silver nanoparticles (AgNPs). For this purpose, and considering that the analytical signal in spICP-MS shows a transient nature, an isotope dilution equation used for online work was adapted and used for the mass determination of individual NPs. The method proposed measures NP isotope ratios in a particle-to-particle approach, which allows for the characterization of NP mass (and size) distributions and not only the mean size of the distribution. For the best results to be obtained, our method development (undertaken through the analysis of the reference material NIST RM 8017) included the optimization of the working conditions for the best precision and accuracy in isotope ratios of individual NPs, which had been only reported to date with multicollector instruments. It is shown that the precision of the measurement of these ratios is limited by the magnitude of the signals obtained for each NP in the mass analyzer (counting statistics). However, the uncertainty obtained for the sizing of NPs in this approach can be improved by careful method optimization, where the most important parameters are shown to be the selection of the spike isotopic composition and concentration. Although only AgNPs were targeted in this study, the method presented, with the corresponding adaptations, could be applied to NPs of any other composition that include an element with different naturally available isotopes.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{D2JA00267A,

title = {Cu fractionation, isotopic analysis, and data processing via machine learning: new approaches for the diagnosis and follow up of Wilson's disease via ICP-MS},

author = {M. Carmen García-Poyo and Sylvain Bérail and Anne Laure Ronzani and Luis Rello and Elena García-González and Flávio V. Nakadi and Maite Aramendía and Javier Resano and Martín Resano and Christophe Pécheyran},

url = {http://dx.doi.org/10.1039/D2JA00267A},

doi = {10.1039/D2JA00267A},

year  = {2023},

date = {2023-01-01},

journal = {J. Anal. At. Spectrom.},

volume = {38},

issue = {1},

pages = {229-242},

publisher = {The Royal Society of Chemistry},

abstract = {Information about Cu fractionation and Cu isotopic composition can be paramount when investigating Wilson's disease (WD). This information can provide a better understanding of the metabolism of Cu. Most importantly, it may provide an easy way to diagnose and to follow the evolution of WD patients. For such purposes, protocols for Cu determination and Cu isotopic analysis via inductively coupled plasma mass spectrometry were investigated in this work, both in bulk serum and in the exchangeable copper (CuEXC) fractions. The CuEXC protocol provided satisfactory recovery values. Also, no significant mass fractionation during the whole analytical procedure (CuEXC production and/or Cu isolation) was detected. Analyses were carried out in controls (healthy persons), newborns, patients with hepatic disorders, and WD patients. While the results for Cu isotopic analysis are relevant (e.g., δ65Cu values were lower for both WD patients under chelating treatment and patients with hepatic problems in comparison with those values obtained for WD patients under Zn treatments, controls, and newborns) to comprehend Cu metabolism and to follow up the disease, the parameter that can help to better discern between WD patients and the rest of the patients tested (non-WD) was found to be the REC (relative exchangeable Cu). In this study, all the WD patients showed a REC higher than 17%, while the rest showed lower values. However, since establishing a universal threshold is complicated, machine learning was investigated to produce a model that can differentiate between WD and non-WD samples with excellent results (100% accuracy, albeit for a limited sample set). Most importantly, unlike other ML approaches, our model can also provide an uncertainty metric to indicate the reliability of the prediction, overall opening new ways to diagnose WD.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{lopez2023accurate,

title = {Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code},

author = {Lorién López-Villellas and Carl Christian Kjelgaard Mikkelsen and Juan José Galano-Frutos and Santiago Marco-Sola and Jesús Alastruey-Benedé and Pablo Ibáñez and Miquel Moretó and Javier Sancho and Pablo García-Risueño},

year  = {2023},

date = {2023-01-01},

journal = {Computer Physics Communications},

volume = {288},

pages = {108742},

publisher = {North-Holland},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Muñoz2022,

title = {Gated-CNN: Combating NBTI and HCI aging effects in on-chip activation memories of Convolutional Neural Network accelerators},

author = {Nicolás Landeros Muñoz and Alejandro Valero and Rubén Gran Tejero and Davide Zoni},

url = {https://www.sciencedirect.com/science/article/pii/S1383762122001072},

doi = {https://doi.org/10.1016/j.sysarc.2022.102553},

issn = {1383-7621},

year  = {2022},

date = {2022-07-01},

urldate = {2022-07-01},

journal = {Journal of Systems Architecture},

volume = {128},

pages = {1-13},

abstract = {Negative Bias Temperature Instability (NBTI) and Hot Carrier Injection (HCI) are two of the main reliability threats in current technology nodes. These aging phenomena degrade the transistor’s threshold voltage (Vth) over the lifetime of a digital circuit, resulting in slower transistors that eventually lead to a faulty operation when the critical paths become longer than the processor cycle time. Among all the transistors on a chip, the most vulnerable transistors to such wearout effects are those used to implement SRAM storage, since memory cells are continuously degrading. In particular, NBTI ages PMOS cell transistors when a given logic value is stored for a long period (i.e., a long duty cycle), whereas HCI ages NMOS cell transistors not only when the stored value flips but also when it is accessed. This work focuses on mitigating aging in the on-chip SRAM memories of Convolutional Neural Network (CNN) accelerators storing activations. This paper makes two main contributions. At the software level, we quantify the aging induced by current CNN benchmarks with a characterization study of duty cycle, flip, and access patterns in every activation memory cell. Based on the insights from this study, this work proposes a novel microarchitectural technique, Gated-CNN, that ensures a uniform aging degradation of every memory cell. To do so, Gated-CNN exploits power-gating and address rotation techniques tailored to the memory demands and temporal/spatial localities exhibited by CNN applications, as well as the memory organization and management of CNN accelerators. Experimental results show that, compared to a conventional design, the average Vth degradation savings are at least as much as 49% depending on the type of transistor.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DBLP:journals/tcbb/LangaritaASIAM22,

title = {Compressed Sparse FM-Index: Fast Sequence Alignment Using Large K-Steps},

author = {Rubén Langarita and Adrià Armejach and Javier Setoain and Pablo Ibáñez-Marín and Jesús Alastruey-Benedé and Miquel Moretó},

url = {https://doi.org/10.1109/TCBB.2020.3000253},

doi = {10.1109/TCBB.2020.3000253},

year  = {2022},

date = {2022-01-01},

journal = {IEEE ACM Trans. Comput. Biol. Bioinform.},

volume = {19},

number = {1},

pages = {355--368},

keywords = {},

pubstate = {published},

tppubtype = {article}

}