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DOE OSTI2026

Mitigating Algorithmic Bias in Cancer Site Classification Models

Purpose Integrating artificial intelligence in cancer diagnostics has improved tumor classification beyond rule-based systems. Despite these advancements, these models may still encode demographic biases. We conducted a large-scale, applied bias-probing study of a deep learning–based cancer site classifier to quantify race information encoded in document embeddings. We then evaluated how performance changes when race-correlated embedding dimensions are removed in a post-training sensitivity analysis. Methods The cancer site classifier was trained using 3.5 million electronic cancer pathology reports from six of the National Cancer Institute's SEER registries. We trained a hierarchical self-attention network to generate 400-dimensional document embeddings. These embeddings were used to train two downstream, gradient-boosted decision tree classifiers: one to classify the cancer sites and another to predict racial categories. We identified overlapping features by intersecting the top 50 feature-importance rankings from the site and race models and computed their cumulative feature importance in each model. As a post hoc sensitivity analysis, we progressively pruned these overlapping dimensions, retrained the site model, and compared overall macro-F1 and accuracy, race-stratified macro-F1, and group fairness metrics on the basis of demographic parity and equalized odds before and after pruning. Results The analysis revealed minimal feature overlap between the cancer site and race prediction models, and the cumulative importance scores indicated a negligible influence of racial information on clinical predictions. Post-training pruning of overlapping features did not compromise the models' diagnostic accuracy, with a 0.07% loss in accuracy. Conclusion Our findings demonstrate that HiSAN-generated embeddings from SEER data can be used effectively in cancer site classification without significant demographic bias influencing the outcomes. Post-training pruning therefore functions as a practical audit and sensitivity check.

Shivanna, Abhishek [ORNL] (ORCID:0009000665228593)↗

DOE OSTI2024

Personalized, disease-stage specific, rapid identification of immunosuppression in sepsis

Introduction Data overlapping of different biological conditions prevents personalized medical decision-making. For example, when the neutrophil percentages of surviving septic patients overlap with those of non-survivors, no individualized assessment is possible. To ameliorate this problem, an immunological method was explored in the context of sepsis. Methods Blood leukocyte counts and relative percentages as well as the serum concentration of several proteins were investigated with 4072 longitudinal samples collected from 331 hospitalized patients classified as septic (n=286), non-septic (n=43), or not assigned (n=2). Two methodological approaches were evaluated: (i) a reductionist alternative, which analyzed variables in isolation; and (ii) a non-reductionist version, which examined interactions among six (leukocyte-, bacterial-, temporal-, personalized-, population-, and outcome-related) dimensions. Results The reductionist approach did not distinguish outcomes: the leukocyte and serum protein data of survivors and non-survivors overlapped. In contrast, the non-reductionist alternative differentiated several data groups, of which at least one was only composed of survivors (a finding observable since hospitalization day 1). Hence, the non-reductionist approach promoted personalized medical practices: every patient classified within a subset associated with 100% survival subset was likely to survive. The non-reductionist method also revealed five inflammatory or disease-related stages (provisionally named ‘early inflammation, early immunocompetence, intermediary immuno-suppression, late immuno-suppression, or other’). Mortality data validated these labels: both ‘suppression’ subsets revealed 100% mortality, the ‘immunocompetence’ group exhibited 100% survival, while the remaining sets reported two-digit mortality percentages. While the ‘intermediary’ suppression expressed an impaired monocyte-related function, the ‘late’ suppression displayed renal-related dysfunctions, as indicated by high concentrations of urea and creatinine. Discussion The data-driven differentiation of five data groups may foster early and non-overlapping biomedical decision-making, both upon admission and throughout their hospitalization. This approach could evaluate therapies, at personalized level, earlier. To ascertain repeatability and investigate the dynamics of the ‘other’ group, additional studies are recommended.

Immunology↗

NASA NTRS1985

Application of homomorphic signal processing to stress wave factor analysis

The stress wave factor (SWF) signal, which is the output of an ultrasonic testing system where the transmitting and receiving transducers are coupled to the same face of the test structure, is analyzed in the frequency domain. The SWF signal generated in an isotropic elastic plate is modelled as the superposition of successive reflections. The reflection which is generated by the stress waves which travel p times as a longitudinal (P) wave and s times as a shear (S) wave through the plate while reflecting back and forth between the bottom and top faces of the plate is designated as the reflection with p, s. Short-time portions of the SWF signal are considered for obtaining spectral information on individual reflections. If the significant reflections are not overlapped, the short-time Fourier analysis is used. A summary of the elevant points of homomorphic signal processing, which is also called cepstrum analysis, is given. Homomorphic signal processing is applied to short-time SWF signals to obtain estimates of the log spectra of individual reflections for cases in which the reflections are overlapped. Two typical SWF signals generated in aluminum plates (overlapping and non-overlapping reflections) are analyzed.

Karagulle, H.↗

NASA NTRS1985

Gamma-ray burster recurrence time scales

In the decade since gamma-ray bursters (GRBs) were discovered by Klebesadel et al. (1973), many models have been proposed to explain the GRB phenomenon. A difficulty is related to the small number of predictions which would make it possible to evaluate the models. One verifiable prediction is the recurrence time scale, tau-gamma. One method to measure tau-gamma is to look for possible cases of recurrence as indicated by overlapping error boxes. The analysis considered in the present investigation is composed of three procedures. One of these involves a search through known error regions for cases where the error regions overlap. In addition, the number of overlaps expected by chance coincidence alone has been determined, and a calculation has been performed regarding the number of overlaps which are expected due to recurrence for various assumed tau-gamma and luminosity functions.

Schaefer, B. E.↗

NASA NTRS1985

Application of homomorphic signal processing to stress wave factor analysis

The stress wave factor (SWF) signal, which is the output of an ultrasonic testing system where the transmitting and receiving transducers are coupled to the same face of the test structure, is analyzed in the frequency domain. The SWF signal generated in an isotropic elastic plate is modelled as the superposition of successive reflections. The reflection which is generated by the stress waves which travel P times as a longitudinal (P) wave and s times as a shear (S) wave through the plate while reflecting back and forth between the bottom and top faces of the plate is designated as the reflection with P, s. Short-time portions of the SWF signal are considered for obtaining spectral information on individual reflections. If the significant reflections are not overlapped, the short-time Fourier analysis is used. A summary of the elevant points of homomorphic signal processing, which is also called cepstrum analysis, is given. Homomorphic signal processing is applied to short-time SWF signals to obtain estimates of the log spectra of individual reflections for cases in which the reflections are overlapped. Two typical SWF signals generated in aluminum plates (overlapping and non-overlapping reflections) are analyzed.

Williams, J. H., Jr.↗

NASA NTRS1986

Transformation of two and three-dimensional regions by elliptic systems

Efforts in transferring computational work from the LRC computer to the IRIS Graphics Workstation at MSU are reported and the computation of a conservative solution of a simple hyperbolic equation on an overlapping grid is discussed. Several conclusions concerning computations on overlapping grids are apparent. Problems only occur when there is a major difference in grid spacing on the individual component grids. In the case of hyperbolic equations, it is necessary that both interpolation and extrapolation be applied at the grid boundaries. When interpolated values are used at outflow boundary points, excessive oscillations in the numerical solution may be the result. The same conclusions would be valid for more complicated systems of hyperbolic equations such as the Euler equations for inviscid flow. Some of the solution values would be extrapolated at the overlap boundary, the exact number depending on the number of characteristics pointing out of the overlap region. It is also possible that similar boundary conditions may be needed for some parabolic equations such as high Reynolds number viscous flow equations. Efforts were also expended on the development of three-dimensional conservative interpolation procedures. Finally, the investigation of grid smoothing procedures were initiated during this reporting period. It was decided that the first grid smoothing algorithms will be based on the concepts of variational grid generation.

Mastin, C. W.↗

NASA NTRS1988

Microplate and shear zone models for oceanic spreading center reorganizations

The kinematics of rift propagation and the resulting goemetries of various tectonic elements for two plates is reviewed with no overlap zone. The formation and evolution of overlap regions using schematic models is discussed. The models are scaled in space and time to approximate the Easter plate, but are simplified to emphasize key elements. The tectonic evolution of overlap regions which act as rigid microplates and shear zones is discussed, and the use of relative motion and structural data to discriminate between the two types of models is investigated. The effect of propagation rate and rise time on the size, shape, and deformation of the overlap region is demonstrated.

Engeln, Joseph F.↗

NASA NTRS1992

Real-time edge-enhanced optical correlator

The performance of five symbol lock detectors are compared. They are the square-law detector with overlapping (SQOD) and non-overlapping (SQNOD) integrators, the absolute value detectors with overlapping and non-overlapping (AVNOD) integrators and the signal power estimator detector (SPED). The analysis considers various scenarios when the observation interval is much larger or equal to the symbol synchronizer loop bandwidth, which has not been considered in previous analyses. Also, the case of threshold setting in the absence of signal is considered. It is shown that the SQOD outperforms all others when the threshold is set in the presence of signal, independent of the relationship between loop bandwidth and observation period. On the other hand, the SPED outperforms all others when the threshold is set in the presence of noise only.

Shihabi, Mazen M.↗

NASA NTRS1992

Locus of the single-channel bottleneck in dual-task interference

Two experiments used the locus-of-cognitive-slack method to determine whether dual-task interference occurs before or after the response selection stage. The experiments used the overlapping tasks paradigm, in which two signals, each requiring a different speeded choice response, are presented in rapid succession. In Experiment 1, stimulus-response (S-R) compatibility was manipulated by varying whether Task 2 stimuli were mapped onto their responses by a rule or arbitrarily. Compatibility effects were additive with the effects of degree of task overlap, manipulated by varying the stimulus onset asynchrony between the signals. Experiment 2 examined 2 additional forms of S-R compatibility: symbolic compatability (arrows vs. letters) and spatial compatibility (the 'Simon' effect). Effects of symbolic compatibility were additive with effects of degree of task overlap, whereas the effects of spatial compatibility and degree of task overlap were underadditive. It is argued that only a central-bottleneck model provides a consistent account of these results. The nature of the central bottleneck is considered.

Mccann, Robert S.↗

NASA NTRS1993

Intercomparison of haloe and ER-2 aircraft H2O and CH4 observations collected during the second Airborne Arctic Stratospheric Experiment (AASE-II)

HALOE observations of H2O and CH4 are compared with in situ techniques aboard the ER-2 aircraft during the northern winter of 1991/92, in particular for the dates 911208, 920108, 920217, 920222, and 920320 when the spatial coincidences are close, within +/- 1 deg latitude and +/- 12 deg longitude. The results reveal the limitations of comparing high resolution in situ aircraft data with a remote sounding limb scanner. Of the five comparison dates, three had HALOE/ER-2 coincidences which occurred near the edge of the Arctic vortex; the vertical variability in the HALOE results and the horizontal variability in the ER-2 observations on these days show that the vortex edge is not a region where exact agreement can be expected except by chance. On a 4th comparison date, there was substantial overlap away from the vortex edge, although for some species the aircraft data show considerable variability near the coincidence point. On the 5th comparison date, the ER-2 had no overlap in altitude with the lowest HALOE observations; however, a short linear interpolation over about 1 km altitude results in smooth composite profiles. Generally speaking the agreement between HALOE and the ER-2 at overlap altitudes is about 12 percent in the case of water vapor, which shows low horizontal and vertical variability. The agreement for methane, with limited data having altitude overlap, is better than 6 percent.

Tuck, A. F.↗

NASA NTRS1996

User's Manual for FOMOCO Utilities-Force and Moment Computation Tools for Overset Grids

In the numerical computations of flows around complex configurations, accurate calculations of force and moment coefficients for aerodynamic surfaces are required. When overset grid methods are used, the surfaces on which force and moment coefficients are sought typically consist of a collection of overlapping surface grids. Direct integration of flow quantities on the overlapping grids would result in the overlapped regions being counted more than once. The FOMOCO Utilities is a software package for computing flow coefficients (force, moment, and mass flow rate) on a collection of overset surfaces with accurate accounting of the overlapped zones. FOMOCO Utilities can be used in stand-alone mode or in conjunction with the Chimera overset grid compressible Navier-Stokes flow solver OVERFLOW. The software package consists of two modules corresponding to a two-step procedure: (1) hybrid surface grid generation (MIXSUR module), and (2) flow quantities integration (OVERINT module). Instructions on how to use this software package are described in this user's manual. Equations used in the flow coefficients calculation are given in Appendix A.

Chan, William M.↗

NASA NTRS2005

Regression Analysis of Long-Term Profile Ozone Data Set from BUV Instruments

We have produced a profile merged ozone data set (MOD) based on the SBUV/SBUV2 series of nadir-viewing satellite backscatter instruments, covering the period from November 1978 - December 2003. In 2004, data from the Nimbus 7 SBUV and NOAA 9, ll, and 16 SBUV/2 instruments were reprocessed using the Version 8 (V8) algorithm and most recent calibrations. More recently, data from the Nimbus 4 BUT instrument, which was operational from 1970 - 1977, were also reprocessed using the V8 algorithm. As part of the V8 profile calibration, the Nimbus 7 and NOAA 9 (1993-1997 only) instrument calibrations have been adjusted to match the NOAA 11 calibration, which was established based on comparisons with SSBUV shuttle flight data. Differences between NOAA 11, Nimbus 7 and NOAA 9 profile zonal means are within plus or minus 5% at all levels when averaged over the respective periods of data overlap. NOAA 16 SBUV/2 data have insufficient overlap with NOAA 11, so its calibration is based on pre-flight information. Mean differences over 4 months of overlap are within plus or minus 7%. Given the level of agreement between the data sets, we simply average the ozone values during periods of instrument overlap to produce the MOD profile data set. Initial comparisons of coincident matches of N4 BUV and Arosa Umkehr data show mean differences of 0.5 (0.5)% at 30km; 7.5 (0.5)% at 35 km; and 11 (0.7)% at 40 km, where the number in parentheses is the standard error of the mean. In this study, we use the MOD profile data set (1978-2003) to estimate the change in profile ozone due to changing stratospheric chlorine levels. We use a standard linear regression model with proxies for the seasonal cycle, solar cycle, QBO, and ozone trend. To account for the non-linearity of stratospheric chlorine levels since the late 1990s, we use a time series of Effective Chlorine, defined as the global average of Chlorine + 50 * Bromine at 1 hPa, as the trend proxy. The Effective Chlorine data are taken from the 3-D Goddard CTM. We will show the latest trend results using this statistical model. In addition, the Nimbus 4 BUV data offer an opportunity to test the physical properties of our statistical model. From ground-based comparisons we will establish an uncertainty range for the Nimbus 4 data. We then extrapolate our statistical model fit backwards in time and compare to the Nimbus 4 data. We compare the characteristics of the residual, defined as the difference between the data and statistical regression fit, during the Nimbus 4 time period and the 1978-2003 period over which the statistical model coefficients were estimated, and present these results.

Stolarski, Richard S.↗

NASA NTRS2008

WGM Resonators for Terahertz-to-Optical Frequency Conversion

Progress has been made toward solving some practical problems in the implementation of terahertz-to-optical frequency converters utilizing whispering-gallery-mode (WGM) resonators. Such frequency converters are expected to be essential parts of non-cryogenic terahertz- radiation receivers that are, variously, under development or contemplated for a variety of applications in airborne and spaceborne instrumentation for astronomical and military uses. In most respects, the basic principles of terahertz-to-optical frequency conversion in WGM resonators are the same as those of microwave (sub-terahertz)-to-optical frequency conversion in WGM resonators, various aspects of which were discussed in the three preceeding articles. To recapitulate: In a receiver following this approach, a preamplified incoming microwave signal (in the present case, a terahertz signal) is up-converted to an optical signal by a technique that exploits the nonlinearity of the electromagnetic response of a whispering-gallery-mode (WGM) resonator made of LiNbO3 or another suitable electro-optical material. Upconversion takes place by three-wave mixing in the resonator. To ensure the required interaction among the optical and terahertz signals, the WGM resonator must be designed and fabricated to function as an electro-optical modulator while simultaneously exhibiting (1) resonance at the required microwave and optical operating frequencies and (2) phase matching among the microwave and optical signals circulating in the resonator. Downstream of the WGM resonator, the up-converted signal is processed photonically by use of a tunable optical filter or local oscillator and is then detected. The practical problems addressed in the present development effort are the following: Satisfaction of the optical and terahertz resonance-frequency requirement is a straightforward matter, inasmuch as the optical and terahertz spectra can be measured. However, satisfaction of the phase-matching requirement is more difficult. The approach followed in the present development is to perform computer simulations of the microwave and optical signals circulating in the resonator to test for phase matching. To enable excitation of the terahertz WGM resonator mode, it is also necessary to ensure phase matching between that mode and the incoming terahertz radiation. In the present development, the incoming signal is coupled into the WGM resonator via a tapered waveguide in the form of a fused silica rod. The phase-matching requirement is satisfied at one point along the taper; the rod is positioned with this point in proximity to the WGM resonator. To maximize the conversion efficiency, it is necessary to maximize the spatial overlap among the terahertz and optical modes in the WGM resonator. In the absence of a special design effort to address this issue, there would be little such overlap because, as a consequence of a large difference between wavelengths, the optical and terahertz modes would be concentrated at different depths from the rim of a WGM resonator. In the present development, overlap is ensured by constructing the WGM resonator as a ring (see figure) so thin that the optical and terahertz modes are effectively forced to overlap.

Strekalov,Dmitry↗

NASA NTRS2012

Evidence of Multiple Reconnection Lines at the Magnetopause from Cusp Observations

Recent global hybrid simulations investigated the formation of flux transfer events (FTEs) and their convection and interaction with the cusp. Based on these simulations, we have analyzed several Polar cusp crossings in the Northern Hemisphere to search for the signature of such FTEs in the energy distribution of downward precipitating ions: precipitating ion beams at different energies parallel to the ambient magnetic field and overlapping in time. Overlapping ion distributions in the cusp are usually attributed to a combination of variable ion acceleration during the magnetopause crossing together with the time-of-flight effect from the entry point to the observing satellite. Most "step up" ion cusp structures (steps in the ion energy dispersions) only overlap for the populations with large pitch angles and not for the parallel streaming populations. Such cusp structures are the signatures predicted by the pulsed reconnection model, where the reconnection rate at the magnetopause decreased to zero, physically separating convecting flux tubes and their parallel streaming ions. However, several Polar cusp events discussed in this study also show an energy overlap for parallel-streaming precipitating ions. This condition might be caused by reopening an already reconnected field line, forming a magnetic island (flux rope) at the magnetopause similar to that reported in global MHD and Hybrid simulations

flux transfer events↗

NASA NTRSDate not supplied

RESIDUAL DEFORMATION ANALYSIS IN COMPOSITE SHELL STRUCTURES MANUFACTURED USING AUTOMATED FIBER PLACEMENT

The manufacturing of composites typically produces residual stresses that can significantly affect the final shape of the structure. The process of automated fiber placement (AFP) has become a prominent manufacturing technique in developing layups with tailored, variable stiffness morphology. The steered patterns of fiber tows with and without overlaps produce residual deformations that are distinctive from traditional layups. Digital image correlation was used to measure the AFP lamina coefficients of thermal expansion, which were incorporated into finite element analyses (FEA) to model the cooling phase of the cure cycle. The effects of nonlinear analysis and temperature-dependent lamina properties calculated using self-consistent field micromechanics, on the resulting residual deformation of shells, were also modeled. The predicted residual deformation was analyzed by considering out-of-roundness in cylindrical shells and compared to the experimental results. The shell FEA results were well-correlated with the overall deformed shape of the AFP cylinder with overlaps, while the shell FEA model of the AFP cylinder without overlaps did not show as good of qualitative match of the deformation pattern. Analytical correlation with measured results were insensitive to material softening at elevated temperatures, geometric nonlinearities, and variations in measured lamina thermal properties. To improve the accuracy of the residual deformation analysis, these results suggest that the thermo-chemical shrinkages preceding the cooldown should be considered, as well as possible variations in ply level microstructure due to the presence of the embedded fiber tow gaps and overlaps.

Composites↗

NASA NTRS2021

The role of analysis error in the convergence of reanalysis production streams in MERRA-2

Due to production time constraints, most reanalyses are produced in multiple parallel streams instead of a single continuous one. These streams cover separate segments of the reanalysis time period with short overlaps to allow reconstruction of the official record. A fundamental assumption justifying this approach is that the streams will be assimilating the same observations during the periods where they overlap, and so will eventually converge to a similar atmospheric state, making discontinuities at stream junctions negligible. This assumption is revisited in this work by examining the impact of analysis error on the differences between MERRA-2 overlapping streams in three historical periods. Comparison results are shown in terms of standard deviations of stream differences as well as the spectral decomposition of the variance of their differences. Residual differences were found at the end of each year of overlap, with larger values observed in the earlier segments of the presatellite era. By drawing parallels with analysis error statistics estimated from the GMAO OSSE system, these differences are shown to reflect the varying constraint of data with the varying observing network, and to further carry the imprint of errors that the data assimilation process is not able to mitigate. As such, they are unlikely to be reduced by longer spinup periods. The ability of data assimilation to ensure continuity in the parallel streams is put into question when the observing system coverage is inadequate or simply when the data assimilation system as a whole is suboptimal.

Amal El Akkraoui↗

DOE OSTI2026

Exact chiral symmetry with quantum signal processing

We give a quantum signal processing (QSP) algorithm for the overlap fermion Hamiltonian which preserves the Ginsparg-Wilson relation up to a controllable error $ε_e$. Quantum simulations of Dirac fermions with exact chiral symmetry are thus nearly free: applying the overlap Hamiltonian costs only a factor logarithmic in $ε_e$ more than the Wilson-Dirac Hamiltonian. Comparing to domain-wall fermions, a mild overhead is found in circuit complexity while reducing qubit costs. We show how QSP effectively constructs an extra dimension when simulating the overlap operator, illustrating that the scaling of quantum algorithms reflects the deeper physics of overlap fermions arising at the boundary of domain-wall fermions.

Lamm, Henry [Fermilab] (ORCID:0000000330330791)↗

DOE OSTI2024

Measuring Thread Timing to Assess the Feasibility of Early-Bird Message Delivery Across Systems and Scales

Early-bird communication is a communication/computation overlap technique that leverages fine-grained communication to improve application run-time. Communication is divided such that each individual thread can initiate transmission of its portion of the data upon completion rather than waiting for a dedicated communication phase. The benefit of early-bird communication depends on the completion timing of the individual threads: On the one hand, if all threads are complete at nearly the same time, the overheads of sending multiple messages will accumulate, leading to performance that is worse than if a single message had been sent. On the other hand, if thread completions are spread out in time, those that complete earlier can send data while others continue working, leading to performance that is better than if a single message had been sent. The challenge is that the completion times are currently unknown and can vary based on application, problem size, system software, and underlying hardware. In this paper, we address this lacuna by measuring and evaluating the potential overlap afforded by early-bird communication for a selection of proxy applications. These measurements help us understand whether a given application could benefit from early-bird communication. Here, we present our technique for gathering this data and evaluate data collected from three proxy applications: MiniFE, MiniMD, and MiniQMC. Each application is run on three systems with distinct CPU architectures and strong scales across three run sizes. To characterize the behavior of these workloads, we study the trends of thread timings at both a macro level, across all threads across all runs of an application, and a micro level, that is, within a single process of a single run. We observe that our tested applications exhibit significantly different thread arrival distributions. The machine used had a significant impact, with the window of potential overlap varying by as much as an order of magnitude.

97 MATHEMATICS AND COMPUTING↗