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1. Fully Functional Parameterized Suffix Trees in Compact Space

   Ganguly, Arnab ; Shah, Rahul ; Thankachan, Sharma V. ( June 2022 , 49th International Colloquium on Automata, Languages, and Programming (ICALP 2022))

   Mikolaj Bojanczyk ; Emanuela Merelli ; David P. Woodruff (Ed.)

   Two equal length strings are a parameterized match (p-match) iff there exists a one-to-one function that renames the symbols in one string to those in the other. The Parameterized Suffix Tree (PST) [Baker, STOC' 93] is a fundamental data structure that handles various string matching problems under this setting. The PST of a text T[1,n] over an alphabet Σ of size σ takes O(nlog n) bits of space. It can report any entry in (parameterized) (i) suffix array, (ii) inverse suffix array, and (iii) longest common prefix (LCP) array in O(1) time. Given any pattern P as a query, a position i in T is an occurrence iff T[i,i+|P|-1] and P are a p-match. The PST can count the number of occurrences of P in T in time O(|P|log σ) and then report each occurrence in time proportional to that of accessing a suffix array entry. An important question is, can we obtain a compressed version of PST that takes space close to the text’s size of nlogσ bits and still support all three functionalities mentioned earlier? In SODA' 17, Ganguly et al. answered this question partially by presenting an O(nlogσ) bit index that can support (parameterized) suffix array and inverse suffix array operations in O(log n) time. However, the compression of the (parameterized) LCP array and the possibility of faster suffix array and inverse suffix array queries in compact space were left open. In this work, we obtain a compact representation of the (parameterized) LCP array. With this result, in conjunction with three new (parameterized) suffix array representations, we obtain the first set of PST representations in o(nlog n) bits (when logσ = o(log n)) as follows. Here ε > 0 is an arbitrarily small constant. - Space O(n logσ) bits and query time O(log_σ^ε n); - Space O(n logσlog log_σ n) bits and query time O(log log_σ n); and - Space O(n logσ log^ε_σ n) bits and query time O(1). The first trade-off is an improvement over Ganguly et al.’s result, whereas our third trade-off matches the optimal time performance of Baker’s PST while squeezing the space by a factor roughly log_σ n. We highlight that our trade-offs match the space-and-time bounds of the best-known compressed text indexes for exact pattern matching and further improvement is highly unlikely. 

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2. Quantum SDP Solvers: Large Speed-Ups, Optimality, and Applications to Quantum Learning

   Brand ; Kalev, Amir ; Li, Tongyang ; Lin, Cedric Yen-Yu ; Svore, Krysta M. ; Wu, Xiaodi ( July 2019 , Leibniz international proceedings in informatics)

   We give two new quantum algorithms for solving semidefinite programs (SDPs) providing quantum speed-ups. We consider SDP instances with m constraint matrices, each of dimension n, rank at most r, and sparsity s. The first algorithm assumes an input model where one is given access to an oracle to the entries of the matrices at unit cost. We show that it has run time O~(s^2 (sqrt{m} epsilon^{-10} + sqrt{n} epsilon^{-12})), with epsilon the error of the solution. This gives an optimal dependence in terms of m, n and quadratic improvement over previous quantum algorithms (when m ~~ n). The second algorithm assumes a fully quantum input model in which the input matrices are given as quantum states. We show that its run time is O~(sqrt{m}+poly(r))*poly(log m,log n,B,epsilon^{-1}), with B an upper bound on the trace-norm of all input matrices. In particular the complexity depends only polylogarithmically in n and polynomially in r. We apply the second SDP solver to learn a good description of a quantum state with respect to a set of measurements: Given m measurements and a supply of copies of an unknown state rho with rank at most r, we show we can find in time sqrt{m}*poly(log m,log n,r,epsilon^{-1}) a description of the state as a quantum circuit preparing a density matrix which has the same expectation values as rho on the m measurements, up to error epsilon. The density matrix obtained is an approximation to the maximum entropy state consistent with the measurement data considered in Jaynes' principle from statistical mechanics. As in previous work, we obtain our algorithm by "quantizing" classical SDP solvers based on the matrix multiplicative weight update method. One of our main technical contributions is a quantum Gibbs state sampler for low-rank Hamiltonians, given quantum states encoding these Hamiltonians, with a poly-logarithmic dependence on its dimension, which is based on ideas developed in quantum principal component analysis. We also develop a "fast" quantum OR lemma with a quadratic improvement in gate complexity over the construction of Harrow et al. [Harrow et al., 2017]. We believe both techniques might be of independent interest. 

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3. Simple and efficient pseudorandom genera- tors from Gaussian processes.

   Chattopadhyay, Eshan ; De, Anindya ; Servedio, Rocco ( July 2019 , Leibniz international proceedings in informatics)

   Abstract We show that a very simple pseudorandom generator fools intersections of k linear threshold functions (LTFs) and arbitrary functions of k LTFs over n-dimensional Gaussian space. The two analyses of our PRG (for intersections versus arbitrary functions of LTFs) are quite different from each other and from previous analyses of PRGs for functions of halfspaces. Our analysis for arbitrary functions of LTFs establishes bounds on the Wasserstein distance between Gaussian random vectors with similar covariance matrices, and combines these bounds with a conversion from Wasserstein distance to "union-of-orthants" distance from [Xi Chen et al., 2014]. Our analysis for intersections of LTFs uses extensions of the classical Sudakov-Fernique type inequalities, which give bounds on the difference between the expectations of the maxima of two Gaussian random vectors with similar covariance matrices. For all values of k, our generator has seed length O(log n) + poly(k) for arbitrary functions of k LTFs and O(log n) + poly(log k) for intersections of k LTFs. The best previous result, due to [Gopalan et al., 2010], only gave such PRGs for arbitrary functions of k LTFs when k=O(log log n) and for intersections of k LTFs when k=O((log n)/(log log n)). Thus our PRG achieves an O(log n) seed length for values of k that are exponentially larger than previous work could achieve. By combining our PRG over Gaussian space with an invariance principle for arbitrary functions of LTFs and with a regularity lemma, we obtain a deterministic algorithm that approximately counts satisfying assignments of arbitrary functions of k general LTFs over {0,1}^n in time poly(n) * 2^{poly(k,1/epsilon)} for all values of k. This algorithm has a poly(n) runtime for k =(log n)^c for some absolute constant c>0, while the previous best poly(n)-time algorithms could only handle k = O(log log n). For intersections of LTFs, by combining these tools with a recent PRG due to [R. O'Donnell et al., 2018], we obtain a deterministic algorithm that can approximately count satisfying assignments of intersections of k general LTFs over {0,1}^n in time poly(n) * 2^{poly(log k, 1/epsilon)}. This algorithm has a poly(n) runtime for k =2^{(log n)^c} for some absolute constant c>0, while the previous best poly(n)-time algorithms for intersections of k LTFs, due to [Gopalan et al., 2010], could only handle k=O((log n)/(log log n)). 

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4. Algorithms for covering multiple submodular constraints and applications

   https://doi.org/10.1007/s10878-022-00874-x  

   Chekuri, Chandra ; Inamdar, Tanmay ; Quanrud, Kent ; Varadarajan, Kasturi ; Zhang, Zhao ( June 2022 , Journal of Combinatorial Optimization)

   We consider the problem of covering multiple submodular constraints. Given a finite ground setN, a weight function$$w: N \rightarrow \mathbb {R}_+$$$w:N\to R_{+}$,rmonotone submodular functions$$f_1,f_2,\ldots ,f_r$$$f_1,f_2,\dots ,f_r$overNand requirements$$k_1,k_2,\ldots ,k_r$$$k_1,k_2,\dots ,k_r$the goal is to find a minimum weight subset$$S \subseteq N$$$S\subseteq N$such that$$f_i(S) \ge k_i$$$f_i\left(S\right)\ge k_i$for$$1 \le i \le r$$$1\le i\le r$. We refer to this problem asMulti-Submod-Coverand it was recently considered by Har-Peled and Jones (Few cuts meet many point sets. CoRR.arxiv:abs1808.03260Har-Peled and Jones 2018) who were motivated by an application in geometry. Even with$$r=1$$$r=1$Multi-Submod-Covergeneralizes the well-known Submodular Set Cover problem (Submod-SC), and it can also be easily reduced toSubmod-SC. A simple greedy algorithm gives an$$O(\log (kr))$$$O(log(kr\left)\right)$approximation where$$k = \sum _i k_i$$$k={\sum }_i{k}_i$and this ratio cannot be improved in the general case. In this paper, motivated by several concrete applications, we consider two ways to improve upon the approximation given by the greedy algorithm. First, we give a bicriteria approximation algorithm forMulti-Submod-Coverthat covers each constraint to within a factor of$$(1-1/e-\varepsilon )$$$(1-1/e-\epsilon )$while incurring an approximation of$$O(\frac{1}{\epsilon }\log r)$$$O(\frac{1}{ϵ}logr)$in the cost. Second, we consider the special case when each$$f_i$$$f_i$is a obtained from a truncated coverage function and obtain an algorithm that generalizes previous work on partial set cover (Partial-SC), covering integer programs (CIPs) and multiple vertex cover constraints Bera et al. (Theoret Comput Sci 555:2–8 Bera et al. 2014). Both these algorithms are based on mathematical programming relaxations that avoid the limitations of the greedy algorithm. We demonstrate the implications of our algorithms and related ideas to several applications ranging from geometric covering problems to clustering with outliers. Our work highlights the utility of the high-level model and the lens of submodularity in addressing this class of covering problems.

    

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5. The Temple University Digital Pathology Corpus: The Breast Tissue Subset

   https://doi.org/10.1109/SPMB52430.2021.9672275  

   Wevodau, Z. ; Doshna, B. ; Jhala, N. ; Akhtar, I. ; Obeid, I. ; Picone, J. ( December 2021 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, I. (Ed.)

   The Neural Engineering Data Consortium (NEDC) is developing the Temple University Digital Pathology Corpus (TUDP), an open source database of high-resolution images from scanned pathology samples [1], as part of its National Science Foundation-funded Major Research Instrumentation grant titled “MRI: High Performance Digital Pathology Using Big Data and Machine Learning” [2]. The long-term goal of this project is to release one million images. We have currently scanned over 100,000 images and are in the process of annotating breast tissue data for our first official corpus release, v1.0.0. This release contains 3,505 annotated images of breast tissue including 74 patients with cancerous diagnoses (out of a total of 296 patients). In this poster, we will present an analysis of this corpus and discuss the challenges we have faced in efficiently producing high quality annotations of breast tissue. It is well known that state of the art algorithms in machine learning require vast amounts of data. Fields such as speech recognition [3], image recognition [4] and text processing [5] are able to deliver impressive performance with complex deep learning models because they have developed large corpora to support training of extremely high-dimensional models (e.g., billions of parameters). Other fields that do not have access to such data resources must rely on techniques in which existing models can be adapted to new datasets [6]. A preliminary version of this breast corpus release was tested in a pilot study using a baseline machine learning system, ResNet18 [7], that leverages several open-source Python tools. The pilot corpus was divided into three sets: train, development, and evaluation. Portions of these slides were manually annotated [1] using the nine labels in Table 1 [8] to identify five to ten examples of pathological features on each slide. Not every pathological feature is annotated, meaning excluded areas can include focuses particular to these labels that are not used for training. A summary of the number of patches within each label is given in Table 2. To maintain a balanced training set, 1,000 patches of each label were used to train the machine learning model. Throughout all sets, only annotated patches were involved in model development. The performance of this model in identifying all the patches in the evaluation set can be seen in the confusion matrix of classification accuracy in Table 3. The highest performing labels were background, 97% correct identification, and artifact, 76% correct identification. A correlation exists between labels with more than 6,000 development patches and accurate performance on the evaluation set. Additionally, these results indicated a need to further refine the annotation of invasive ductal carcinoma (“indc”), inflammation (“infl”), nonneoplastic features (“nneo”), normal (“norm”) and suspicious (“susp”). This pilot experiment motivated changes to the corpus that will be discussed in detail in this poster presentation. To increase the accuracy of the machine learning model, we modified how we addressed underperforming labels. One common source of error arose with how non-background labels were converted into patches. Large areas of background within other labels were isolated within a patch resulting in connective tissue misrepresenting a non-background label. In response, the annotation overlay margins were revised to exclude benign connective tissue in non-background labels. Corresponding patient reports and supporting immunohistochemical stains further guided annotation reviews. The microscopic diagnoses given by the primary pathologist in these reports detail the pathological findings within each tissue site, but not within each specific slide. The microscopic diagnoses informed revisions specifically targeting annotated regions classified as cancerous, ensuring that the labels “indc” and “dcis” were used only in situations where a micropathologist diagnosed it as such. Further differentiation of cancerous and precancerous labels, as well as the location of their focus on a slide, could be accomplished with supplemental immunohistochemically (IHC) stained slides. When distinguishing whether a focus is a nonneoplastic feature versus a cancerous growth, pathologists employ antigen targeting stains to the tissue in question to confirm the diagnosis. For example, a nonneoplastic feature of usual ductal hyperplasia will display diffuse staining for cytokeratin 5 (CK5) and no diffuse staining for estrogen receptor (ER), while a cancerous growth of ductal carcinoma in situ will have negative or focally positive staining for CK5 and diffuse staining for ER [9]. Many tissue samples contain cancerous and non-cancerous features with morphological overlaps that cause variability between annotators. The informative fields IHC slides provide could play an integral role in machine model pathology diagnostics. Following the revisions made on all the annotations, a second experiment was run using ResNet18. Compared to the pilot study, an increase of model prediction accuracy was seen for the labels indc, infl, nneo, norm, and null. This increase is correlated with an increase in annotated area and annotation accuracy. Model performance in identifying the suspicious label decreased by 25% due to the decrease of 57% in the total annotated area described by this label. A summary of the model performance is given in Table 4, which shows the new prediction accuracy and the absolute change in error rate compared to Table 3. The breast tissue subset we are developing includes 3,505 annotated breast pathology slides from 296 patients. The average size of a scanned SVS file is 363 MB. The annotations are stored in an XML format. A CSV version of the annotation file is also available which provides a flat, or simple, annotation that is easy for machine learning researchers to access and interface to their systems. Each patient is identified by an anonymized medical reference number. Within each patient’s directory, one or more sessions are identified, also anonymized to the first of the month in which the sample was taken. These sessions are broken into groupings of tissue taken on that date (in this case, breast tissue). A deidentified patient report stored as a flat text file is also available. Within these slides there are a total of 16,971 total annotated regions with an average of 4.84 annotations per slide. Among those annotations, 8,035 are non-cancerous (normal, background, null, and artifact,) 6,222 are carcinogenic signs (inflammation, nonneoplastic and suspicious,) and 2,714 are cancerous labels (ductal carcinoma in situ and invasive ductal carcinoma in situ.) The individual patients are split up into three sets: train, development, and evaluation. Of the 74 cancerous patients, 20 were allotted for both the development and evaluation sets, while the remain 34 were allotted for train. The remaining 222 patients were split up to preserve the overall distribution of labels within the corpus. This was done in hope of creating control sets for comparable studies. Overall, the development and evaluation sets each have 80 patients, while the training set has 136 patients. In a related component of this project, slides from the Fox Chase Cancer Center (FCCC) Biosample Repository (https://www.foxchase.org/research/facilities/genetic-research-facilities/biosample-repository -facility) are being digitized in addition to slides provided by Temple University Hospital. This data includes 18 different types of tissue including approximately 38.5% urinary tissue and 16.5% gynecological tissue. These slides and the metadata provided with them are already anonymized and include diagnoses in a spreadsheet with sample and patient ID. We plan to release over 13,000 unannotated slides from the FCCC Corpus simultaneously with v1.0.0 of TUDP. Details of this release will also be discussed in this poster. Few digitally annotated databases of pathology samples like TUDP exist due to the extensive data collection and processing required. The breast corpus subset should be released by November 2021. By December 2021 we should also release the unannotated FCCC data. We are currently annotating urinary tract data as well. We expect to release about 5,600 processed TUH slides in this subset. We have an additional 53,000 unprocessed TUH slides digitized. Corpora of this size will stimulate the development of a new generation of deep learning technology. In clinical settings where resources are limited, an assistive diagnoses model could support pathologists’ workload and even help prioritize suspected cancerous cases. ACKNOWLEDGMENTS This material is supported by the National Science Foundation under grants nos. CNS-1726188 and 1925494. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation. REFERENCES [1] N. Shawki et al., “The Temple University Digital Pathology Corpus,” in Signal Processing in Medicine and Biology: Emerging Trends in Research and Applications, 1st ed., I. Obeid, I. Selesnick, and J. Picone, Eds. New York City, New York, USA: Springer, 2020, pp. 67 104. https://www.springer.com/gp/book/9783030368432. [2] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning.” Major Research Instrumentation (MRI), Division of Computer and Network Systems, Award No. 1726188, January 1, 2018 – December 31, 2021. https://www. isip.piconepress.com/projects/nsf_dpath/. [3] A. Gulati et al., “Conformer: Convolution-augmented Transformer for Speech Recognition,” in Proceedings of the Annual Conference of the International Speech Communication Association (INTERSPEECH), 2020, pp. 5036-5040. https://doi.org/10.21437/interspeech.2020-3015. [4] C.-J. Wu et al., “Machine Learning at Facebook: Understanding Inference at the Edge,” in Proceedings of the IEEE International Symposium on High Performance Computer Architecture (HPCA), 2019, pp. 331–344. https://ieeexplore.ieee.org/document/8675201. [5] I. Caswell and B. Liang, “Recent Advances in Google Translate,” Google AI Blog: The latest from Google Research, 2020. [Online]. Available: https://ai.googleblog.com/2020/06/recent-advances-in-google-translate.html. [Accessed: 01-Aug-2021]. [6] V. Khalkhali, N. Shawki, V. Shah, M. Golmohammadi, I. Obeid, and J. Picone, “Low Latency Real-Time Seizure Detection Using Transfer Deep Learning,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2021, pp. 1 7. https://www.isip. piconepress.com/publications/conference_proceedings/2021/ieee_spmb/eeg_transfer_learning/. [7] J. Picone, T. Farkas, I. Obeid, and Y. Persidsky, “MRI: High Performance Digital Pathology Using Big Data and Machine Learning,” Philadelphia, Pennsylvania, USA, 2020. https://www.isip.piconepress.com/publications/reports/2020/nsf/mri_dpath/. [8] I. Hunt, S. Husain, J. Simons, I. Obeid, and J. Picone, “Recent Advances in the Temple University Digital Pathology Corpus,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB), 2019, pp. 1–4. https://ieeexplore.ieee.org/document/9037859. [9] A. P. Martinez, C. Cohen, K. Z. Hanley, and X. (Bill) Li, “Estrogen Receptor and Cytokeratin 5 Are Reliable Markers to Separate Usual Ductal Hyperplasia From Atypical Ductal Hyperplasia and Low-Grade Ductal Carcinoma In Situ,” Arch. Pathol. Lab. Med., vol. 140, no. 7, pp. 686–689, Apr. 2016. https://doi.org/10.5858/arpa.2015-0238-OA. 

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