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The accurate prediction of B-cell epitopes is critical for guiding vaccine development against infectious diseases, including SARS and COVID-19. This study explores the use of a deep neural network (DNN) model to predict B-cell epitopes for SARS-CoVandSARS-CoV-2,leveraging a dataset that incorporates essential protein and peptide features. Traditional sequence-based methods often struggle with large, complex datasets, but deep learning offers promising improvements in predictive accuracy. Our model employs regularization techniques, such as dropout and early stopping, to enhance generalization, while also analyzing key features, including isoelectric point and aromaticity, that influence epitope recognition. Results indicate an overall accuracy of 82% in predicting COVID-19 negative and positive cases, with room for improvement in detecting positive samples. This research demonstrates the applicability of deep learning in epitope mapping, suggesting that such approaches can enhance the speed and precision of vaccine design for emerging pathogens. Future work could incorporate structural data and diverse viral strains to further refine prediction capabilities.

We explore the relationship between two popular concepts on allocating divisible items: competitive equilibrium (CE) and allocations with maximum Nash welfare, i.e., allocations where the weighted geometric mean of the utilities is maximal. When agents have homogeneous concave utility functions, these two concepts coincide: the classical Eisenberg-Gale convex program that maximizes Nash welfare over feasible allocations yields a competitive equilibrium. However, these two concepts diverge for non-homogeneous utilities. From a computational perspective, maximizing Nash welfare amounts to solving a convex program for any concave utility functions, computing CE becomes PPAD-hard already for separable piecewise linear concave (SPLC) utilities. We introduce the concept of Gale-substitute utility functions, an analogue of the weak gross substitutes (WGS) property for the so-called Gale demand system. For Gale-substitutes utilities, we show that any allocation maximizing Nash welfare provides an approximate-CE with surprisingly strong guarantees, where every agent gets at least half the maximum utility they can get at any CE, and is approximately envy-free. Gale-substitutes include examples of utilities where computing CE is PPAD hard: in particular, all separable concave utilities, and the previously studied non-separable class of Leontief-free utilities. We introduce a new, general class of utility functions called generalized network utilities based on the generalized flow model; this class includes SPLC and Leontief-free utilities. We show that all such utilities are Gale-substitutes. Conversely, although some agents may get much higher utility at a Nash welfare maximizing allocation than at a CE, we show a price of anarchy type result: for general concave utilities, every CE achieves at least $(1/e)^{1/e} > 0.69$ fraction of the maximum Nash welfare, and this factor is tight.

Various first order approaches have been proposed in the literature to solve Linear Programming (LP) problems, recently leading to practically efficient solvers for large-scale LPs. From a theoretical perspective, linear convergence rates have been established for first order LP algorithms, despite the fact that the underlying formulations are not strongly convex. However, the convergence rate typically depends on the Hoffman constant of a large matrix that contains the constraint matrix, as well as the right hand side, cost, and capacity vectors. We introduce a first order approach for LP optimization with a convergence rate depending polynomially on the circuit imbalance measure, which is a geometric parameter of the constraint matrix, and depending logarithmically on the right hand side, capacity, and cost vectors. This provides much stronger convergence guarantees. For example, if the constraint matrix is totally unimodular, we obtain polynomial-time algorithms, whereas the convergence guarantees for approaches based on primal-dual formulations may have arbitrarily slow convergence rates for this class. Our approach is based on a fast gradient method due to Necoara, Nesterov, and Glineur (Math. Prog. 2019); this algorithm is called repeatedly in a framework that gradually fixes variables to the boundary. This technique is based on a new approximate version of Tardos's method, that was used to obtain a strongly polynomial algorithm for combinatorial LPs (Oper. Res. 1986).

Optimal auction design is a fundamental problem in algorithmic game theory. This problem is notoriously difficult already in very simple settings. Recent work in differentiable economics showed that neural networks can efficiently learn known optimal auction mechanisms and discover interesting new ones. In an attempt to theoretically justify their empirical success, we focus on one of the first such networks, RochetNet, and a generalized version for affine maximizer auctions. We prove that they satisfy mode connectivity, i.e., locally optimal solutions are connected by a simple, piecewise linear path such that every solution on the path is almost as good as one of the two local optima. Mode connectivity has been recently investigated as an intriguing empirical and theoretically justifiable property of neural networks used for prediction problems. Our results give the first such analysis in the context of differentiable economics, where neural networks are used directly for solving non-convex optimization problems., Comment: Conference paper published at NeurIPS 2023

We study the equilibrium computation problem in the Fisher market model with constrained piecewise linear concave (PLC) utilities. This general class captures many well-studied special cases, including markets with PLC utilities, markets with satiation, and matching markets. For the special case of PLC utilities, although the problem is PPAD-hard, Devanur and Kannan (FOCS 2008) gave a polynomial-time algorithm when the number of items is constant. Our main result is a fixed parameter approximation scheme for computing an approximate equilibrium, where the parameters are the number of agents and the approximation accuracy. This provides an answer to an open question by Devanur and Kannan for PLC utilities, and gives a simpler and faster algorithm for matching markets as the one by Alaei, Jalaly and Tardos (EC 2017). The main technical idea is to work with the stronger concept of thrifty equilibria, and approximating the input utility functions by `robust' utilities that have favorable marginal properties. With some restrictions, the results also extend to the Arrow--Debreu exchange market model.

In a dynamic matching market, such as a marriage or job market, how should agents balance accepting a proposed match with the cost of continuing their search? We consider this problem in a discrete setting, in which agents have cardinal values and finite lifetimes, and proposed matches are random. We seek to quantify how well the agents can do. We provide upper and lower bounds on the collective losses of the agents, with a polynomially small failure probability, where the notion of loss is with respect to a plausible baseline we define. These bounds are tight up to constant factors. We highlight two aspects of this work. First, in our model, agents have a finite time in which to enjoy their matches, namely the minimum of their remaining lifetime and that of their partner; this implies that unmatched agents become less desirable over time, and suggests that their decision rules should change over time. Second, we use a discrete rather than a continuum model for the population. The discreteness causes variance which induces localized imbalances in the two sides of the market. One of the main technical challenges we face is to bound these imbalances. In addition, we present the results of simulations on moderate-sized problems for both the discrete and continuum versions. For these size problems, there are substantial ongoing fluctuations in the discrete setting whereas the continuum version converges reasonably quickly.

Machine learning processes, e.g. ''learning in games'', can be viewed as non-linear dynamical systems. In general, such systems exhibit a wide spectrum of behaviors, ranging from stability/recurrence to the undesirable phenomena of chaos (or ''butterfly effect''). Chaos captures sensitivity of round-off errors and can severely affect predictability and reproducibility of ML systems, but AI/ML community's understanding of it remains rudimentary. It has a lot out there that await exploration. Recently, Cheung and Piliouras employed volume-expansion argument to show that Lyapunov chaos occurs in the cumulative payoff space, when some popular learning algorithms, including Multiplicative Weights Update (MWU), Follow-the-Regularized-Leader (FTRL) and Optimistic MWU (OMWU), are used in several subspaces of games, e.g. zero-sum, coordination or graphical constant-sum games. It is natural to ask: can these results generalize to much broader families of games? We take on a game decomposition approach and answer the question affirmatively. Among other results, we propose a notion of ''matrix domination'' and design a linear program, and use them to characterize bimatrix games where MWU is Lyapunov chaotic almost everywhere. Such family of games has positive Lebesgue measure in the bimatrix game space, indicating that chaos is a substantial issue of learning in games. For multi-player games, we present a local equivalence of volume change between general games and graphical games, which is used to perform volume and chaos analyses of MWU and OMWU in potential games.

A major goal in Algorithmic Game Theory is to justify equilibrium concepts from an algorithmic and complexity perspective. One appealing approach is to identify robust natural distributed algorithms that converge quickly to an equilibrium. This paper addresses a lack of robustness in existing convergence results for discrete forms of tatonnement, including the fact that it need not converge when buyers have linear utility functions. This work achieves greater robustness by seeking approximate rather than exact convergence in large market settings. More specifically, this paper shows that for Fisher markets with buyers having CES utility functions, including linear utility functions, tatonnement will converge quickly to an approximate equilibrium (i.e. at a linear rate), modulo a suitable large market assumption. The quality of the approximation is a function of the parameters of the large market assumption.

Envy-freeness and Pareto Efficiency are two major goals in welfare economics. The existence of an allocation that satisfies both conditions has been studied for a long time. Whether items are indivisible or divisible, it is impossible to achieve envy-freeness and Pareto Efficiency ex post even in the case of two people and two items. In contrast, in this work, we prove that, for any cardinal utility functions (including complementary utilities for example) and for any number of items and players, there always exists an ex ante mixed allocation which is envy-free and Pareto Efficient, assuming the allowable assignments are closed under swaps, i.e. if given a legal assignment, swapping any two players' allocations produces another legal assignment. The problem remains open in the divisible case. We also investigate the communication complexity for finding a Pareto Efficient and envy-free allocation.

Several works have shown linear speedup is achieved by an asynchronous parallel implementation of stochastic coordinate descent so long as there is not too much parallelism. More specifically, it is known that if all updates are of similar duration, then linear speedup is possible with up to $\Theta(\sqrt n L_{\max}/L_{\overline{\mathrm{res}}})$ processors, where $L_{\max}$ and $L_{\overline{\mathrm{res}}}$ are suitable Lipschitz parameters. This paper shows the bound is tight for almost all possible values of these parameters.

We seek tight bounds on the viable parallelism in asynchronous implementations of coordinate descent that achieves linear speedup. We focus on asynchronous coordinate descent (ACD) algorithms on convex functions which consist of the sum of a smooth convex part and a possibly non-smooth separable convex part. We quantify the shortfall in progress compared to the standard sequential stochastic gradient descent. This leads to a simple yet tight analysis of the standard stochastic ACD in a partially asynchronous environment, generalizing and improving the bounds in prior work. We also give a considerably more involved analysis for general asynchronous environments in which the only constraint is that each update can overlap with at most q others. The new lower bound on the maximum degree of parallelism attaining linear speedup is tight and improves the best prior bound almost quadratically., Comment: Accepted for publication in Mathematical Programming (Series A)

Gradient descent, and coordinate descent in particular, are core tools in machine learning and elsewhere. Large problem instances are common. To help solve them, two orthogonal approaches are known: acceleration and parallelism. In this work, we ask whether they can be used simultaneously. The answer is "yes". More specifically, we consider an asynchronous parallel version of the accelerated coordinate descent algorithm proposed and analyzed by Lin, Liu and Xiao (SIOPT'15). We give an analysis based on the efficient implementation of this algorithm. The only constraint is a standard bounded asynchrony assumption, namely that each update can overlap with at most q others. (q is at most the number of processors times the ratio in the lengths of the longest and shortest updates.) We obtain the following three results: 1. A linear speedup for strongly convex functions so long as q is not too large. 2. A substantial, albeit sublinear, speedup for strongly convex functions for larger q. 3. A substantial, albeit sublinear, speedup for convex functions.

A major goal in Algorithmic Game Theory is to justify equilibrium concepts from an algorithmic and complexity perspective. One appealing approach is to identify natural distributed algorithms that converge quickly to an equilibrium. This paper established new convergence results for two generalizations of Proportional Response in Fisher markets with buyers having CES utility functions. The starting points are respectively a new convex and a new convex-concave formulation of such markets. The two generalizations correspond to suitable mirror descent algorithms applied to these formulations. Several of our new results are a consequence of new notions of strong Bregman convexity and of strong Bregman convex-concave functions, and associated linear rates of convergence, which may be of independent interest. Among other results, we analyze a damped generalized Proportional Response and show a linear rate of convergence in a Fisher market with buyers whose utility functions cover the full spectrum of CES utilities aside the extremes of linear and Leontief utilities; when these utilities are included, we obtain an empirical O(1/T) rate of convergence.

As is well known, many classes of markets have efficient equilibria, but this depends on agents being non-strategic, i.e. that they declare their true demands when offered goods at particular prices, or in other words, that they are price-takers. An important question is how much the equilibria degrade in the face of strategic behavior, i.e. what is the Price of Anarchy (PoA) of the market viewed as a mechanism? Often, PoA bounds are modest constants such as 4/3 or 2. Nonetheless, in practice a guarantee that no more than 25% or 50% of the economic value is lost may be unappealing. This paper asks whether significantly better bounds are possible under plausible assumptions. In particular, we look at how these worst case guarantees improve in the following large settings. Large Walrasian auctions: These are auctions with many copies of each item and many agents. We show that the PoA tends to 1 as the market size increases, under suitable conditions, mainly that there is some uncertainty about the numbers of copies of each good and demands obey the gross substitutes condition. We also note that some such assumption is unavoidable. Large Fisher markets: Fisher markets are a class of economies that has received considerable attention in the computer science literature. A large market is one in which at equilibrium, each buyer makes only a small fraction of the total purchases; the smaller the fraction, the larger the market. Here the main condition is that demands are based on homogeneous monotone utility functions that satisfy the gross substitutes condition. Again, the PoA tends to 1 as the market size increases. Furthermore, in each setting, we quantify the tradeoff between market size and the PoA.

Generalized Second Price (GSP) auctions are widely used by search engines today to sell their ad slots. Most search engines have supported broad match between queries and bid keywords when executing GSP auctions, however, it has been revealed that GSP auction with the standard broad-match mechanism they are currently using (denoted as SBM-GSP) has several theoretical drawbacks (e.g., its theoretical properties are known only for the single-slot case and full-information setting, and even in this simple setting, the corresponding worst-case social welfare can be rather bad). To address this issue, we propose a novel broad-match mechanism, which we call the Probabilistic Broad-Match (PBM) mechanism. Different from SBM that puts together the ads bidding on all the keywords matched to a given query for the GSP auction, the GSP with PBM (denoted as PBM-GSP) randomly samples a keyword according to a predefined probability distribution and only runs the GSP auction for the ads bidding on this sampled keyword. We perform a comprehensive study on the theoretical properties of the PBM-GSP. Specifically, we study its social welfare in the worst equilibrium, in both full-information and Bayesian settings. The results show that PBM-GSP can generate larger welfare than SBM-GSP under mild conditions. Furthermore, we also study the revenue guarantee for PBM-GSP in Bayesian setting. To the best of our knowledge, this is the first work on broad-match mechanisms for GSP that goes beyond the single-slot case and the full-information setting.