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1. On Matrix Momentum Stochastic Approximation and Applications to Q-learning

   https://doi.org/10.1109/ALLERTON.2019.8919828  

   Devraj, Adithya M. ; Busic, Ana ; Meyn, Sean ( September 2019 , Allerton Conference on Communication, Control, and Computing)

   Stochastic approximation (SA) algorithms are recursive techniques used to obtain the roots of functions that can be expressed as expectations of a noisy parameterized family of functions. In this paper two new SA algorithms are introduced: 1) PolSA, an extension of Polyak's momentum technique with a specially designed matrix momentum, and 2) NeSA, which can either be regarded as a variant of Nesterov's acceleration method, or a simplification of PolSA. The rates of convergence of SA algorithms is well understood. Under special conditions, the mean square error of the parameter estimates is bounded by σ 2 /n+o(1/n), where σ 2 ≥ 0 is an identifiable constant. If these conditions fail, the rate is typically sub-linear. There are two well known SA algorithms that ensure a linear rate, with minimal value of variance, σ 2 : the Ruppert-Polyak averaging technique, and the stochastic Newton-Raphson (SNR) algorithm. It is demonstrated here that under mild technical assumptions, the PolSA algorithm also achieves this optimality criteria. This result is established via novel coupling arguments: It is shown that the parameter estimates obtained from the PolSA algorithm couple with those of the optimal variance (but computationally more expensive) SNR algorithm, at a rate O(1/n 2more »). The newly proposed algorithms are extended to a reinforcement learning setting to obtain new Q-learning algorithms, and numerical results confirm the coupling of PolSA and SNR.« less
2. 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 notmore »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.« less
3. Differentiable Programming for Hyperspectral Unmixing using a Physics-based Dispersion Model

   Janiczek, John ; Thaker, Parth ; Dasarathy, Gautam ; Edwards, Christopher ; Christensen, Philip ; Jayasuriya, Suren ( January 2020 , European Conference on Computer Vision (ECCV))

   Hyperspectral unmixing is an important remote sensing task with applications including material identification and analysis. Characteristic spectral features make many pure materials identifiable from their visible-to-infrared spectra, but quantifying their presence within a mixture is a challenging task due to nonlinearities and factors of variation. In this paper, spectral variation is considered from a physics-based approach and incorporated into an end-to-end spectral unmixing algorithm via differentiable programming. The dispersion model is introduced to simulate realistic spectral variation, and an efficient method to fit the parameters is presented. Then, this dispersion model is utilized as a generative model within an analysis-by-synthesis spectral unmixing algorithm. Further, a technique for inverse rendering using a convolutional neural network to predict parameters of the generative model is introduced to enhance performance and speed when training data is available. Results achieve state-of-the-art on both infrared and visible-to-near-infrared (VNIR) datasets, and show promise for the synergy between physicsbased models and deep learning in hyperspectral unmixing in the future.
4. Improved Merlin–Arthur Protocols for Central Problems in Fine-Grained Complexity

   https://doi.org/10.1007/s00453-023-01102-6  

   Akmal, Shyan ; Chen, Lijie ; Jin, Ce ; Raj, Malvika ; Williams, Ryan ( February 2023 , Algorithmica)

   In a Merlin–Arthur proof system, the proof verifier (Arthur) accepts valid proofs (from Merlin) with probability 1, and rejects invalid proofs with probability arbitrarily close to 1. The running time of such a system is defined to be the length of Merlin’s proof plus the running time of Arthur. We provide new Merlin–Arthur proof systems for some key problems in fine-grained complexity. In several cases our proof systems have optimal running time. Our main results include:

   Certifying that a list ofnintegers has no 3-SUM solution can be done in Merlin–Arthur time$$\tilde{O}(n)$$$\tilde{O}\left(n\right)$. Previously, Carmosino et al. [ITCS 2016] showed that the problem has a nondeterministic algorithm running in$$\tilde{O}(n^{1.5})$$$\tilde{O}\left(n^{1.5}\right)$time (that is, there is a proof system with proofs of length$$\tilde{O}(n^{1.5})$$$\tilde{O}\left(n^{1.5}\right)$and a deterministic verifier running in$$\tilde{O}(n^{1.5})$$$\tilde{O}\left(n^{1.5}\right)$time).

   Counting the number ofk-cliques with total edge weight equal to zero in ann-node graph can be done in Merlin–Arthur time$${\tilde{O}}(n^{\lceil k/2\rceil })$$$\tilde{O}\left(n^{\lceil k/2\rceil }\right)$(where$$k\ge 3$$$k\ge 3$). For oddk, this bound can be further improved for sparse graphs: for example, counting the number of zero-weight triangles in anm-edge graph can be done in Merlin–Arthur time$${\tilde{O}}(m)$$$\tilde{O}\left(m\right)$. Previous Merlin–Arthur protocols by Williams [CCC’16] and Björklund and Kaski [PODC’16] could only countk-cliques in unweighted graphs, and had worse running times for smallk.

   Computing the All-Pairsmore »Shortest Distances matrix for ann-node graph can be done in Merlin–Arthur time$$\tilde{O}(n^2)$$$\tilde{O}\left(n^2\right)$. Note this is optimal, as the matrix can have$$\Omega (n^2)$$$\Omega \left(n^2\right)$nonzero entries in general. Previously, Carmosino et al. [ITCS 2016] showed that this problem has an$$\tilde{O}(n^{2.94})$$$\tilde{O}\left(n^{2.94}\right)$nondeterministic time algorithm.

   Certifying that ann-variablek-CNF is unsatisfiable can be done in Merlin–Arthur time$$2^{n/2 - n/O(k)}$$$2^{n/2-n/O\left(k\right)}$. We also observe an algebrization barrier for the previous$$2^{n/2}\cdot \textrm{poly}(n)$$$2^{n/2}·\text{poly}\left(n\right)$-time Merlin–Arthur protocol of R. Williams [CCC’16] for$$\#$$$\#$SAT: in particular, his protocol algebrizes, and we observe there is no algebrizing protocol fork-UNSAT running in$$2^{n/2}/n^{\omega (1)}$$$2^{n/2}/n^{\omega \left(1\right)}$time. Therefore we have to exploit non-algebrizing properties to obtain our new protocol.

   Certifying a Quantified Boolean Formula is true can be done in Merlin–Arthur time$$2^{4n/5}\cdot \textrm{poly}(n)$$$2^{4n/5}·\text{poly}\left(n\right)$. Previously, the only nontrivial result known along these lines was an Arthur Merlin–Arthur protocol (where Merlin’s proof depends on some of Arthur’s coins) running in$$2^{2n/3}\cdot \textrm{poly}(n)$$$2^{2n/3}·\text{poly}\left(n\right)$time.

   Due to the centrality of these problems in fine-grained complexity, our results have consequences for many other problems of interest. For example, our work implies that certifying there is no Subset Sum solution tonintegers can be done in Merlin–Arthur time$$2^{n/3}\cdot \textrm{poly}(n)$$$2^{n/3}·\text{poly}\left(n\right)$, improving on the previous best protocol by Nederlof [IPL 2017] which took$$2^{0.49991n}\cdot \textrm{poly}(n)$$$2^{0.49991n}·\text{poly}\left(n\right)$time.

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5. 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 PRGmore »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)).« less