4 Search Results for "Pu, Justin"

Document
DOI: 10.4230/LIPIcs.SEA.2025.20
SimdMinimizers: Computing Random Minimizers, fast

Authors: Ragnar Groot Koerkamp and Igor Martayan

Published in: LIPIcs, Volume 338, 23rd International Symposium on Experimental Algorithms (SEA 2025)

Abstract
Motivation. Because of the rapidly-growing amount of sequencing data, computing sketches of large textual datasets has become an essential preprocessing task. These sketches are typically much smaller than the input sequences, but preserve sufficient information for downstream analysis. Minimizers are an especially popular sketching technique and used in a wide variety of applications. They sample at least one out of every w consecutive k-mers. As DNA sequencers are getting more accurate, some applications can afford to use a larger w and hence sparser and smaller sketches. And as sketches get smaller, their analysis becomes faster, so the time spent sketching the full-sized input becomes more of a bottleneck. Methods. Our library simd-minimizers implements a random minimizer algorithm using SIMD instructions. It supports both AVX2 and NEON architectures. Its main novelty is two-fold. First, it splits the input into 8 chunks that are streamed over in parallel through all steps of the algorithm. This is enabled by using the completely deterministic two-stacks sliding window minimum algorithm, which seems not to have been used before for finding minimizers. Results. Our library is up to 6.8× faster than a scalar implementation of the rescan method when w = 5 is small, and 3.4× faster for larger w = 19. Computing canonical minimizers is less than 50% slower than computing forward minimizers, and over 15× faster than the existing implementation in the minimizer-iter crate. Our library finds all (canonical) minimizers of a 3.2 Gbp human genome in 5.2 (resp. 6.7) seconds.
Cite as

Ragnar Groot Koerkamp and Igor Martayan. SimdMinimizers: Computing Random Minimizers, fast. In 23rd International Symposium on Experimental Algorithms (SEA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 338, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{grootkoerkamp_et_al:LIPIcs.SEA.2025.20,
  author =	{Groot Koerkamp, Ragnar and Martayan, Igor},
  title =	{{SimdMinimizers: Computing Random Minimizers, fast}},
  booktitle =	{23rd International Symposium on Experimental Algorithms (SEA 2025)},
  pages =	{20:1--20:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-375-1},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{338},
  editor =	{Mutzel, Petra and Prezza, Nicola},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2025.20},
  URN =		{urn:nbn:de:0030-drops-232581},
  doi =		{10.4230/LIPIcs.SEA.2025.20},
  annote =	{Keywords: Minimizers, Randomized algorithms, Sketching, Hashing}
}
Document
Survey
DOI: 10.4230/TGDK.1.1.4
Knowledge Graph Embeddings: Open Challenges and Opportunities

Authors: Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
While Knowledge Graphs (KGs) have long been used as valuable sources of structured knowledge, in recent years, KG embeddings have become a popular way of deriving numeric vector representations from them, for instance, to support knowledge graph completion and similarity search. This study surveys advances as well as open challenges and opportunities in this area. For instance, the most prominent embedding models focus primarily on structural information. However, there has been notable progress in incorporating further aspects, such as semantics, multi-modal, temporal, and multilingual features. Most embedding techniques are assessed using human-curated benchmark datasets for the task of link prediction, neglecting other important real-world KG applications. Many approaches assume a static knowledge graph and are unable to account for dynamic changes. Additionally, KG embeddings may encode data biases and lack interpretability. Overall, this study provides an overview of promising research avenues to learn improved KG embeddings that can address a more diverse range of use cases.
Cite as

Russa Biswas, Lucie-Aimée Kaffee, Michael Cochez, Stefania Dumbrava, Theis E. Jendal, Matteo Lissandrini, Vanessa Lopez, Eneldo Loza Mencía, Heiko Paulheim, Harald Sack, Edlira Kalemi Vakaj, and Gerard de Melo. Knowledge Graph Embeddings: Open Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 4:1-4:32, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{biswas_et_al:TGDK.1.1.4,
  author =	{Biswas, Russa and Kaffee, Lucie-Aim\'{e}e and Cochez, Michael and Dumbrava, Stefania and Jendal, Theis E. and Lissandrini, Matteo and Lopez, Vanessa and Menc{\'\i}a, Eneldo Loza and Paulheim, Heiko and Sack, Harald and Vakaj, Edlira Kalemi and de Melo, Gerard},
  title =	{{Knowledge Graph Embeddings: Open Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{4:1--4:32},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.4},
  URN =		{urn:nbn:de:0030-drops-194783},
  doi =		{10.4230/TGDK.1.1.4},
  annote =	{Keywords: Knowledge Graphs, KG embeddings, Link prediction, KG applications}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2020.25
Scala with Explicit Nulls

Authors: Abel Nieto, Yaoyu Zhao, Ondřej Lhoták, Angela Chang, and Justin Pu

Published in: LIPIcs, Volume 166, 34th European Conference on Object-Oriented Programming (ECOOP 2020)

Abstract
The Scala programming language makes all reference types implicitly nullable. This is a problem, because null references do not support most operations that do make sense on regular objects, leading to runtime errors. In this paper, we present a modification to the Scala type system that makes nullability explicit in the types. Specifically, we make reference types non-nullable by default, while still allowing for nullable types via union types. We have implemented this design for explicit nulls as a fork of the Dotty (Scala 3) compiler. We evaluate our scheme by migrating a number of Scala libraries to use explicit nulls. Finally, we give a denotational semantics of type nullification, the interoperability layer between Java and Scala with explicit nulls. We show a soundness theorem stating that, for variants of System F_ω that model Java and Scala, nullification preserves values of types.
Cite as

Abel Nieto, Yaoyu Zhao, Ondřej Lhoták, Angela Chang, and Justin Pu. Scala with Explicit Nulls. In 34th European Conference on Object-Oriented Programming (ECOOP 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 166, pp. 25:1-25:26, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@InProceedings{nieto_et_al:LIPIcs.ECOOP.2020.25,
  author =	{Nieto, Abel and Zhao, Yaoyu and Lhot\'{a}k, Ond\v{r}ej and Chang, Angela and Pu, Justin},
  title =	{{Scala with Explicit Nulls}},
  booktitle =	{34th European Conference on Object-Oriented Programming (ECOOP 2020)},
  pages =	{25:1--25:26},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-154-2},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{166},
  editor =	{Hirschfeld, Robert and Pape, Tobias},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2020.25},
  URN =		{urn:nbn:de:0030-drops-131821},
  doi =		{10.4230/LIPIcs.ECOOP.2020.25},
  annote =	{Keywords: Scala, Java, nullability, language interoperability, type systems}
}
Document
Artifact
DOI: 10.4230/DARTS.6.2.14
Scala with Explicit Nulls (Artifact)

Authors: Abel Nieto, Yaoyu Zhao, Ondřej Lhoták, Angela Chang, and Justin Pu

Published in: DARTS, Volume 6, Issue 2, Special Issue of the 34th European Conference on Object-Oriented Programming (ECOOP 2020)

Abstract
This artifact is a companion to the paper "Scala with Explicit Nulls", where we present a modification to the Scala type system that makes nullability explicit in the types. Specifically, we make reference types non-nullable by default, while still allowing for nullable types via union types. The artifact contains an implementation of this new type system design as a fork of the Dotty (Scala 3) compiler. Additionally, the artifact contains the source code of multiple Scala libraries that we used to evaluate our design.
Cite as

Abel Nieto, Yaoyu Zhao, Ondřej Lhoták, Angela Chang, and Justin Pu. Scala with Explicit Nulls (Artifact). In Special Issue of the 34th European Conference on Object-Oriented Programming (ECOOP 2020). Dagstuhl Artifacts Series (DARTS), Volume 6, Issue 2, pp. 14:1-14:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

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@Article{nieto_et_al:DARTS.6.2.14,
  author =	{Nieto, Abel and Zhao, Yaoyu and Lhot\'{a}k, Ond\v{r}ej and Chang, Angela and Pu, Justin},
  title =	{{Scala with Explicit Nulls (Artifact)}},
  pages =	{14:1--14:2},
  journal =	{Dagstuhl Artifacts Series},
  ISSN =	{2509-8195},
  year =	{2020},
  volume =	{6},
  number =	{2},
  editor =	{Nieto, Abel and Zhao, Yaoyu and Lhot\'{a}k, Ond\v{r}ej and Chang, Angela and Pu, Justin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DARTS.6.2.14},
  URN =		{urn:nbn:de:0030-drops-132117},
  doi =		{10.4230/DARTS.6.2.14},
  annote =	{Keywords: Scala, Java, nullability, language interoperability, type systems}
}
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