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Whether the strong coupling to thermal baths can improve the performance of quantum thermal machines remains an open issue under active debate. Here, we revisit quantum thermal machines operating with the quasi-static Carnot cycle and aim to unveil the role of strong coupling in maximum efficiency. Our analysis builds upon definitions of excess work and heat derived from an exact formulation of the first law of thermodynamics for the working substance, which captures the non-Gibbsian thermal equilibrium state that emerges at strong couplings during quasi-static isothermal processes. These excess definitions differ from conventional ones by an energetic cost for maintaining the non-Gibbsian characteristics. With this distinction, we point out that one can introduce two different yet thermodynamically allowed definitions for efficiency of both the heat engine and refrigerator modes. We dub them excess and hybrid definitions which differ in the way of defining the gain for the thermal machines at strong couplings by either just analyzing the energetics of the working substance or instead evaluating the performance from an external system upon which the thermal machine acts, respectively. We analytically demonstrate that the excess definition predicts that the Carnot limit remains the upper bound for both operation modes at strong couplings, whereas the hybrid one reveals that strong coupling can suppress the maximum efficiency rendering the Carnot limit unattainable. These seemingly incompatible predictions thus indicate that it is imperative to first gauge the definition for efficiency before elucidating the exact role of strong coupling, thereby shedding light on the on-going investigation on strong-coupling quantum thermal machines., Comment: 9 pages, 1 figure. Comments are highly welcome!

We introduce a general method based on the operators of the Dyson-Masleev transformation to map the Hamiltonian of an arbitrary model system into the Hamiltonian of a circuit Quantum Electrodynamics (cQED) processor. Furthermore, we introduce a modular approach to program a cQED processor with components corresponding to the mapping Hamiltonian. The method is illustrated as applied to quantum dynamics simulations of the Fenna-Matthews-Olson (FMO) complex and the spin-boson model of charge transfer. Beyond applications to molecular Hamiltonians, the mapping provides a general approach to implement any unitary operator in terms of a sequence of unitary transformations corresponding to powers of creation and annihilation operators of a single bosonic mode in a cQED processor.

Electron transfer at electrode interfaces to molecules in solution or at the electrode surface plays a vital role in numerous technological processes. However, treating these processes requires a unified and accurate treatment of the fermionic states of the electrode and their coupling to the molecule being oxidized or reduced in the electrochemical processes and, in turn, the way the molecular energy levels are modulated by the bosonic nuclear modes of the molecule and solvent. Here we present a physically transparent quasiclassical scheme to treat these electrochemical electron transfer processes in the presence of molecular vibrations by using an appropriately chosen mapping of the fermionic variables. We demonstrate that this approach, which is exact in the limit of non-interacting fermions, is able to accurately capture the electron transfer dynamics from the electrode even when the process is coupled to vibrational motions in regimes of weak coupling. This approach thus provides a scalable strategy to explicitly treat electron transfer from electrode interfaces in condensed-phase molecular systems.

The nonequilibrium steady state (NESS) of a quantum network is central to a host of physical and biological scenarios. Examples include natural processes such as vision and photosynthesis, as well as technical devices such as photocells, both activated by incoherent light (e.g. sunlight) and leading to quantum transport. Here, a completely general approach to defining components of a quantum network in the NESS, and obtaining rates of processes between these components is provided. Quantum effects are explicitly included throughout, both in (a) defining network components via projection operators, and (b) in determining the role of coherences in rate processes. As examples, the methodology is applied to model cases, two versions of the V-level system, and to the spin-boson model, wherein the role of the environment and of internal system properties in determining the rates is examined. In addition, the role of Markovian vs. non-Markovian contributions is quantified, exposing conditions under which NESS rates can be obtained by perturbing the nonequilibrium steady state.

The third-order response lies at the heart of simulating and interpreting nonlinear spectroscopies ranging from two dimensional infrared (2D-IR) to 2D electronic (2D-ES), and 2D sum frequency generation (2D-SFG). The extra time and frequency dimensions in these spectroscopies provides access to rich information on the electronic and vibrational states present, the coupling between them, and the resulting rates at which they exchange energy that are obscured in linear spectroscopy, particularly for condensed phase systems that usually contain many overlapping features. While the exact quantum expression for the third-order response is well established it is incompatible with the methods that are practical for calculating the atomistic dynamics of large condensed phase systems. These methods, which include both classical mechanics and quantum dynamics methods that retain quantum statistical properties while obeying the symmetries of classical dynamics, such as LSC-IVR, Centroid Molecular Dynamics (CMD) and Ring Polymer Molecular Dynamics (RPMD) naturally provide short-time approximations to the multi-time symmetrized Kubo transformed correlation function. Here, we show how the third-order response can be formulated in terms of equilibrium symmetrized Kubo transformed correlation functions. We demonstrate the utility and accuracy of our approach by showing how it can be used to obtain the third-order response of a series of model systems using both classical dynamics and RPMD. In particular, we show that this approach captures features such as anharmonically induced vertical splittings and peak shifts while providing a physically transparent framework for understanding multidimensional spectroscopies.

Uncovering whether strong system-bath coupling can be an advantageous operation resource for energy conversion can facilitate the development of efficient quantum heat engines (QHEs). Yet, a consensus on this ongoing debate is still lacking owing to challenges arising from treating strong couplings. Here we conclude the debate for optimal linear cyclic QHEs operated under a small temperature difference by revealing the detrimental role of strong system-bath coupling in their optimal operations. We analytically demonstrate that both the efficiency at maximum power and maximum efficiency of strong-coupling linear cyclic QHEs are upper bounded by their weak-coupling counterparts and, particularly, experience a quadratic suppression relative to the Carnot limit under strong time-reversal symmetry breaking., Comment: Submitted. Comments are highly welcome

Time-resolved scattering experiments enable imaging of materials at the molecular scale with femtosecond time resolution. However, in disordered media they provide access to just one radial dimension thus limiting the study of orientational structure and dynamics. Here we introduce a rigorous and practical theoretical framework for predicting and interpreting experiments combining optically induced anisotropy and time-resolved scattering. Using impulsive nuclear Raman and ultrafast X-ray scattering experiments of chloroform and simulations, we demonstrate that this framework can accurately predict and elucidate both the spatial and temporal features of these experiments.

Theoretical treatments of periodically-driven quantum thermal machines (PD-QTMs) are largely focused on the limit-cycle stage of operation characterized by a periodic state of the system. Yet, this regime is not immediately accessible for experimental verification. Here, we present a general thermodynamic framework that can handle the performance of PD-QTMs both before and during the limit-cycle stage of operation. It is achieved by observing that periodicity may break down at the ensemble average level, even in the limit-cycle phase. With this observation, and using conventional thermodynamic expressions for work and heat, we find that a complete description of the first law of thermodynamics for PD-QTMs requires a new contribution, which vanishes only in the limit-cycle phase under rather weak system-bath couplings. Significantly, this contribution is substantial at strong couplings even at limit cycle, thus largely affecting the behavior of the thermodynamic efficiency. We demonstrate our framework by simulating a quantum Otto engine building upon a driven resonant level model. Our results provide new insights towards a complete description of PD-QTMs, from turn-on to the limit-cycle stage and, particularly, shed light on the development of quantum thermodynamics at strong coupling., Comment: submitted. Comments and suggestions are highly welcome

In the case of quantum systems interacting with multiple environments, the time-evolution of the reduced density matrix is described by the Liouvillian. For a variety of physical observables, the long-time limit or steady state solution is needed for the computation of desired physical observables. For inverse design or optimal control of such systems, the common approaches are based on brute-force search strategies. Here, we present a novel methodology, based on automatic differentiation, capable of differentiating the steady state solution with respect to any parameter of the Liouvillian. Our approach has a low memory cost, and is agnostic to the exact algorithm for computing the steady state. We illustrate the advantage of this method by inverse designing the parameters of a quantum heat transfer device that maximizes the heat current and the rectification coefficient. Additionally, we optimize the parameters of various Lindblad operators used in the simulation of energy transfer under natural incoherent light. We also present a sensitivity analysis of the steady state for energy transfer under natural incoherent light as a function of the incoherent-light pumping rate., Comment: Main work 10 pages and 5 Figures. Supplemental Material 12 pages, 1 Figure, 3 Tables

Inverse design of a property that depends on the steady-state of an open quantum system is commonly done by grid-search type of methods. In this paper we present a new methodology that allows us to compute the gradient of the steady-state of an open quantum system with respect to any parameter of the Hamiltonian using the implicit differentiation theorem. As an example, we present a simulation of a spin-boson model where the steady-state solution is obtained using Redfield theory., Comment: 6 pages, 2 figures, accepted for publication in Third Workshop on Machine Learning and the Physical Sciences (NeurIPS 2020), Vancouver, Canada

The non-equilibrium stationary coherences that form in donor-acceptor systems are investigated to determine their relationship to the efficiency of energy transfer to a neighboring reaction center. It is found that the effects of asymmetry in the dimer are generally detrimental to the transfer of energy. Four types of systems are examined, arising from combinations of localized trapping, delocalized (Forster) trapping, eigenstate dephasing and site basis dephasing. In the cases of site basis dephasing the interplay between the energy gap of the excited dimer states and the environment is shown to give rise to a turnover effect in the efficiency under weak dimer coupling conditions. Furthermore, the nature of the coherences and associated flux are interpreted in terms of pathway interference effects. In addition, regardless of the cases considered, the ratio of the real part and the imaginary part of the coherences in the energy-eigenbasis tends to a constant value in the steady state limit.

Identifying patients who will be discharged within 24 hours can improve hospital resource management and quality of care. We studied this problem using eight years of Electronic Health Records (EHR) data from Stanford Hospital. We fit models to predict 24 hour discharge across the entire inpatient population. The best performing models achieved an area under the receiver-operator characteristic curve (AUROC) of 0.85 and an AUPRC of 0.53 on a held out test set. This model was also well calibrated. Finally, we analyzed the utility of this model in a decision theoretic framework to identify regions of ROC space in which using the model increases expected utility compared to the trivial always negative or always positive classifiers.

Matsubara dynamics has recently emerged as the most general form of a quantum-Boltzmann-conserving classical dynamics theory for the calculation of single-time correlation functions. Here, we present a generalization of Matsubara dynamics for the evaluation of multi-time correlation functions. We show that the Matsubara approximation can also be used to approximate the two-time symmetrized double Kubo transformed correlation function. By a straightforward extension of these ideas to the multi-time realm, a multi-time Matsubara dynamics approximation can be obtained for the multi-time fully symmetrized Kubo transformed correlation function. Although not a practical method, due to the presence of a phase-term, this multi-time formulation of Matsubara dynamics represents a benchmark theory for future development of Boltzmann preserving semi-classical approximations to general higher order multi-time correlation functions.

Electronic phenotyping is the task of ascertaining whether an individual has a medical condition of interest by analyzing their medical record and is foundational in clinical informatics. Increasingly, electronic phenotyping is performed via supervised learning. We investigate the effectiveness of multitask learning for phenotyping using electronic health records (EHR) data. Multitask learning aims to improve model performance on a target task by jointly learning additional auxiliary tasks and has been used in disparate areas of machine learning. However, its utility when applied to EHR data has not been established, and prior work suggests that its benefits are inconsistent. We present experiments that elucidate when multitask learning with neural nets improves performance for phenotyping using EHR data relative to neural nets trained for a single phenotype and to well-tuned logistic regression baselines. We find that multitask neural nets consistently outperform single-task neural nets for rare phenotypes but underperform for relatively more common phenotypes. The effect size increases as more auxiliary tasks are added. Moreover, multitask learning reduces the sensitivity of neural nets to hyperparameter settings for rare phenotypes. Last, we quantify phenotype complexity and find that neural nets trained with or without multitask learning do not improve on simple baselines unless the phenotypes are sufficiently complex., Comment: Pacific Symposium on Biocomputing (PSB) 2019, Hawaii, https://psb.stanford.edu/psb-online/; 13 pages, 7 figures

Probabilistic survival predictions from models trained with Maximum Likelihood Estimation (MLE) can have high, and sometimes unacceptably high variance. The field of meteorology, where the paradigm of maximizing sharpness subject to calibration is popular, has addressed this problem by using scoring rules beyond MLE, such as the Continuous Ranked Probability Score (CRPS). In this paper we present the \emph{Survival-CRPS}, a generalization of the CRPS to the survival prediction setting, with right-censored and interval-censored variants. We evaluate our ideas on the mortality prediction task using two different Electronic Health Record (EHR) data sets (STARR and MIMIC-III) covering millions of patients, with suitable deep neural network architectures: a Recurrent Neural Network (RNN) for STARR and a Fully Connected Network (FCN) for MIMIC-III. We compare results between the two scoring rules while keeping the network architecture and data fixed, and show that models trained with Survival-CRPS result in sharper predictive distributions compared to those trained by MLE, while still maintaining calibration., Comment: UAI 2019

Improving the quality of end-of-life care for hospitalized patients is a priority for healthcare organizations. Studies have shown that physicians tend to over-estimate prognoses, which in combination with treatment inertia results in a mismatch between patients wishes and actual care at the end of life. We describe a method to address this problem using Deep Learning and Electronic Health Record (EHR) data, which is currently being piloted, with Institutional Review Board approval, at an academic medical center. The EHR data of admitted patients are automatically evaluated by an algorithm, which brings patients who are likely to benefit from palliative care services to the attention of the Palliative Care team. The algorithm is a Deep Neural Network trained on the EHR data from previous years, to predict all-cause 3-12 month mortality of patients as a proxy for patients that could benefit from palliative care. Our predictions enable the Palliative Care team to take a proactive approach in reaching out to such patients, rather than relying on referrals from treating physicians, or conduct time consuming chart reviews of all patients. We also present a novel interpretation technique which we use to provide explanations of the model's predictions., Comment: IEEE International Conference on Bioinformatics and Biomedicine 2017

When devising a course of treatment for a patient, doctors often have little quantitative evidence on which to base their decisions, beyond their medical education and published clinical trials. Stanford Health Care alone has millions of electronic medical records (EMRs) that are only just recently being leveraged to inform better treatment recommendations. These data present a unique challenge because they are high-dimensional and observational. Our goal is to make personalized treatment recommendations based on the outcomes for past patients similar to a new patient. We propose and analyze three methods for estimating heterogeneous treatment effects using observational data. Our methods perform well in simulations using a wide variety of treatment effect functions, and we present results of applying the two most promising methods to data from The SPRINT Data Analysis Challenge, from a large randomized trial of a treatment for high blood pressure.

Clinical notes are a rich source of information about patient state. However, using them to predict clinical events with machine learning models is challenging. They are very high dimensional, sparse and have complex structure. Furthermore, training data is often scarce because it is expensive to obtain reliable labels for many clinical events. These difficulties have traditionally been addressed by manual feature engineering encoding task specific domain knowledge. We explored the use of neural networks and transfer learning to learn representations of clinical notes that are useful for predicting future clinical events of interest, such as all causes mortality, inpatient admissions, and emergency room visits. Our data comprised 2.7 million notes and 115 thousand patients at Stanford Hospital. We used the learned representations, along with commonly used bag of words and topic model representations, as features for predictive models of clinical events. We evaluated the effectiveness of these representations with respect to the performance of the models trained on small datasets. Models using the neural network derived representations performed significantly better than models using the baseline representations with small ($N < 1000$) training datasets. The learned representations offer significant performance gains over commonly used baseline representations for a range of predictive modeling tasks and cohort sizes, offering an effective alternative to task specific feature engineering when plentiful labeled training data is not available.