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Jarek Duda

Publications and source records attributed to Jarek Duda.

At least 55 records · Page 3Linked to original sources

Exploiting statistical dependencies of time series with hierarchical correlation reconstruction

While we are usually focused on forecasting future values of time series, it is often valuable to additionally predict their entire probability distributions, e.g. to evaluate risk, Monte Carlo simulations. On example of time series of $\approx$ 30000 Dow Jones Industrial Averages, there will be presented application of hierarchical correlation reconstruction for this purpose: MSE estimating polynomial as joint density for (current value, context), where context is for example a few previous values. Then substituting the currently observed context and normalizing density to 1, we get predicted probability distribution for the current value. In contrast to standard machine learning approaches like neural networks, optimal polynomial coefficients here have inexpensive direct formula, have controllable accuracy, are unique and independently calculated, each has a specific cumulant-like interpretation, and such approximation can asymptotically approach complete description of any real joint distribution - providing universal tool to quantitatively describe and exploit statistical dependencies in time series, systematically enhancing ARMA/ARCH-like approaches, also based on different distributions than Gaussian which turns out improper for daily log returns. There is also discussed application for non-stationary time series like calculating linear time trend, or adapting coefficients to local statistical behavior.

cs.LG↗

Gaussian AutoEncoder

Generative AutoEncoders require a chosen probability distribution in latent space, usually multivariate Gaussian. The original Variational AutoEncoder (VAE) uses randomness in encoder - causing problematic distortion, and overlaps in latent space for distinct inputs. It turned out unnecessary: we can instead use deterministic encoder with additional regularizer to ensure that sample distribution in latent space is close to the required. The original approach (WAE) uses Wasserstein metric, what required comparing with random sample and using an arbitrarily chosen kernel. Later CWAE finally derived a non-random analytic formula by averaging $L_2$ distance of Gaussian-smoothened sample over all 1D projections. However, these arbitrarily chosen regularizers do not lead to Gaussian distribution. This article proposes approach for regularizers directly optimizing agreement between empirical distribution function and its desired CDF for chosen properties, for example radii and distances for Gaussian distribution, or coordinate-wise, to directly attract this distribution in latent space of AutoEncoder. We can also attract different distributions with this general approach, for example latent space uniform distribution on $[0,1]^D$ hypercube or torus would allow for data compression without entropy coding, increased density near codewords would optimize for the required quantization.

cs.LG↗

Modeling joint probability distribution of yield curve parameters

US Yield curve has recently collapsed to its most flattened level since subprime crisis and is close to the inversion. This fact has gathered attention of investors around the world and revived the discussion of proper modeling and forecasting yield curve, since changes in interest rate structure are believed to represent investors expectations about the future state of economy and have foreshadowed recessions in the United States. While changes in term structure of interest rates are relatively easy to interpret they are however very difficult to model and forecast due to no proper economic theory underlying such events. Yield curves are usually represented by multivariate sparse time series, at any point in time infinite dimensional curve is portrayed via relatively few points in a multivariate space of data and as a consequence multimodal statistical dependencies behind these curves are relatively hard to extract and forecast via typical multivariate statistical methods.We propose to model yield curves via reconstruction of joint probability distribution of parameters in functional space as a high degree polynomial. Thanks to adoption of an orthonormal basis, the MSE estimation of coefficients of a given function is an average over a data sample in the space of functions. Since such polynomial coefficients are independent and have cumulant-like interpretation ie.describe corresponding perturbation from an uniform joint distribution, our approach can also be extended to any d-dimensional space of yield curve parameters (also in neighboring times) due to controllable accuracy. We believe that this approach to modeling of local behavior of a sparse multivariate curved time series can complement prediction from standard models like ARIMA, that are using long range dependencies, but provide only inaccurate prediction of probability distribution, often as just Gaussian with constant width.

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Hierarchical correlation reconstruction with missing data, for example for biology-inspired neuron

Machine learning often needs to model density from a multidimensional data sample, including correlations between coordinates. Additionally, we often have missing data case: that data points can miss values for some of coordinates. This article adapts rapid parametric density estimation approach for this purpose: modelling density as a linear combination of orthonormal functions, for which $L^2$ optimization says that (independently) estimated coefficient for a given function is just average over the sample of value of this function. Hierarchical correlation reconstruction first models probability density for each separate coordinate using all its appearances in data sample, then adds corrections from independently modelled pairwise correlations using all samples having both coordinates, and so on independently adding correlations for growing numbers of variables using often decreasing evidence in data sample. A basic application of such modelled multidimensional density can be imputation of missing coordinates: by inserting known coordinates to the density, and taking expected values for the missing coordinates, or even their entire joint probability distribution. Presented method can be compared with cascade correlations approach, offering several advantages in flexibility and accuracy. It can be also used as artificial neuron: maximizing prediction capabilities for only local behavior - modelling and predicting local connections.

cs.LG↗

Polynomial-based rotation invariant features

One of basic difficulties of machine learning is handling unknown rotations of objects, for example in image recognition. A related problem is evaluation of similarity of shapes, for example of two chemical molecules, for which direct approach requires costly pairwise rotation alignment and comparison. Rotation invariants are useful tools for such purposes, allowing to extract features describing shape up to rotation, which can be used for example to search for similar rotated patterns, or fast evaluation of similarity of shapes e.g. for virtual screening, or machine learning including features directly describing shape. A standard approach are rotationally invariant cylindrical or spherical harmonics, which can be seen as based on polynomials on sphere, however, they provide very few invariants - only one per degree of polynomial. There will be discussed a general approach to construct arbitrarily large sets of rotation invariants of polynomials, for degree $D$ in $\mathbb{R}^n$ up to $O(n^D)$ independent invariants instead of $O(D)$ offered by standard approaches, possibly also a complete set: providing not only necessary, but also sufficient condition for differing only by rotation (and reflectional symmetry).

cs.LG↗

Improving Pyramid Vector Quantizer with power projection

Pyramid Vector Quantizer (PVQ) is a promising technique especially for multimedia data compression, already used in Opus audio codec and considered for AV1 video codec. It quantizes vectors from Euclidean unit sphere by first projecting them to $L^1$ norm unit sphere, then quantizing and encoding there. This paper shows that the used standard radial projection is suboptimal and proposes to tune its deformations by using parameterized power projection: $x\to x^p/\|x^p\|$ instead, where the optimized power $p$ is applied coordinate-wise, getting usually $\geq 0.5\, dB$ improvement comparing to radial projection.

math.OC↗

Rapid parametric density estimation

Parametric density estimation, for example as Gaussian distribution, is the base of the field of statistics. Machine learning requires inexpensive estimation of much more complex densities, and the basic approach is relatively costly maximum likelihood estimation (MLE). There will be discussed inexpensive density estimation, for example literally fitting a polynomial (or Fourier series) to the sample, which coefficients are calculated by just averaging monomials (or sine/cosine) over the sample. Another discussed basic application is fitting distortion to some standard distribution like Gaussian - analogously to ICA, but additionally allowing to reconstruct the disturbed density. Finally, by using weighted average, it can be also applied for estimation of non-probabilistic densities, like modelling mass distribution, or for various clustering problems by using negative (or complex) weights: fitting a function which sign (or argument) determines clusters. The estimated parameters are approaching the optimal values with error dropping like $1/\sqrt{n}$, where $n$ is the sample size.

cs.LG↗

Lightweight compression with encryption based on Asymmetric Numeral Systems

Data compression combined with effective encryption is a common requirement of data storage and transmission. Low cost of these operations is often a high priority in order to increase transmission speed and reduce power usage. This requirement is crucial for battery-powered devices with limited resources, such as autonomous remote sensors or implants. Well-known and popular encryption techniques are frequently too expensive. This problem is on the increase as machine-to-machine communication and the Internet of Things are becoming a reality. Therefore, there is growing demand for finding trade-offs between security, cost and performance in lightweight cryptography. This article discusses Asymmetric Numeral Systems -- an innovative approach to entropy coding which can be used for compression with encryption. It provides compression ratio comparable with arithmetic coding at similar speed as Huffman coding, hence, this coding is starting to replace them in new compressors. Additionally, by perturbing its coding tables, the Asymmetric Numeral System makes it possible to simultaneously encrypt the encoded message at nearly no additional cost. The article introduces this approach and analyzes its security level. The basic application is reducing the number of rounds of some cipher used on ANS-compressed data, or completely removing additional encryption layer if reaching a satisfactory protection level.

cs.IT↗

Practical estimation of rotation distance and induced partial order for binary trees

Tree rotations (left and right) are basic local deformations allowing to transform between two unlabeled binary trees of the same size. Hence, there is a natural problem of practically finding such transformation path with low number of rotations, the optimal minimal number is called the rotation distance. Such distance could be used for instance to quantify similarity between two trees for various machine learning problems, for example to compare hierarchical clusterings or arbitrarily chosen spanning trees of two graphs, like in SMILES notation popular for describing chemical molecules. There will be presented inexpensive practical greedy algorithm for finding a short rotation path, optimality of which has still to be determined. It uses introduced partial order for binary trees of the same size: $t_1 \leq t_2$ iff $t_2$ can be obtained from $t_1$ by a sequence of only right rotations. Intuitively, the shortest rotation path should go through the least upper bound or the greatest lower bound for this partial order. The algorithm finds a path through candidates for both points in representation of binary tree as stack graph: describing evolution of content of stack while processing a formula described by a given binary tree. The article is accompanied with Mathematica implementation of all used procedures (Appendix).

cs.DS↗

Nonuniform probability modulation for reducing energy consumption of remote sensors

One of the main goals of 5G wireless telecommunication technology is improving energy efficiency, especially of remote sensors which should be able for example to transmit on average 1bit/s for 10 years from a single AAA battery. There will be discussed using modulation with nonuniform probability distribution of symbols for improving energy efficiency of transmission at cost of reduced throughput. While the zero-signal (silence) has zero energy cost to emit, it can carry information if used alongside other symbols. If used more frequently than others, for example for majority of time slots or OFDM subcarriers, the number of bits transmitted per energy unit can be significantly increased. For example for hexagonal modulation and zero noise, this amount of bits per energy unit can be doubled by reducing throughput 2.7 times, thanks to using the zero-signal with probability $\approx$ 0.84. There will be discussed models and methods for such nonuniform probability modulations (NPM).

cs.IT↗

Distortion-Resistant Hashing for rapid search of similar DNA subsequence

One of the basic tasks in bioinformatics is localizing a short subsequence $S$, read while sequencing, in a long reference sequence $R$, like the human geneome. A natural rapid approach would be finding a hash value for $S$ and compare it with a prepared database of hash values for each of length $|S|$ subsequences of $R$. The problem with such approach is that it would only spot a perfect match, while in reality there are lots of small changes: substitutions, deletions and insertions. This issue could be repaired if having a hash function designed to tolerate some small distortion accordingly to an alignment metric (like Needleman-Wunch): designed to make that two similar sequences should most likely give the same hash value. This paper discusses construction of Distortion-Resistant Hashing (DRH) to generate such fingerprints for rapid search of similar subsequences. The proposed approach is based on the rate distortion theory: in a nearly uniform subset of length $|S|$ sequences, the hash value represents the closest sequence to $S$. This gives some control of the distance of collisions: sequences having the same hash value.

cs.DS↗

Fundamental Bounds and Approaches to Sequence Reconstruction from Nanopore Sequencers

Nanopore sequencers are emerging as promising new platforms for high-throughput sequencing. As with other technologies, sequencer errors pose a major challenge for their effective use. In this paper, we present a novel information theoretic analysis of the impact of insertion-deletion (indel) errors in nanopore sequencers. In particular, we consider the following problems: (i) for given indel error characteristics and rate, what is the probability of accurate reconstruction as a function of sequence length; (ii) what is the number of `typical' sequences within the distortion bound induced by indel errors; (iii) using replicated extrusion (the process of passing a DNA strand through the nanopore), what is the number of replicas needed to reduce the distortion bound so that only one typical sequence exists within the distortion bound. Our results provide a number of important insights: (i) the maximum length of a sequence that can be accurately reconstructed in the presence of indel and substitution errors is relatively small; (ii) the number of typical sequences within the distortion bound is large; and (iii) replicated extrusion is an effective technique for unique reconstruction. In particular, we show that the number of replicas is a slow function (logarithmic) of sequence length -- implying that through replicated extrusion, we can sequence large reads using nanopore sequencers. Our model considers indel and substitution errors separately. In this sense, it can be viewed as providing (tight) bounds on reconstruction lengths and repetitions for accurate reconstruction when the two error modes are considered in a single model.

cs.IT↗

Designing dedicated data compression for physics experiments within FPGA already used for data acquisition

Physics experiments produce enormous amount of raw data, counted in petabytes per day. Hence, there is large effort to reduce this amount, mainly by using some filters. The situation can be improved by additionally applying some data compression techniques: removing redundancy and optimally encoding the actual information. Preferably, both filtering and data compression should fit in FPGA already used for data acquisition - reducing requirements of both data storage and networking architecture. We will briefly explain and discuss some basic techniques, for a better focus applied to design a dedicated data compression system basing on a sample data from a prototype of a tracking detector: 10000 events for 48 channels. We will focus on the time data here, which after neglecting the headers and applying data filtering, requires on average 1170 bits/event using the current coding. Encoding relative times (differences) and grouping data by channels, reduces this number to 798 bits/channel, still using fixed length coding: a fixed number of bits used for a given value. Using variable length Huffman coding to encode numbers of digital pulses for a channel and the most significant bits of values (simple binning) reduces further this number to 552 bits/event. Using adaptive binning: denser for frequent values, and an accurate entropy coder we get further down to 455 bits/event - this option can easily fit unused resources of FPGA currently used for data acquisition. Finally, using separate probability distributions for different channels, what could be done by a software compressor, leads to 437bits/event, what is 2.67 times less than the original 1170 bits/event.

cs.IT↗

Normalized rotation shape descriptors and lossy compression of molecular shape

There is a common need to search of molecular databases for compounds resembling some shape, what suggests having similar biological activity while searching for new drugs. The large size of the databases requires fast methods for such initial screening, for example based on feature vectors constructed to fulfill the requirement that similar molecules should correspond to close vectors. Ultrafast Shape Recognition (USR) is a popular approach of this type. It uses vectors of 12 real number as 3 first moments of distances from 4 emphasized points. These coordinates might contain unnecessary correlations and does not allow to reconstruct the approximated shape. In contrast, spherical harmonic (SH) decomposition uses orthogonal coordinates, suggesting their independence and so lager informational content of the feature vector. There is usually considered rotationally invariant SH descriptors, what means discarding of some essential information. This article discusses framework for descriptors with normalized rotation, for example by using principal component analysis (PCA-SH). As one of the most interesting are ligands which have to slide into a protein, we will introduce descriptors optimized for such flat elongated shapes. Bent deformed cylinder (BDC) describes the molecule as a cylinder which was first bent, then deformed such that its cross-sections became ellipses of evolving shape. Legendre polynomials are used to describe the central axis of such bent cylinder. Additional polynomials are used to define evolution of such elliptic cross-section along the main axis. There will be also discussed bent cylindrical harmonics (BCH), which uses cross-sections described by cylindrical harmonics instead of ellipses. All these normalized rotation descriptors allow to reconstruct (decode) the approximated representation of the shape, hence can be also used for lossy compression purposes.

cs.CE↗

Joint error correction enhancement of the fountain codes concept

Fountain codes like LT or Raptor codes, also known as rateless erasure codes, allow to encode a message as some number of packets, such that any large enough subset of these packets is sufficient to fully reconstruct the message. It requires undamaged packets, while the packets which were not lost are usually damaged in real scenarios. Hence, an additional error correction layer is often required: adding some level of redundancy to each packet to be able to repair eventual damages. This approach requires a priori knowledge of the final damage level of every packet - insufficient redundancy leads to packet loss, overprotection means suboptimal channel rate. However, the sender may have inaccurate or even no a priori information about the final damage levels, for example in applications like broadcasting, degradation of a storage medium or damage of picture watermarking. Joint Reconstruction Codes (JRC) setting is introduced and discussed in this paper for the purpose of removing the need of a priori knowledge of damage level and sub-optimality caused by overprotection and discarding underprotected packets. It is obtained by combining both processes: reconstruction from multiple packets and forward error correction. The decoder combines the resultant informational content of all received packets accordingly to their actual noise level, which can be estimated a posteriori individually for each packet. Assuming binary symmetric channel (BSC) of $ε$ bit-flip probability, every potentially damaged bit carries $R_0(ε)=1-h_1(ε)$ bits of information, where $h_1$ is the Shannon entropy. The minimal requirement to fully reconstruct the message is that the sum of rate $R_0(ε)$ over all bits is at least the size of the message. We will discuss sequential decoding for the reconstruction purpose, which statistical behavior can be estimated using Renyi entropy.

cs.IT↗

Asymmetric numeral systems: entropy coding combining speed of Huffman coding with compression rate of arithmetic coding

The modern data compression is mainly based on two approaches to entropy coding: Huffman (HC) and arithmetic/range coding (AC). The former is much faster, but approximates probabilities with powers of 2, usually leading to relatively low compression rates. The latter uses nearly exact probabilities - easily approaching theoretical compression rate limit (Shannon entropy), but at cost of much larger computational cost. Asymmetric numeral systems (ANS) is a new approach to accurate entropy coding, which allows to end this trade-off between speed and rate: the recent implementation [1] provides about $50\%$ faster decoding than HC for 256 size alphabet, with compression rate similar to provided by AC. This advantage is due to being simpler than AC: using single natural number as the state, instead of two to represent a range. Beside simplifying renormalization, it allows to put the entire behavior for given probability distribution into a relatively small table: defining entropy coding automaton. The memory cost of such table for 256 size alphabet is a few kilobytes. There is a large freedom while choosing a specific table - using pseudorandom number generator initialized with cryptographic key for this purpose allows to simultaneously encrypt the data. This article also introduces and discusses many other variants of this new entropy coding approach, which can provide direct alternatives for standard AC, for large alphabet range coding, or for approximated quasi arithmetic coding.

cs.IT↗

Embedding grayscale halftone pictures in QR Codes using Correction Trees

Barcodes like QR Codes have made that encoded messages have entered our everyday life, what suggests to attach them a second layer of information: directly available to human receiver for informational or marketing purposes. We will discuss a general problem of using codes with chosen statistical constrains, for example reproducing given grayscale picture using halftone technique. If both sender and receiver know these constrains, the optimal capacity can be easily approached by entropy coder. The problem is that this time only the sender knows them - we will refer to these scenarios as constrained coding. Kuznetsov and Tsybakov problem in which only the sender knows which bits are fixed can be seen as a special case, surprisingly approaching the same capacity as if both sides would know the constrains. We will analyze Correction Trees to approach analogous capacity in the general case - use weaker: statistical constrains, what allows to apply them to all bits. Finding satisfying coding is similar to finding the proper correction in error correction problem, but instead of single ensured possibility, there are now statistically expected some. While in standard steganography we hide information in the least important bits, this time we create codes resembling given picture - hide information in the freedom of realizing grayness by black and white pixels using halftone technique. We will also discuss combining with error correction and application to rate distortion problem.

cs.IT↗

Optimal compression of hash-origin prefix trees

There is a common problem of operating on hash values of elements of some database. In this paper there will be analyzed informational content of such general task and how to practically approach such found lower boundaries. Minimal prefix tree which distinguish elements turns out to require asymptotically only about 2.77544 bits per element, while standard approaches use a few times more. While being certain of working inside the database, the cost of distinguishability can be reduced further to about 2.33275 bits per elements. Increasing minimal depth of nodes to reduce probability of false positives leads to simple relation with average depth of such random tree, which is asymptotically larger by about 1.33275 bits than lg(n) of the perfect binary tree. This asymptotic case can be also seen as a way to optimally encode n large unordered numbers - saving lg(n!) bits of information about their ordering, which can be the major part of contained information. This ability itself allows to reduce memory requirements even to about 0.693 of required in Bloom filter for the same false positive probability.

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