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1. Covering entropy for types in tracial W*-algebras

   https://doi.org/10.4115/jla.2023.15.2  

   Jekel, David ( June 2023 , Journal of Logic and Analysis)

   We study embeddings of tracial $\mathrm{W}^*$-algebras into a ultraproduct of matrix algebras through an amalgamation of free probabilistic and model-theoretic techniques.  Jung implicitly and Hayes explicitly defined \emph{$1$-bounded entropy} through the asymptotic covering numbers of Voiculescu's microstate spaces, that is, spaces of matrix tuples $(X_1^{(N)},X_2^{(N)},\dots)$ having approximately the same $*$-moments as the generators $(X_1,X_2,\dots)$ of a given tracial $\mathrm{W}^*$-algebra.  We study the analogous covering entropy for microstate spaces defined through formulas that use suprema and infima, not only $*$-algebra operations and the trace | formulas such as arise in the model theory of tracial $\mathrm{W}^*$-algebras initiated by Farah, Hart, and Sherman.  By relating the new theory with the original $1$-bounded entropy, we show that if $\mathcal{M}$ is a separable tracial $\mathrm{W}^*$-algebra with $h(\cN:\cM) \geq 0$, then there exists an embedding of $\cM$ into a matrix ultraproduct $\cQ = \prod_{n \to \cU} M_n(\C)$ such that $h(\cN:\cQ)$ is arbitrarily close to $h(\cN:\cM)$.  We deduce that if all embeddings of $\cM$ into $\cQ$ are automorphically equivalent, then $\cM$ is strongly $1$-bounded and in fact has $h(\cM) \leq 0$. 

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2. L oo p D e l t a : E m b e dd i n g L o c a li t y - a w a r e O pp o r t un i s t i c D e l t a C o m p r e ss i o n i n I n li n e D e dup li c a t i o n f o r Hi g h l y E ffic i e n t D a t a R e du c t i o n

   Zhang, Yucheng ; Jiang, Hong ; Feng, Dan ; Jiang Nan ; Qui, Taorong ; Huang, Wei ( July 2023 , USENIX annual technical conference)

   A s a c om pl e men t t o da ta d edupli cat ion , de lta c om p ress i on fu r- t he r r edu c es t h e dat a vo l u m e by c o m pr e ssi n g n o n - dup li c a t e d ata chunk s r e l a t iv e to t h e i r s i m il a r chunk s (bas e chunk s). H ow ever, ex is t i n g p o s t - d e dup li c a t i o n d e l t a c o m pr e ssi o n a p- p ro a ches fo r bac kup s t or ag e e i t h e r su ffe r f ro m t h e l ow s i m - il a r i t y b e twee n m any de te c ted c hun ks o r m i ss so me po t e n - t i a l s i m il a r c hunks , o r su ffer f r om l ow (ba ckup and r es t ore ) th r oug hpu t du e t o extr a I/ Os f or r e a d i n g b a se c hun ks o r a dd a dd i t i on a l s e r v i c e - d i s r up t ive op e r a t i on s to b a ck up s ys t em s. I n t h i s pa p e r, w e pr opo se L oop D e l t a t o a dd ress the above - m e n t i on e d prob l e m s by an e nha nced em b e ddi n g d e l t a c o m p - r e ss i on sc heme i n d e dup li c a t i on i n a non - i n t ru s ive way. T h e e nha nce d d elt a c o mpr ess ion s che m e co m b in e s f our key t e c h - ni qu e s : (1) du a l - l o c a li t y - b a s e d s i m il a r i t y t r a c k i n g to d e t ect po t e n t i a l si m il a r chun k s b y e x p l o i t i n g both l o g i c a l and ph y - s i c a l l o c a li t y, ( 2 ) l o c a li t y - a wa r e pr e f e t c h i n g to pr efe tc h ba se c hun ks to a vo i d ex t ra I/ Os fo r r e a d i n g ba s e chun ks on t h e w r i t e p at h , (3) c a che -aware fil t e r to avo i d ext r a I/Os f or b a se c hunk s on t he read p at h, a nd (4) i nver sed de l ta co mpressi on t o perf orm de lt a co mpress i o n fo r d at a chunk s t hat a re o th e r wi se f o r b i dd e n to s er ve as ba se c hunk s by r ew r i t i n g t e c hn i qu e s d e s i g n e d t o i m p r ove r es t o re pe rf o rma nc e. E x p e r i m e n t a l re su lts indi ca te t hat L oop D e l t a i ncr ea se s t he c o m pr e ss i o n r a t i o by 1 .2410 .97 t i m e s on t op of d e dup li c a - t i on , wi t hou t no t a b l y a ffe c t i n g th e ba ck up th rou ghpu t, a nd i t i m p r ove s t he res to re p er fo r m an ce b y 1.23.57 t i m e 

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3. A Deep Learning-Based Real-time Seizure Detection System

   https://doi.org/10.1109/SPMB50085.2020.9353623  

   Shawki, N. ; Elseify, T. ; Cap, T. ; Shah, V. ; Obeid, I. ; Picone, J. ( December 2020 , Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium (SPMB))

   Obeid, Iyad Selesnick (Ed.)

   Electroencephalography (EEG) is a popular clinical monitoring tool used for diagnosing brain-related disorders such as epilepsy [1]. As monitoring EEGs in a critical-care setting is an expensive and tedious task, there is a great interest in developing real-time EEG monitoring tools to improve patient care quality and efficiency [2]. However, clinicians require automatic seizure detection tools that provide decisions with at least 75% sensitivity and less than 1 false alarm (FA) per 24 hours [3]. Some commercial tools recently claim to reach such performance levels, including the Olympic Brainz Monitor [4] and Persyst 14 [5]. In this abstract, we describe our efforts to transform a high-performance offline seizure detection system [3] into a low latency real-time or online seizure detection system. An overview of the system is shown in Figure 1. The main difference between an online versus offline system is that an online system should always be causal and has minimum latency which is often defined by domain experts. The offline system, shown in Figure 2, uses two phases of deep learning models with postprocessing [3]. The channel-based long short term memory (LSTM) model (Phase 1 or P1) processes linear frequency cepstral coefficients (LFCC) [6] features from each EEG channel separately. We use the hypotheses generated by the P1 model and create additional features that carry information about the detected events and their confidence. The P2 model uses these additional features and the LFCC features to learn the temporal and spatial aspects of the EEG signals using a hybrid convolutional neural network (CNN) and LSTM model. Finally, Phase 3 aggregates the results from both P1 and P2 before applying a final postprocessing step. The online system implements Phase 1 by taking advantage of the Linux piping mechanism, multithreading techniques, and multi-core processors. To convert Phase 1 into an online system, we divide the system into five major modules: signal preprocessor, feature extractor, event decoder, postprocessor, and visualizer. The system reads 0.1-second frames from each EEG channel and sends them to the feature extractor and the visualizer. The feature extractor generates LFCC features in real time from the streaming EEG signal. Next, the system computes seizure and background probabilities using a channel-based LSTM model and applies a postprocessor to aggregate the detected events across channels. The system then displays the EEG signal and the decisions simultaneously using a visualization module. The online system uses C++, Python, TensorFlow, and PyQtGraph in its implementation. The online system accepts streamed EEG data sampled at 250 Hz as input. The system begins processing the EEG signal by applying a TCP montage [8]. Depending on the type of the montage, the EEG signal can have either 22 or 20 channels. To enable the online operation, we send 0.1-second (25 samples) length frames from each channel of the streamed EEG signal to the feature extractor and the visualizer. Feature extraction is performed sequentially on each channel. The signal preprocessor writes the sample frames into two streams to facilitate these modules. In the first stream, the feature extractor receives the signals using stdin. In parallel, as a second stream, the visualizer shares a user-defined file with the signal preprocessor. This user-defined file holds raw signal information as a buffer for the visualizer. The signal preprocessor writes into the file while the visualizer reads from it. Reading and writing into the same file poses a challenge. The visualizer can start reading while the signal preprocessor is writing into it. To resolve this issue, we utilize a file locking mechanism in the signal preprocessor and visualizer. Each of the processes temporarily locks the file, performs its operation, releases the lock, and tries to obtain the lock after a waiting period. The file locking mechanism ensures that only one process can access the file by prohibiting other processes from reading or writing while one process is modifying the file [9]. The feature extractor uses circular buffers to save 0.3 seconds or 75 samples from each channel for extracting 0.2-second or 50-sample long center-aligned windows. The module generates 8 absolute LFCC features where the zeroth cepstral coefficient is replaced by a temporal domain energy term. For extracting the rest of the features, three pipelines are used. The differential energy feature is calculated in a 0.9-second absolute feature window with a frame size of 0.1 seconds. The difference between the maximum and minimum temporal energy terms is calculated in this range. Then, the first derivative or the delta features are calculated using another 0.9-second window. Finally, the second derivative or delta-delta features are calculated using a 0.3-second window [6]. The differential energy for the delta-delta features is not included. In total, we extract 26 features from the raw sample windows which add 1.1 seconds of delay to the system. We used the Temple University Hospital Seizure Database (TUSZ) v1.2.1 for developing the online system [10]. The statistics for this dataset are shown in Table 1. A channel-based LSTM model was trained using the features derived from the train set using the online feature extractor module. A window-based normalization technique was applied to those features. In the offline model, we scale features by normalizing using the maximum absolute value of a channel [11] before applying a sliding window approach. Since the online system has access to a limited amount of data, we normalize based on the observed window. The model uses the feature vectors with a frame size of 1 second and a window size of 7 seconds. We evaluated the model using the offline P1 postprocessor to determine the efficacy of the delayed features and the window-based normalization technique. As shown by the results of experiments 1 and 4 in Table 2, these changes give us a comparable performance to the offline model. The online event decoder module utilizes this trained model for computing probabilities for the seizure and background classes. These posteriors are then postprocessed to remove spurious detections. The online postprocessor receives and saves 8 seconds of class posteriors in a buffer for further processing. It applies multiple heuristic filters (e.g., probability threshold) to make an overall decision by combining events across the channels. These filters evaluate the average confidence, the duration of a seizure, and the channels where the seizures were observed. The postprocessor delivers the label and confidence to the visualizer. The visualizer starts to display the signal as soon as it gets access to the signal file, as shown in Figure 1 using the “Signal File” and “Visualizer” blocks. Once the visualizer receives the label and confidence for the latest epoch from the postprocessor, it overlays the decision and color codes that epoch. The visualizer uses red for seizure with the label SEIZ and green for the background class with the label BCKG. Once the streaming finishes, the system saves three files: a signal file in which the sample frames are saved in the order they were streamed, a time segmented event (TSE) file with the overall decisions and confidences, and a hypotheses (HYP) file that saves the label and confidence for each epoch. The user can plot the signal and decisions using the signal and HYP files with only the visualizer by enabling appropriate options. For comparing the performance of different stages of development, we used the test set of TUSZ v1.2.1 database. It contains 1015 EEG records of varying duration. The any-overlap performance [12] of the overall system shown in Figure 2 is 40.29% sensitivity with 5.77 FAs per 24 hours. For comparison, the previous state-of-the-art model developed on this database performed at 30.71% sensitivity with 6.77 FAs per 24 hours [3]. The individual performances of the deep learning phases are as follows: Phase 1’s (P1) performance is 39.46% sensitivity and 11.62 FAs per 24 hours, and Phase 2 detects seizures with 41.16% sensitivity and 11.69 FAs per 24 hours. We trained an LSTM model with the delayed features and the window-based normalization technique for developing the online system. Using the offline decoder and postprocessor, the model performed at 36.23% sensitivity with 9.52 FAs per 24 hours. The trained model was then evaluated with the online modules. The current performance of the overall online system is 45.80% sensitivity with 28.14 FAs per 24 hours. Table 2 summarizes the performances of these systems. The performance of the online system deviates from the offline P1 model because the online postprocessor fails to combine the events as the seizure probability fluctuates during an event. The modules in the online system add a total of 11.1 seconds of delay for processing each second of the data, as shown in Figure 3. In practice, we also count the time for loading the model and starting the visualizer block. When we consider these facts, the system consumes 15 seconds to display the first hypothesis. The system detects seizure onsets with an average latency of 15 seconds. Implementing an automatic seizure detection model in real time is not trivial. We used a variety of techniques such as the file locking mechanism, multithreading, circular buffers, real-time event decoding, and signal-decision plotting to realize the system. A video demonstrating the system is available at: https://www.isip.piconepress.com/projects/nsf_pfi_tt/resources/videos/realtime_eeg_analysis/v2.5.1/video_2.5.1.mp4. The final conference submission will include a more detailed analysis of the online performance of each module. ACKNOWLEDGMENTS Research reported in this publication was most recently supported by the National Science Foundation Partnership for Innovation award number IIP-1827565 and the Pennsylvania Commonwealth Universal Research Enhancement Program (PA CURE). Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the official views of any of these organizations. REFERENCES [1] A. Craik, Y. He, and J. L. Contreras-Vidal, “Deep learning for electroencephalogram (EEG) classification tasks: a review,” J. Neural Eng., vol. 16, no. 3, p. 031001, 2019. https://doi.org/10.1088/1741-2552/ab0ab5. [2] A. C. Bridi, T. Q. Louro, and R. C. L. Da Silva, “Clinical Alarms in intensive care: implications of alarm fatigue for the safety of patients,” Rev. Lat. Am. Enfermagem, vol. 22, no. 6, p. 1034, 2014. https://doi.org/10.1590/0104-1169.3488.2513. [3] M. Golmohammadi, V. Shah, I. Obeid, and J. Picone, “Deep Learning Approaches for Automatic Seizure Detection from Scalp Electroencephalograms,” 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, New York, USA: Springer, 2020, pp. 233–274. https://doi.org/10.1007/978-3-030-36844-9_8. [4] “CFM Olympic Brainz Monitor.” [Online]. Available: https://newborncare.natus.com/products-services/newborn-care-products/newborn-brain-injury/cfm-olympic-brainz-monitor. [Accessed: 17-Jul-2020]. [5] M. L. Scheuer, S. B. Wilson, A. Antony, G. Ghearing, A. Urban, and A. I. Bagic, “Seizure Detection: Interreader Agreement and Detection Algorithm Assessments Using a Large Dataset,” J. Clin. Neurophysiol., 2020. https://doi.org/10.1097/WNP.0000000000000709. [6] A. Harati, M. Golmohammadi, S. Lopez, I. Obeid, and J. Picone, “Improved EEG Event Classification Using Differential Energy,” in Proceedings of the IEEE Signal Processing in Medicine and Biology Symposium, 2015, pp. 1–4. https://doi.org/10.1109/SPMB.2015.7405421. [7] V. Shah, C. Campbell, I. Obeid, and J. Picone, “Improved Spatio-Temporal Modeling in Automated Seizure Detection using Channel-Dependent Posteriors,” Neurocomputing, 2021. [8] W. Tatum, A. Husain, S. Benbadis, and P. Kaplan, Handbook of EEG Interpretation. New York City, New York, USA: Demos Medical Publishing, 2007. [9] D. P. Bovet and C. Marco, Understanding the Linux Kernel, 3rd ed. O’Reilly Media, Inc., 2005. https://www.oreilly.com/library/view/understanding-the-linux/0596005652/. [10] V. Shah et al., “The Temple University Hospital Seizure Detection Corpus,” Front. Neuroinform., vol. 12, pp. 1–6, 2018. https://doi.org/10.3389/fninf.2018.00083. [11] F. Pedregosa et al., “Scikit-learn: Machine Learning in Python,” J. Mach. Learn. Res., vol. 12, pp. 2825–2830, 2011. https://dl.acm.org/doi/10.5555/1953048.2078195. [12] J. Gotman, D. Flanagan, J. Zhang, and B. Rosenblatt, “Automatic seizure detection in the newborn: Methods and initial evaluation,” Electroencephalogr. Clin. Neurophysiol., vol. 103, no. 3, pp. 356–362, 1997. https://doi.org/10.1016/S0013-4694(97)00003-9. 

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4. Rate-independent Computation in Continuous Chemical Reaction Networks

   https://doi.org/10.1145/3590776  

   Chen, Ho-Lin ; Doty, David ; Reeves, Wyatt ; Soloveichik, David ( June 2023 , Journal of the ACM)

   Understanding the algorithmic behaviors that are in principle realizable in a chemical system is necessary for a rigorous understanding of the design principles of biological regulatory networks. Further, advances in synthetic biology herald the time when we will be able to rationally engineer complex chemical systems and when idealized formal models will become blueprints for engineering. Coupled chemical interactions in a well-mixed solution are commonly formalized as chemical reaction networks (CRNs). However, despite the widespread use of CRNs in the natural sciences, the range of computational behaviors exhibited by CRNs is not well understood. Here, we study the following problem: What functions f : ℝ k → ℝ can be computed by a CRN, in which the CRN eventually produces the correct amount of the “output” molecule, no matter the rate at which reactions proceed? This captures a previously unexplored but very natural class of computations: For example, the reaction X 1 + X 2 → Y can be thought to compute the function y = min ( x 1 , x 2 ). Such a CRN is robust in the sense that it is correct whether its evolution is governed by the standard model of mass-action kinetics, alternatives such as Hill-function or Michaelis-Menten kinetics, or other arbitrary models of chemistry that respect the (fundamentally digital) stoichiometric constraints (what are the reactants and products?). We develop a reachability relation based on a broad notion of “what could happen” if reaction rates can vary arbitrarily over time. Using reachability, we define stable computation analogously to probability 1 computation in distributed computing and connect it with a seemingly stronger notion of rate-independent computation based on convergence in the limit t → ∞ under a wide class of generalized rate laws. Besides the direct mapping of a concentration to a nonnegative analog value, we also consider the “dual-rail representation” that can represent negative values as the difference of two concentrations and allows the composition of CRN modules. We prove that a function is rate-independently computable if and only if it is piecewise linear (with rational coefficients) and continuous (dual-rail representation), or non-negative with discontinuities occurring only when some inputs switch from zero to positive (direct representation). The many contexts where continuous piecewise linear functions are powerful targets for implementation, combined with the systematic construction we develop for computing these functions, demonstrate the potential of rate-independent chemical computation. 

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5. Universal Tensor Categories Generated by Dual Pairs

   https://doi.org/10.1007/s10485-021-09640-2  

   Chirvasitu, Alexandru ; Penkov, Ivan ( October 2021 , Applied Categorical Structures)

   Abstract Let $$V_*\otimes V\rightarrow {\mathbb {C}}$$ V ∗ ⊗ V → C be a non-degenerate pairing of countable-dimensional complex vector spaces V and $$V_*$$ V ∗ . The Mackey Lie algebra $${\mathfrak {g}}=\mathfrak {gl}^M(V,V_*)$$ g = gl M ( V , V ∗ ) corresponding to this pairing consists of all endomorphisms $$\varphi $$ φ of V for which the space $$V_*$$ V ∗ is stable under the dual endomorphism $$\varphi ^*: V^*\rightarrow V^*$$ φ ∗ : V ∗ → V ∗ . We study the tensor Grothendieck category $${\mathbb {T}}$$ T generated by the $${\mathfrak {g}}$$ g -modules V , $$V_*$$ V ∗ and their algebraic duals $$V^*$$ V ∗ and $$V^*_*$$ V ∗ ∗ . The category $${{\mathbb {T}}}$$ T is an analogue of categories considered in prior literature, the main difference being that the trivial module $${\mathbb {C}}$$ C is no longer injective in $${\mathbb {T}}$$ T . We describe the injective hull I of $${\mathbb {C}}$$ C in $${\mathbb {T}}$$ T , and show that the category $${\mathbb {T}}$$ T is Koszul. In addition, we prove that I is endowed with a natural structure of commutative algebra. We then define another category $$_I{\mathbb {T}}$$ I T of objects in $${\mathbb {T}}$$ T which are free as I -modules. Our main result is that the category $${}_I{\mathbb {T}}$$ I T is also Koszul, and moreover that $${}_I{\mathbb {T}}$$ I T is universal among abelian $${\mathbb {C}}$$ C -linear tensor categories generated by two objects X , Y with fixed subobjects $$X'\hookrightarrow X$$ X ′ ↪ X , $$Y'\hookrightarrow Y$$ Y ′ ↪ Y and a pairing $$X\otimes Y\rightarrow {\mathbf{1 }}$$ X ⊗ Y → 1 where 1 is the monoidal unit. We conclude the paper by discussing the orthogonal and symplectic analogues of the categories $${\mathbb {T}}$$ T and $${}_I{\mathbb {T}}$$ I T . 

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