愛というのは軛である。パラドックスの間を縫うようにして在る我々の、よすがない機能を果たしているという慰みに等しい。
□
AstroSamantha:
Hello #Budapest! That's where 2014 started for me. Great memories! Il 2014 e' iniziato qui per me. Bei ricordi!
□ Grow your own snowflakes. DIY instructions
>>
http://www.futurity.org/grow-your-own-snowflakes-826602/ … @Caltech #snowflakes
□ Computational self-assembly of a one-component icosahedral quasicrystal: World's most complex crystal never repeats
>>
http://www.nature.com/nmat/journal/v14/n1/abs/nmat4152.html …
□ Snowflakes have an infinitely repeating self-similarity, making all snowflakes a unique shape
>>
http://oxford.ly/1B6RVuO
□ Six Degrees to the Emergence of Reality: a new model of quantum complex networks physical nature of time & paradoxes
>>
http://fqxi.org/community/articles/display/197 …
□ Chiral Quantum Walks: the physical effect of time-symmetry breaking plays an essential role in coherent transport
>>
http://arxiv.org/pdf/1405.6209v1.pdf …
applying local gates in an otherwise time-symmetric circuit to induce time-reversal asymmetry and thereby achieve.
The probability time-symmetry condition |Uij|^2=|Uji|^2 ∀ i,j can be expressed as
sinh(iHt)ji cosh(iHt)ij = sinh(iHt)ij cosh(iHt)ji
∀ i,j.
□ Deep learning and genomics: the splicing code:
>>
https://followthedata.wordpress.com/2015/01/05/deep-learning-and-genomics-the-splicing-code/ …
□ Hebel: a GPU-accelerated deep learning library for DNA sequence data for Python
>>
https://github.com/hannes-brt/hebel …
Hebel implements stochastic gradient descent regular/Nesterov momentum. Convolutional neural net & Restricted Boltzman machines are planned.
(ISA framework conceptual layers: from syntactic layer up to linkedISA layer: hierarchical structure of ISATab format)
□ linkedISA: semantic representation of ISA-Tab experimental metadata
>>
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4255742/
the Bio-GraphIIn interface hides most of the complexities to the users, exposing a familiar tabular view of the experimental description with the RDF representation, and visualising descriptors to drive the query over the semantic representation of the experimental design.
expand the conversion tool beyond the current experimental steps represented in ISA-Tab, to consider analysis results, by relying on the STATistics Ontology (STATO)
(The empirical pattern probability distribution is the point {P} and the goal is to find the surface it is close to: )
□ The two cultures of mathematics and biology: Bits of DNA
>>
http://liorpachter.wordpress.com/2014/12/30/the-two-cultures-of-mathematics-and-biology/ …
the 4-state general Markov model with independent processes on each branch, one writes p_{ij} for {P}(B=i,M=j) where i,j are one of A,C,G,T, then it must be the case that p_{ij}p_{kl} = p_{il}p_{jk}. In other words, the polynomial
p_{ij}p_{kl} - p_{il}p_{jk}=0.
“ring of polynomials with the geometric properties of the locus” are the phylogenetic invariants. f(P)=0 and g(P)=0 for any pattern probabilities from the model, so therefore f+g is also a phylogenetic invariant because f(P)+g(P)=0 for any pattern probabilities from the model (the same is true for c \cdot f for any constant c).
□ DeepDive: a inference based approach machine learning to leverage on domain-specific knowledge and data analysis.
>>
http://deepdive.stanford.edu
以下、DeepDiveアルゴリズムの基幹エンジン。
□ Tuffy: Scaling up Statistical Inference in Markov Logic Networks using an RDBMS:
>>
http://www.cs.stanford.edu/people/chrismre/papers/tuffy-vldb11.pdf …
□ An Asynchronous Parallel Stochastic Coordinate Descent Algorithm:
>>
http://arxiv.org/pdf/1311.1873v3.pdf …
□ Elementary: Large-scale Knowledge-base Construction via Machine Learning and Statistical Inference
>>
http://www.cs.stanford.edu/people/chrismre/papers/elementary_journal.pdf
Markov Logic in Elementary
AdjacentMentions(m1, m2) :=
Mentions(m1, p1) ∧ Mentions(m2, p2) ∧ p1 = p2 － 1
MLN rule
wgt(w, l) :
Tokens(tok) ∧ HasWord(tok, w) => TokenLabel(tok, l)
□ Determining the quality and complexity of next-generation sequencing data without a reference genome:
>>
http://genomebiology.com/2014/15/12/555/abstract …
an open-source kPAL package that facilitates alignment-free assessment of quality/comparability of seq data by analysing k-mer frequencies. kPAL uses an efficient k-mer processing as it encodes into a binary code using specific keys and quick conversion to its reverse complement. Counts from k-mers that share the first (n – 1) nucleotides are merged to collapse k-mer profiles to a size k – 1
□ LFCseq: a data-driven nonparametric approach for differential expression analysis of RNA-seq data
>>
http://www.biomedcentral.com/1471-2164/15/S10/S7 …
LFCseq estimates a null or noise probability distribution by contrasting log fold changes for a selected genes at similar expression levels.
PRE (precision) = TP/(TP+FP), SEN (sensitivity) =TP/(TP+FN), and FS (F-score) =2 × PRE × SEN/(PRE + SEN)
□ iRNA-seq: computational method for genome-wide assessment of acute transcriptional regulation from total RNA-seq data
>>
http://www.ncbi.nlm.nih.gov/pubmed/25564527
□ Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools
http://www.ncbi.nlm.nih.gov/pubmed/25566532
□ IVT-seq reveals extreme bias in RNA sequencing:
>>
http://genomebiology.com/2014/15/6/R86?utm_content=buffer33d85 …
over 50% showing greater than 2-fold changes in w/transcript coverage & 10% having more than 10-fold differences attributable to sequencing
□
ecSeq:
Benchmark - Comparison of Different NGS Mappers (
http://www.ecseq.com/support/benchmark.html …)
The transcript isoform abundance parameter, indicator variable for transcript isoform choice, nucleotide sequence
□ TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
>>
http://www.biomedcentral.com/1471-2164/15/S10/S5 …
based on gapped-alignments of reads to the reference cDNA sequences so that sensitive read-aligners such as Bowtie2 and BWA-MEM are effectively incorporated in our pipeline. Also, a heuristic algorithm is implemented in variational Bayesian inference for faster computation.
(100 bp, 250 bp, 500 bp, and 1000 bp of both single-end and paired-end) and variable-length reads, especially for reads longer than 250 bp.
P(Znt|θ) is the conditional probability of Znt given θ
P(Znt | θ) = P(Tn | θ) P(Fn | Tn) P(Sn | Tn,Fn) P(On | Tn) P(A1n,A2n | Tn,Fn,Sn,On)
□ HyLiTE (Hybrid Lineage Transcriptome Explorer) analyzes high-throughput transcriptome data from allopolyploid species
>>
http://hylite.sourceforge.net
HyLiTE temporarily agregates the different lanes of an organism. Thus, the coverage becomes the sum of the coverage for the different lanes. Then, HyLiTE counts and compares every genotype to its expected count if it were an error.
□ SPANR: Splicing-based Analysis of Variants using deep learning algorithms
>>
http://tools.genes.toronto.edu
□
yuifu:
SPANR http://tools.genes.toronto.edu/
Freyらによる、深層学習を利用したスプライシング予測ツール。ヒトのSNVの解釈に利用できる。スプライス部位からイントロン300 nt・エキソン100 ntまで対応。
http://www.sciencemag.org/content/347/6218/1254806 …
□ XBitPar: Bit-parallel String Comparison Tools on Accelerators specified for biological data (i.e DNA, RNA sequences
>>
http://sourceforge.net/projects/xbitpar/?source=directory …
□ Discovery of Substrates for a SET Domain Lysine Methyltransferase Predict by Multistate Computational Protein Design
>>
http://www.cell.com/structure/abstract/S0969-2126(14)00369-4 …
SMYD2 activity is dictated by the motif [LFM]－1-K∗-[AFYMSHRK]+1-[LYK]+2 around the target lysine K∗. Comprehensive motif-based searches.
SMYD2 methylates transcription factors and chromatin remodeling complexes in vitro
□
aaronquinlan:
We are improving the speed & func. of the closest tool in #bedtools. Mulli-file support & k-closest soon. cc @brentp
http://bedtools.readthedocs.org/en/latest/content/tools/closest.html …
□ Evolutionary meandering of intermolecular interactions along the drift barrier:
>>
http://www.pnas.org/content/early/2014/12/18/1421641112.short …
The conflict between mutation pressure toward reduced affinity and selective pressure for greater interaction results in an evolutionary equilibrium distribution for the affinity between interacting partners.
most phylogenetic differences in the sequences of binding interfaces are the result of a simple consequence of random genetic drift.
□ Computational Analysis of Multiple Inositol Polyphosphate Phosphatase 1 Adapt in Higher Organisms Through Evolution
>>
http://www.la-press.com/computational-analysis-reveals-a-successive-adaptation-of-multiple-ino-article-a4587-abstract …
a bioinformatics approach to explore the extent of evolutionary diversification in Minpp1 structure. The human Minpp1 amino acid (AA) sequence was BLAST searched against available national protein databases.
Three signature motifs for phytases were also identified in Minpp1. AAs 126–128 (DLG), AAs 103–200 (QHYH), and AAs 48–53 (GTKTRY).
□ Are there more true codes found in biology besides the central dogma?: mathematical sense of finite-state machines.
>>
http://biology.stackexchange.com/questions/26357/are-there-more-true-codes-found-in-biology-besides-the-central-
□
nygenome:
This Thursday night, @joe_pickrell will speak on combining #genomics & machine learning. More info:
http://bit.ly/13LfsXk #NYGClectures
□ United States Patent (US 8,847,799 B1): Methods and Systems for Storing Sequence read data
>>
https://drive.google.com/viewerng/viewer?url=patentimages.storage.googleapis.com/pdfs/US8847799.pdf
□ Heng Li’s Mysterious New Program: Heng Li is developing a new Bloom filter-based short read error-correction program
>>
http://www.homolog.us/blogs/blog/2015/01/08/heng-lis-mysterious-new-program/ …
an input fastq file and the program will output the error-corrected file with erroneous nucleotide marked in small letters.
-b INT set Bloom filter size to pow(2,INT) bits [33]
-H INT use INT hash functions for Bloom filter [4]
-w INT no more than 5 ec or 2 highQ ec in INT-bp window [10]
-c INT min k-mer coverage [3]
□ Python for Finance: NumPy/SciPy/SymPy Framework Monte Carlo simulation-based risk analytics
>>
http://cdn.oreillystatic.com/oreilly/booksamplers/9781491945285_sampler.pdf …
□ Applications of Information Theory to Analysis of Neural Data
http://arxiv.org/abs/1501.01860
□
SciPyTip:
sys.float_info.epsilon is the smallest number that can be added to 1 and make a difference.
□ Data Visualization Japan Meetup #2「数字を見せろ」から「コードを見せろ」へ ～過程の透明性を確保したデータ可視化を目指す～ on @slideshare
http://www.slideshare.net/keiono/ss-43018012 …
□ Programming Computer Vision with Python
http://bit.ly/13GVdJe (cmts
http://bit.ly/13GVdJf )
□ Transforming data with zeros
http://bit.ly/fspptd
□ Random paths and current fluctuations in nonequilibrium statistical mechanics in time or spacetime:
>>
http://scitation.aip.org/content/aip/journal/jmp/55/7/10.1063/1.4881534
Open classical Hamiltonian systems can be considered in the escape-rate formalism. These systems are set in transient non equilibrium regimes allowing trajectories to escape from some phase-space domain delimited by absorbing boundary conditions which define first-passage problems.
open systems: γ = ∑ λ(i)>0 ⟨λ(i)⟩－hKS
□ A system-level pathway-phenotype association analysis using synthetic feature random forest:
>>
http://www.ncbi.nlm.nih.gov/pubmed/24535726
complement SF-RF with pathway-based Statistical Epistasis Network (SEN) analysis that evaluates interactions among pathways.
□ Dynamic acoustic field activated cell separation: new method to separate clinically useful cells from cellular debris
>>
http://pubs.rsc.org/en/content/articlepdf/2015/lc/c4lc01153h
The large particles move with greater velocity than smallers, when the phase shift reaches the rest period at 360° large particles continue forward and reach the next acoustic node and are trapped. the small, light particles relax back to the initial node.
□
brembs:
#PLOSBiology: The Transformative Nature of Transparency in Research Funding
http://buff.ly/14koH0U
□
rahman_nazneen:
NHS hampered by over-complex management structure that limits progress and performance, Rose report claims. Indeed!
http://gu.com/p/44f7n/stw
□
erlichya:
Here is the Vogelstein data but this time Organ size vs. Life time incident of cancer. Pearson corr = 0.5
経営をやっていると、需要のあるところで「偏ったデータ」に出くわすこともあるけれど、statisticsの方法論が正しく偏ったデータに価値や知見を見出す（表現する）ことと、方法論自体を誤ることは、単純にパースペクティブの違い以上の決定的な線引きがある。
□
ldemare:
Developing new methods for assessing the strength of evidence supporting a hypothesis #beyondthePvalue PNAS [podcast]
http://www.pnas.org/site/podcasts/podcasts.xhtml#Vieland
□
dgmacarthur:
The $60M deal between @23andMe and @genentech is huge news. As usual, @matthewherper has perceptive commentary:
http://www.forbes.com/sites/matthewherper/2015/01/06/surprise-with-60-million-genentech-deal-23andme-has-a-business-plan/ …
□
fperez_org:
Because we can't test string theory, let's redefine science to remove that pesky "empirical testing" requirement...
>>
http://www.nature.com/news/scientific-method-defend-the-integrity-of-physics-1.16535 …
in the absence of adequate data, elegant and compelling ideas led researchers in the wrong direction.
□ Quantum voting & violation of Arrow’s Impossibility Theorem:
>>
http://arxiv.org/pdf/1501.00458v1.pdf …
Superpositions, interference, and entanglement expand voters’ arsenals of manipulation tactics. So does whether monogamy of entanglement limits one voter’s influence on others’ quantum preferences.
□
PlanckScale:
投票制度に関するアローの不可能性定理は、量子論理にはあてはまらないので、投票を量子化すればこの定理を逃れられるという論文
□
SCSanderson:
Two main results in online survey (n=6944) re incidental findings (IFs) from genomic research, by @Genomethics et al
http://www.thelancet.com/journals/lancet/article/PIIS0140-6736%2814%2962119-X/fulltext
□
CraigBosse:
Unbelievable Picture of Ibrahim Albeshari Cruise Yacht in Dubai
□
INTLSpectator:
The Zaatari Syrian refugee camp in Jordan, now equivalent to being the country's fourth largest city.
□ Nietzsche, Dionysus, and the Ontology of Music: Music, Science, and the Interpretation of Existence
>>
http://faculty.hampshire.edu/ccox/Cox.Nietzsche.Dionysus.Music.pdf
