Search

Single-stranded (ss) RNA viruses self-assemble spontaneously in solutions that contain the viral RNA genome molecules and the viral capsid proteins. The self-assembly of empty capsids can be understood on the basis of free energy minimization of rather simple models. However, during the self-assembly of complete viral particles in the cytoplasm of an infected cell, the viral genome molecules must be selected from a large pool of very similar host messenger RNA molecules. It is known that the assembly process takes the form of preferential heterogeneous nucleation of capsid proteins on viral RNA molecules ("selective nucleation"). Recently, a simple mathematical model was proposed for the selective nucleation of small ssRNA viruses. In this paper we present a statistical physics analysis of the thermal equilibrium and kinetic properties of that model and show that it can account, at least qualitatively, for numerous observations of the self-assembly of small ssRNA viruses., Comment: 19 pages, 26 figures. Submitted to Physical Review E. arXiv admin note: text overlap with arXiv:2102.03941

Interdependent values make basic auction design tasks -- in particular maximizing welfare truthfully in single-item auctions -- quite challenging. Eden et al. recently established that if the bidders valuation functions are submodular over their signals (a.k.a. SOS), a truthful 4-approximation to the optimal welfare exists. We show existence of a mechanism that is truthful and achieves a tight 2-approximation to the optimal welfare when signals are binary. Our mechanism is randomized and assigns bidders only 0 or 0.5 probabilities of winning the item. Our results utilize properties of submodular set functions, and extend to matroid settings., Comment: 26 pages, 5 figures

Just-in-time adaptive interventions (JITAIs) are time-varying adaptive interventions that use frequent opportunities for the intervention to be adapted--weekly, daily, or even many times a day. The micro-randomized trial (MRT) has emerged for use in informing the construction of JITAIs. MRTs can be used to address research questions about whether and under what circumstances JITAI components are effective, with the ultimate objective of developing effective and efficient JITAI. The purpose of this article is to clarify why, when, and how to use MRTs; to highlight elements that must be considered when designing and implementing an MRT; and to review primary and secondary analyses methods for MRTs. We briefly review key elements of JITAIs and discuss a variety of considerations that go into planning and designing an MRT. We provide a definition of causal excursion effects suitable for use in primary and secondary analyses of MRT data to inform JITAI development. We review the weighted and centered least-squares (WCLS) estimator which provides consistent causal excursion effect estimators from MRT data. We describe how the WCLS estimator along with associated test statistics can be obtained using standard statistical software such as R (R Core Team, 2019). Throughout we illustrate the MRT design and analyses using the HeartSteps MRT, for developing a JITAI to increase physical activity among sedentary individuals. We supplement the HeartSteps MRT with two other MRTs, SARA and BariFit, each of which highlights different research questions that can be addressed using the MRT and experimental design considerations that might arise., Comment: arXiv admin note: substantial text overlap with arXiv:2005.05880, arXiv:2004.10241

We study contract design for welfare maximization in the well known "common agency" model of [Bernheim and Whinston, 1986]. This model combines the challenges of coordinating multiple principals with the fundamental challenge of contract design: that principals have incomplete information of the agent's choice of action. Motivated by the significant social inefficiency of standard contracts for such settings (which we formally quantify using a price of anarchy/stability analysis), we investigate whether and how a recent toolbox developed for the first set of challenges under a complete-information assumption, VCG contracts [Lavi and Shamash, 2019], can be extended to incomplete information. We define and characterize the class of "incomplete information VCG contracts (IIVCG)", and show it is the unique class guaranteeing truthfulness of the principals and welfare maximization by the agent. Our results reveal an inherent tradeoff between two important properties required to ensure participation in the contract: individual rationality (for the principals) and limited liability (for the agent). We design a polynomial-time algorithm for determining whether a setting has an IIVCG contract with both properties. As our main result we design a polynomial-time "algorithmic IIVCG" contract: given valuation reports from the principals it returns, if possible for the setting, a payment scheme for the agent that constitutes an IIVCG contract with all desired properties. We also give a sufficient graph-theoretic condition on the population of principals that ensures the existence of such an IIVCG contract.

We study a Bayesian persuasion setting with binary actions (adopt and reject) for Receiver. We examine the following question - how well can Sender perform, in terms of persuading Receiver to adopt, when ignorant of Receiver's utility? We take a robust (adversarial) approach to study this problem; that is, our goal is to design signaling schemes for Sender that perform well for all possible Receiver's utilities. We measure performance of signaling schemes via the notion of (additive) regret: the difference between Sender's hypothetically optimal utility had she known Receiver's utility function and her actual utility induced by the given scheme. On the negative side, we show that if Sender has no knowledge at all about Receiver's utility, then Sender has no signaling scheme that performs robustly well. On the positive side, we show that if Sender only knows Receiver's ordinal preferences of the states of nature - i.e., Receiver's utility upon adoption is monotonic as a function of the state - then Sender can guarantee a surprisingly low regret even when the number of states tends to infinity. In fact, we exactly pin down the minimum regret value that Sender can guarantee in this case, which turns out to be at most 1/e. We further show that such positive results are not possible under the alternative performance measure of a multiplicative approximation ratio by proving that no constant ratio can be guaranteed even for monotonic Receiver's utility; this may serve to demonstrate the merits of regret as a robust performance measure that is not too pessimistic. Finally, we analyze an intermediate setting in between the no-knowledge and the ordinal-knowledge settings.

Dynamic treatment regimens (DTRs), also known as treatment algorithms or adaptive interventions, play an increasingly important role in many health domains. DTRs are motivated to address the unique and changing needs of individuals by delivering the type of treatment needed, when needed, while minimizing unnecessary treatment. Practically, a DTR is a sequence of decision rules that specify, for each of several points in time, how available information about the individual's status and progress should be used in practice to decide which treatment (e.g., type or intensity) to deliver. The sequential multiple assignment randomized trial (SMART) is an experimental design widely used to empirically inform the development of DTRs. Sample size planning resources for SMARTs have been developed for continuous, binary, and survival outcomes. However, an important gap exists in sample size estimation methodology for SMARTs with longitudinal count outcomes. Further, in many health domains, count data are overdispersed - having variance greater than their mean. We propose a Monte Carlo-based approach to sample size estimation applicable to many types of longitudinal outcomes and provide a case study with longitudinal overdispersed count outcomes. A SMART for engaging alcohol and cocaine-dependent patients in treatment is used as motivation., Comment: Key words: dynamic treatment regimen (DTR); longitudinal outcome; overdispersed count; sample size estimation; sequential multiple assignment randomized trial (SMART)

Amphiphilic molecules and their self-assembled structures have long been the target of extensive research due to their potential applications in fields ranging from materials design to biomedical and cosmetic applications. Increasing demands for functional complexity have been met with challenges in biochemical engineering, driving researchers to innovate in the design of new amphiphiles. An emerging class of molecules, namely, peptide amphiphiles, combines key advantages and circumvents some of the disadvantages of conventional phospholipids and block-copolymers. Herein, we present new peptide amphiphiles comprised of an intrinsically disordered peptide conjugated to two variants of hydrophobic dendritic domains. These molecules termed intrinsically disordered peptide amphiphiles (IDPA), exhibit a sharp pH-induced micellar phase-transition from low-dispersity spheres to extremely elongated worm-like micelles. We present an experimental characterization of the transition and propose a theoretical model to describe the pH-response. We also present the potential of the shape transition to serve as a mechanism for the design of a cargo hold-and-release application. Such amphiphilic systems demonstrate the power of tailoring the interactions between disordered peptides for various stimuli-responsive biomedical applications., Comment: 27 pages, 4 figures, supplementary information file

Education practice often requires teachers and other school personnel to adapt interventions over time in order to address between-student heterogeneity in response to intervention (e.g., what works for one student may not work for the other) or within-student heterogeneity (e.g., what works now may not work in the future for the same student). An adaptive intervention allows education practitioners to do this in a prespecified, systematic, and replicable way through a sequence of decision rules that guides whether, how, and when to modify interventions. In an adaptive intervention, the practitioner modifies the dosage or type of intervention, or the mode of delivery to meet the unique and changing needs of students as they progress over time. The sequential, multiple assignment, randomized trial (SMART) is one type of multistage, experimental design that can help education researchers build high-quality adaptive interventions. Despite the critical role adaptive interventions can play in various domains of education, research about adaptive interventions and about the use of SMART designs to develop effective adaptive interventions in education is in its infancy. This paper defines an adaptive intervention and reviews the components of this design, discusses the key features of the SMART, and introduces common research questions for which SMARTs may be appropriate. [This guide was completed by the Manhattan Strategy Group.]

Strategic classification studies the interaction between a classification rule and the strategic agents it governs. Under the assumption that the classifier is known, rational agents respond to it by manipulating their features. However, in many real-life scenarios of high-stake classification (e.g., credit scoring), the classifier is not revealed to the agents, which leads agents to attempt to learn the classifier and game it too. In this paper we generalize the strategic classification model to such scenarios. We define the price of opacity as the difference in prediction error between opaque and transparent strategy-robust classifiers, characterize it, and give a sufficient condition for this price to be strictly positive, in which case transparency is the recommended policy. Our experiments show how Hardt et al.'s robust classifier is affected by keeping agents in the dark.

Protein function may be modulated by an event occurring far away from the functional site, a phenomenon termed allostery. While classically allostery involves conformational changes, we recently observed that charge redistribution within an antibody can also lead to an allosteric effect, modulating the kinetics of binding to target antigen. In the present study, we study the association of a poly-histidine tagged enzyme (phosphoglycerate kinase, PGK) to surface-immobilized anti-His antibodies, finding a significant Charge-Reorganization Allostery (CRA) effect. We further observe that the negatively charged nucleotide substrates of PGK modulate CRA substantially, even though they bind far away from the His-tag-antibody interaction interface. In particular, binding of ATP reduces CRA by more than 50%. The results indicate that CRA may be affected by charged substrates bound to a protein and provide further insight into the role of charge redistribution in protein function.

We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and based on small differences between the assembly energy profiles. RNA molecules that win these packaging contests are characterized by having a minimum "Maximum Ladder Distance" and a maximum "Wrapping Number".The former is a topological invariant that measures the "branchiness" of the genome molecule while the latter measures the ability of the genome molecule to maximally associate with the capsid proteins. The model can also be used study the applicability of the theory of nucleation and growth to viral assembly, which breaks down with increasing strength of the RNA-protein interaction., Comment: 18 pages, 25 figures

This paper introduces HeBERT and HebEMO. HeBERT is a Transformer-based model for modern Hebrew text, which relies on a BERT (Bidirectional Encoder Representations for Transformers) architecture. BERT has been shown to outperform alternative architectures in sentiment analysis, and is suggested to be particularly appropriate for MRLs. Analyzing multiple BERT specifications, we find that while model complexity correlates with high performance on language tasks that aim to understand terms in a sentence, a more-parsimonious model better captures the sentiment of entire sentence. Either way, out BERT-based language model outperforms all existing Hebrew alternatives on all common language tasks. HebEMO is a tool that uses HeBERT to detect polarity and extract emotions from Hebrew UGC. HebEMO is trained on a unique Covid-19-related UGC dataset that we collected and annotated for this study. Data collection and annotation followed an active learning procedure that aimed to maximize predictability. We show that HebEMO yields a high F1-score of 0.96 for polarity classification. Emotion detection reaches F1-scores of 0.78-0.97 for various target emotions, with the exception of surprise, which the model failed to capture (F1 = 0.41). These results are better than the best-reported performance, even among English-language models of emotion detection.

This paper presents methods to choose individuals to test for infection during a pandemic such as COVID-19, characterized by high contagion and presence of asymptomatic carriers. The smart-testing ideas presented here are motivated by active learning and multi-armed bandit techniques in machine learning. Our active sampling method works in conjunction with quarantine policies, can handle different objectives, is dynamic and adaptive in the sense that it continually adapts to changes in real-time data. The bandit algorithm uses contact tracing, location-based sampling and random sampling in order to select specific individuals to test. Using a data-driven agent-based model simulating New York City we show that the algorithm samples individuals to test in a manner that rapidly traces infected individuals. Experiments also suggest that smart-testing can significantly reduce the death rates as compared to current methods such as testing symptomatic individuals with or without contact tracing.

Bayesian persuasion is the study of information sharing policies among strategic agents. A prime example is signaling in online ad auctions: what information should a platform signal to an advertiser regarding a user when selling the opportunity to advertise to her? Practical considerations such as preventing discrimination, protecting privacy or acknowledging limited attention of the information receiver impose constraints on information sharing. In this work, we propose and analyze a simple way to mathematically model such constraints as restrictions on Receiver's admissible posterior beliefs. We consider two families of constraints - ex ante and ex post, where the latter limits each instance of Sender-Receiver communication, while the former more general family can also pose restrictions in expectation. For the ex ante family, Doval and Skreta establish the existence of an optimal signaling scheme with a small number of signals - at most the number of constraints plus the number of states of nature; we show this result is tight and provide an alternative proof for it. For the ex post family, we tighten a bound of V{\o}lund, showing that the required number of signals is at most the number of states of nature, as in the original Kamenica-Gentzkow setting. As our main algorithmic result, we provide an additive bi-criteria FPTAS for an optimal constrained signaling scheme assuming a constant number of states; we improve the approximation to single-criteria under a Slater-like regularity condition. The FPTAS holds under standard assumptions; relaxed assumptions yield a PTAS. Finally, we bound the ratio between Sender's optimal utility under convex ex ante constraints and the corresponding ex post constraints. This bound applies to finding an approximately welfare-maximizing constrained signaling scheme in ad auctions.

We present a simple unsupervised approach for answer identification in organizational group chat. In recent years, organizational group chat is on the rise enabling asynchronous text-based collaboration between co-workers in different locations and time zones. Finding answers to questions is often critical for work efficiency. However, group chat is characterized by intertwined conversations and 'always on' availability, making it hard for users to pinpoint answers to questions they care about in real-time or search for answers in retrospective. In addition, structural and lexical characteristics differ between chat groups, making it hard to find a 'one model fits all' approach. Our Kernel Density Estimation (KDE) based clustering approach termed Ans-Chat implicitly learns discussion patterns as a means for answer identification, thus eliminating the need to channel-specific tagging. Empirical evaluation shows that this solution outperforms other approached.

We expand the literature on the price of anarchy (PoA) of simultaneous item auctions by considering settings with correlated values; we do this via the fundamental economic model of interdependent values (IDV). It is well-known that in multi-item settings with private values, correlated values can lead to bad PoA, which can be polynomially large in the number of agents $n$. In the more general model of IDV, we show that the PoA can be polynomially large even in single-item settings. On the positive side, we identify a natural condition on information dispersion in the market, termed $\gamma$-heterogeneity, which enables good PoA guarantees. Under this condition, we show that for single-item settings, the PoA of standard mechanisms degrades gracefully with $\gamma$. For settings with $m>1$ items we show a separation between two domains: If $n \geq m$, we devise a new simultaneous item auction with good PoA (with respect to $\gamma$), under limited information asymmetry. To the best of our knowledge, this is the first positive PoA result for correlated values in multi-item settings. The main technical difficulty in establishing this result is that the standard tool for establishing PoA results -- the smoothness framework -- is unsuitable for IDV settings, and so we must introduce new techniques to address the unique challenges imposed by such settings. In the domain of $n \ll m$, we establish impossibility results even for surprisingly simple scenarios.

Crop type classification using satellite observations is an important tool for providing insights about planted area and enabling estimates of crop condition and yield, especially within the growing season when uncertainties around these quantities are highest. As the climate changes and extreme weather events become more frequent, these methods must be resilient to changes in domain shifts that may occur, for example, due to shifts in planting timelines. In this work, we present an approach for within-season crop type classification using moderate spatial resolution (30 m) satellite data that addresses domain shift related to planting timelines by normalizing inputs by crop growth stage. We use a neural network leveraging both convolutional and recurrent layers to predict if a pixel contains corn, soybeans, or another crop or land cover type. We evaluated this method for the 2019 growing season in the midwestern US, during which planting was delayed by as much as 1-2 months due to extreme weather that caused record flooding. We show that our approach using growth stage-normalized time series outperforms fixed-date time series, and achieves overall classification accuracy of 85.4% prior to harvest (September-November) and 82.8% by mid-season (July-September)., Comment: Presented at KDD 2020 Fragile Earth: Data Science for a Sustainable Planet Workshop

In the $(k,h)$-SetCover problem, we are given a collection $\mathcal{S}$ of sets over a universe $U$, and the goal is to distinguish between the case that $\mathcal{S}$ contains $k$ sets which cover $U$, from the case that at least $h$ sets in $\mathcal{S}$ are needed to cover $U$. Lin (ICALP'19) recently showed a gap creating reduction from the $(k,k+1)$-SetCover problem on universe of size $O_k(\log |\mathcal{S}|)$ to the $\left(k,\sqrt[k]{\frac{\log|\mathcal{S}|}{\log\log |\mathcal{S}|}}\cdot k\right)$-SetCover problem on universe of size $|\mathcal{S}|$. In this paper, we prove a more scalable version of his result: given any error correcting code $C$ over alphabet $[q]$, rate $\rho$, and relative distance $\delta$, we use $C$ to create a reduction from the $(k,k+1)$-SetCover problem on universe $U$ to the $\left(k,\sqrt[2k]{\frac{2}{1-\delta}}\right)$-SetCover problem on universe of size $\frac{\log|\mathcal{S}|}{\rho}\cdot|U|^{q^k}$. Lin established his result by composing the input SetCover instance (that has no gap) with a special threshold graph constructed from extremal combinatorial object called universal sets, resulting in a final SetCover instance with gap. Our reduction follows along the exact same lines, except that we generate the threshold graphs specified by Lin simply using the basic properties of the error correcting code $C$. We use the same threshold graphs mentioned above to prove inapproximability results, under W[1]$\neq$FPT and ETH, for the $k$-MaxCover problem introduced by Chalermsook et al. (SICOMP'20). Our inapproximaiblity results match the bounds obtained by Karthik et al. (JACM'19), although their proof framework is very different, and involves generalization of the distributed PCP framework. Prior to this work, it was not clear how to adopt the proof strategy of Lin to prove inapproximability results for $k$-MaxCover.

The ubiquity of smartphone cameras has led to more and more documents being captured by cameras rather than scanned. Unlike flatbed scanners, photographed documents are often folded and crumpled, resulting in large local variance in text structure. The problem of document rectification is fundamental to the Optical Character Recognition (OCR) process on documents, and its ability to overcome geometric distortions significantly affects recognition accuracy. Despite the great progress in recent OCR systems, most still rely on a pre-process that ensures the text lines are straight and axis aligned. Recent works have tackled the problem of rectifying document images taken in-the-wild using various supervision signals and alignment means. However, they focused on global features that can be extracted from the document's boundaries, ignoring various signals that could be obtained from the document's content. We present CREASE: Content Aware Rectification using Angle Supervision, the first learned method for document rectification that relies on the document's content, the location of the words and specifically their orientation, as hints to assist in the rectification process. We utilize a novel pixel-wise angle regression approach and a curvature estimation side-task for optimizing our rectification model. Our method surpasses previous approaches in terms of OCR accuracy, geometric error and visual similarity., Comment: Presented in ECCV 2020

Spatial information on cropland distribution, often called cropland or crop maps, are critical inputs for a wide range of agriculture and food security analyses and decisions. However, high-resolution cropland maps are not readily available for most countries, especially in regions dominated by smallholder farming (e.g., sub-Saharan Africa). These maps are especially critical in times of crisis when decision makers need to rapidly design and enact agriculture-related policies and mitigation strategies, including providing humanitarian assistance, dispersing targeted aid, or boosting productivity for farmers. A major challenge for developing crop maps is that many regions do not have readily accessible ground truth data on croplands necessary for training and validating predictive models, and field campaigns are not feasible for collecting labels for rapid response. We present a method for rapid mapping of croplands in regions where little to no ground data is available. We present results for this method in Togo, where we delivered a high-resolution (10 m) cropland map in under 10 days to facilitate rapid response to the COVID-19 pandemic by the Togolese government. This demonstrated a successful transition of machine learning applications research to operational rapid response in a real humanitarian crisis. All maps, data, and code are publicly available to enable future research and operational systems in data-sparse regions., Comment: Presented at KDD 2020 Humanitarian Mapping Workshop

Just-in-time adaptive interventions (JITAIs) are time-varying adaptive interventions that use frequent opportunities for the intervention to be adapted such as weekly, daily, or even many times a day. This high intensity of adaptation is facilitated by the ability of digital technology to continuously collect information about an individual's current context and deliver treatments adapted to this information. The micro-randomized trial (MRT) has emerged for use in informing the construction of JITAIs. MRTs operate in, and take advantage of, the rapidly time-varying digital intervention environment. MRTs can be used to address research questions about whether and under what circumstances particular components of a JITAI are effective, with the ultimate objective of developing effective and efficient components. The purpose of this article is to clarify why, when, and how to use MRTs; to highlight elements that must be considered when designing and implementing an MRT; and to discuss the possibilities this emerging optimization trial design offers for future research in the behavioral sciences, education, and other fields. We briefly review key elements of JITAIs, and then describe three case studies of MRTs, each of which highlights research questions that can be addressed using the MRT and experimental design considerations that might arise. We also discuss a variety of considerations that go into planning and designing an MRT, using the case studies as examples.

Accurate crop type maps provide critical information for ensuring food security, yet there has been limited research on crop type classification for smallholder agriculture, particularly in sub-Saharan Africa where risk of food insecurity is highest. Publicly-available ground-truth data such as the newly-released training dataset of crop types in Kenya (Radiant MLHub) are catalyzing this research, but it is important to understand the context of when, where, and how these datasets were obtained when evaluating classification performance and using them as a benchmark across methods. In this paper, we provide context for the new western Kenya dataset which was collected during an atypical 2019 main growing season and demonstrate classification accuracy up to 64% for maize and 70% for cassava using k Nearest Neighbors--a fast, interpretable, and scalable method that can serve as a baseline for future work., Comment: Paper presented at the ICLR 2020 Workshop on Computer Vision for Agriculture (CV4A)

Mobile health (mHealth) applications are a powerful medium for providing behavioral interventions, and systematic reviews suggest that theory-based interventions are more effective. However, how exactly theoretical concepts should be translated into features of technological interventions is often not clear. There is a gulf between the abstract nature of psychological theory and the concreteness of the designs needed to build health technologies. In this paper, we use SARA, a mobile app we developed to support substance-use research among adolescents and young adults, as a case study of a process of translating behavioral theory into mHealth intervention design. SARA was designed to increase adherence to daily self-report in longitudinal epidemiological studies. To achieve this goal, we implemented a number of constructs from the operant conditioning theory. We describe our design process and discuss how we operationalized theoretical constructs in the light of design constraints, user feedback, and empirical data from four formative studies.