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Noam Solomon

Publications and source records attributed to Noam Solomon.

At least 19 recordsLinked to original sources
arXiv2023

Improving Accuracy in Cell-Perturbation Experiments by Leveraging Auxiliary Information

Modern cell-perturbation experiments expose cells to panels of hundreds of stimuli, such as cytokines or CRISPR guides that perform gene knockouts. These experiments are designed to investigate whether a particular gene is upregulated or downregulated by exposure to each treatment. However, due to high levels of experimental noise, typical estimators of whether a gene is up- or down-regulated make many errors. In this paper, we make two contributions. Our first contribution is a new estimator of regulatory effect that makes use of Gaussian processes and factor analysis to leverage auxiliary information about similarities among treatments, such as the chemical similarity among the drugs used to perturb cells. The new estimator typically has lower variance than unregularized estimators, which do not use auxiliary information, but higher bias. To assess whether this new estimator improves accuracy (i.e., achieves a favorable trade-off between bias and variance), we cannot simply compute its error on heldout data as ``ground truth'' about the effects of treatments is unavailable. Our second contribution is a novel data-splitting method to evaluate error rates. This data-splitting method produces valid error bounds using ``sign-valid'' estimators, which by definition have the correct sign more often than not. Using this data-splitting method, through a series of case studies we find that our new estimator, which leverages auxiliary information, can yield a three-fold reduction in type S error rate.

stat.AP↗
arXiv2022

SystemMatch: optimizing preclinical drug models to human clinical outcomes via generative latent-space matching

Translating the relevance of preclinical models ($\textit{in vitro}$, animal models, or organoids) to their relevance in humans presents an important challenge during drug development. The rising abundance of single-cell genomic data from human tumors and tissue offers a new opportunity to optimize model systems by their similarity to targeted human cell types in disease. In this work, we introduce SystemMatch to assess the fit of preclinical model systems to an $\textit{in sapiens}$ target population and to recommend experimental changes to further optimize these systems. We demonstrate this through an application to developing $\textit{in vitro}$ systems to model human tumor-derived suppressive macrophages. We show with held-out $\textit{in vivo}$ controls that our pipeline successfully ranks macrophage subpopulations by their biological similarity to the target population, and apply this analysis to rank a series of 18 $\textit{in vitro}$ macrophage systems perturbed with a variety of cytokine stimulations. We extend this analysis to predict the behavior of 66 $\textit{in silico}$ model systems generated using a perturbational autoencoder and apply a $k$-medoids approach to recommend a subset of these model systems for further experimental development in order to fully explore the space of possible perturbations. Through this use case, we demonstrate a novel approach to model system development to generate a system more similar to human biology.

cs.LG↗
arXiv2022

On rich points and incidences with restricted sets of lines in 3-space

Let $L$ be a set of $n$ lines in $R^3$ that is contained, when represented as points in the four-dimensional Plücker space of lines in $R^3$, in an irreducible variety $T$ of constant degree which is \emph{non-degenerate} with respect to $L$ (see below). We show: \medskip \noindent{\bf (1)} If $T$ is two-dimensional, the number of $r$-rich points (points incident to at least $r$ lines of $L$) is $O(n^{4/3+ε}/r^2)$, for $r \ge 3$ and for any $ε>0$, and, if at most $n^{1/3}$ lines of $L$ lie on any common regulus, there are at most $O(n^{4/3+ε})$ $2$-rich points. For $r$ larger than some sufficiently large constant, the number of $r$-rich points is also $O(n/r)$. As an application, we deduce (with an $ε$-loss in the exponent) the bound obtained by Pach and de Zeeuw (2107) on the number of distinct distances determined by $n$ points on an irreducible algebraic curve of constant degree in the plane that is not a line nor a circle. \medskip \noindent{\bf (2)} If $T$ is two-dimensional, the number of incidences between $L$ and a set of $m$ points in $R^3$ is $O(m+n)$. \medskip \noindent{\bf (3)} If $T$ is three-dimensional and nonlinear, the number of incidences between $L$ and a set of $m$ points in $R^3$ is $O\left(m^{3/5}n^{3/5} + (m^{11/15}n^{2/5} + m^{1/3}n^{2/3})s^{1/3} + m + n \right)$, provided that no plane contains more than $s$ of the points. When $s = O(\min\{n^{3/5}/m^{2/5}, m^{1/2}\})$, the bound becomes $O(m^{3/5}n^{3/5}+m+n)$. As an application, we prove that the number of incidences between $m$ points and $n$ lines in $R^4$ contained in a quadratic hypersurface (which does not contain a hyperplane) is $O(m^{3/5}n^{3/5} + m + n)$. The proofs use, in addition to various tools from algebraic geometry, recent bounds on the number of incidences between points and algebraic curves in the plane.

math.CO↗
arXiv2020

Incidences with curves in three dimensions

We study incidence problems involving points and curves in $R^3$. The current (and in fact only viable) approach to such problems, pioneered by Guth and Katz, requires a variety of tools from algebraic geometry, most notably (i) the polynomial partitioning technique, and (ii) the study of algebraic surfaces that are ruled by lines or, in more recent studies, by algebraic curves of some constant degree. By exploiting and refining these tools, we obtain new and improved bounds for point-curve incidence problems in $R^3$. Incidences of this kind have been considered in several previous studies, starting with Guth and Katz's work on points and lines. Our results, which are based on the work of Guth and Zahl concerning surfaces that are doubly ruled by curves, provide a grand generalization of most of the previous results. We reconstruct the bound for points and lines, and improve, in certain significant ways, recent bounds involving points and circles (in Sharir, Sheffer and Zahl), and points and arbitrary constant-degree algebraic curves (in Sharir, Sheffer and Solomon). While in these latter instances the bounds are not known (and are strongly suspected not) to be tight, our bounds are, in a certain sense, the best that can be obtained with this approach, given the current state of knowledge. As an application of our point-curve incidence bound, we show that the number of triangles spanned by a set of $n$ points in $R^3$ and similar to a given triangle is $O(n^{15/7})$, which improves the bound of Agarwal et al. Our results are also related to a study by Guth et al.~(work in progress), and have been recently applied in Sharir, Solomon and Zlydenko to related incidence problems in three dimensions.

math.CO↗
arXiv2020

Derandomization from Algebraic Hardness

A hitting-set generator (HSG) is a polynomial map $G:\mathbb{F}^k \to \mathbb{F}^n$ such that for all $n$-variate polynomials $C$ of small enough circuit size and degree, if $C$ is nonzero, then $C\circ G$ is nonzero. In this paper, we give a new construction of such an HSG assuming that we have an explicit polynomial of sufficient hardness. Formally, we prove the following over any field of characteristic zero: Let $k\in \mathbb{N}$ and $δ> 0$ be arbitrary constants. Suppose $\{P_d\}_{d\in \mathbb{N}}$ is an explicit family of $k$-variate polynomials such that $\operatorname{deg} P_d = d$ and $P_d$ requires algebraic circuits of size $d^δ$. Then, there are explicit hitting sets of polynomial size for $\mathsf{VP}$. This is the first HSG in the algebraic setting that yields a complete derandomization of polynomial identity testing (PIT) for general circuits from a suitable algebraic hardness assumption. As a direct consequence, we show that even saving a single point from the "trivial" explicit, exponential sized hitting sets for constant-variate polynomials of low individual degree which are computable by small circuits, implies a deterministic polynomial time algorithm for PIT. More precisely, we show the following: Let $k\in \mathbb{N}$ and $δ> 0$ be arbitrary constants. Suppose for every $s$ large enough, there is an explicit hitting set of size at most $((s+1)^k - 1)$ for the class of $k$-variate polynomials of individual degree $s$ that are computable by size $s^δ$ circuits. Then there is an explicit hitting set of size $\operatorname{poly}(s)$ for the class of $s$-variate polynomials, of degree $s$, that are computable by size $s$ circuits. As a consequence, we give a deterministic polynomial time construction of hitting sets for algebraic circuits, if a strengthening of the $τ$-Conjecture of Shub and Smale is true.

cs.CC↗
arXiv2020

Incidences between points and curves with almost two degrees of freedom

We study incidences between points and algebraic curves in three dimensions, taken from a family $C$ of curves that have almost two degrees of freedom, meaning that every pair of curves intersect in $O(1)$ points, for any pair of points $p$, $q$, there are only $O(1)$ curves of $C$ that pass through both points, and a pair $p$, $q$ of points admit a curve of $C$ that passes through both of them iff $F(p,q)=0$ for some polynomial $F$. We study two specific instances, one involving unit circles in $R^3$ that pass through some fixed point (so called anchored unit circles), and the other involving tangencies between directed points (points and directions) and circles in the plane; a directed point is tangent to a circle if the point lies on the circle and the direction is the tangent direction. A lifting transformation of Ellenberg et al. maps these tangencies to incidences between points and curves in three dimensions. In both instances the curves in $R^3$ have almost two degrees of freedom. We show that the number of incidences between $m$ points and $n$ anchored unit circles in $R^3$, as well as the number of tangencies between $m$ directed points and $n$ arbitrary circles in the plane, is $O(m^{3/5}n^{3/5}+m+n)$. We derive a similar incidence bound, with a few additional terms, for more general families of curves in $R^3$ with almost two degrees of freedom. The proofs follow standard techniques, based on polynomial partitioning, but face a novel issue involving surfaces that are infinitely ruled by the respective family of curves, as well as surfaces in a dual 3D space that are infinitely ruled by the respective family of suitably defined dual curves. The general bound that we obtain is $O(m^{3/5}n^{3/5}+m+n)$ plus additional terms that depend on how many curves or dual curves can lie on an infinitely-ruled surface.

cs.CG↗
arXiv2020

A Generalized Matching Reconfiguration Problem

The goal in {\em reconfiguration problems} is to compute a {\em gradual transformation} between two feasible solutions of a problem such that all intermediate solutions are also feasible. In the {\em Matching Reconfiguration Problem} (MRP), proposed in a pioneering work by Ito et al.\ from 2008, we are given a graph $G$ and two matchings $M$ and $M'$, and we are asked whether there is a sequence of matchings in $G$ starting with $M$ and ending at $M'$, each resulting from the previous one by either adding or deleting a single edge in $G$, without ever going through a matching of size $< \min\{|M|,|M'|\}-1$. Ito et al.\ gave a polynomial time algorithm for the problem. In this paper we introduce a natural generalization of the MRP that depends on an integer parameter $Δ\ge 1$: here we are allowed to make $Δ$ changes to the current solution rather than 1 at each step of the {transformation procedure}. There is always a valid sequence of matchings transforming $M$ to $M'$ if $Δ$ is sufficiently large, and naturally we would like to minimize $Δ$. We first devise an optimal transformation procedure for unweighted matching with $Δ= 3$, and then extend it to weighted matchings to achieve asymptotically optimal guarantees. The running time of these procedures is linear. We further demonstrate the applicability of this generalized problem to dynamic graph matchings. In this area, the number of changes to the maintained matching per update step (the \emph{recourse bound}) is an important quality measure. Nevertheless, the \emph{worst-case} recourse bounds of almost all known dynamic matching algorithms are prohibitively large, much larger than the corresponding update times. We fill in this gap via a surprisingly simple black-box reduction: Any dynamic algorithm for maintaining [...]

cs.DS↗
arXiv2019

From DNF compression to sunflower theorems via regularity

The sunflower conjecture is one of the most well-known open problems in combinatorics. It has several applications in theoretical computer science, one of which is DNF compression, due to Gopalan, Meka and Reingold [Computational Complexity 2013]. In this paper, we show that improved bounds for DNF compression imply improved bounds for the sunflower conjecture, which is the reverse direction of [Computational Complexity 2013]. The main approach is based on regularity of set systems and a structure-vs-pseudorandomness approach to the sunflower conjecture.

math.CO↗
arXiv2019

Closure of VP under taking factors: a short and simple proof

In this note, we give a short, simple and almost completely self contained proof of a classical result of Kaltofen [Kal86, Kal87, Kal89] which shows that if an $n$ variate degree $d$ polynomial $f$ can be computed by an arithmetic circuit of size $s$, then each of its factors can be computed by an arithmetic circuit of size at most $\textsf{poly}\left(s, n, d\right)$. However, unlike Kaltofen's argument, our proof does not directly give an efficient algorithm for computing the circuits for the factors of $f$.

cs.CC↗
arXiv2019

Incidence estimates for well spaced tubes

We prove analogues of the Szemerédi-Trotter theorem and other incidence theorems using $δ$-tubes in place of straight lines, assuming that the $δ$-tubes are well-spaced in a strong sense.

math.CA↗
arXiv2018

Traces of Hypergraphs

Let $\text{Tr}(n,m,k)$ denote the largest number of distinct projections onto $k$ coordinates guaranteed in any family of $m$ binary vectors of length $n$. The classical Sauer-Perles-Shelah Lemma implies that $\text{Tr}(n, n^r, k) = 2^k$ for $k \le r$. While determining $\text{Tr}(n,n^r,k)$ precisely for general $k$ seems hopeless even for constant $r$, estimating it, and more generally estimating the function $\text{Tr}(n,m,k)$ for all range of the parameters, remains a widely open problem with connections to important questions in computer science and combinatorics. Here we essentially resolve this problem when $k$ is linear and $m=n^r$ where $r$ is constant, proving that, for any constant $α>0$, $\text{Tr}(n,n^r,αn) = \tildeΘ(n^C)$ with $C=C(r,α)=\frac{r+1-\log(1+α)}{2-\log(1+α)}$. For the proof we establish a "sparse" version of another classical result, the Kruskal-Katona Theorem, which gives a stronger guarantee when the hypergraph does not induce dense sub-hypergraphs. Furthermore, we prove that the parameters in our sparse Kruskal-Katona theorem are essentially best possible. Finally, we mention two simple applications which may be of independent interest.

math.CO↗
arXiv2018

Some Closure Results for Polynomial Factorization and Applications

In a sequence of seminal results in the 80's, Kaltofen showed that the complexity class VP is closed under taking factors. A natural question in this context is to understand if other natural classes of multivariate polynomials, for instance, arithmetic formulas, algebraic branching programs, bounded depth arithmetic circuits or the class VNP, are closed under taking factors. In this paper, we show that all factors of degree at most $\log^a n$ of polynomials with poly(n) size depth $k$ circuits have poly(n) size circuits of depth at most $O(k + a)$. This partially answers a question of Shpilka-Yehudayoff and has applications to hardness-randomness tradeoffs for bounded depth arithmetic circuits. More precisely, this shows that a superpolynomial lower bound for bounded depth arithmetic circuits, for a family of explicit polynomials of degree poly$(\log n)$ implies deterministic sub-exponential time algorithms for polynomial identity testing (PIT) for bounded depth arithmetic circuits. This is incomparable to a beautiful result of Dvir et al., where they showed that super-polynomial lower bounds for constant depth arithmetic circuits for any explicit family of polynomials (of potentially high degree) implies sub-exponential time deterministic PIT for bounded depth circuits of bounded individual degree. Thus, we remove the "bounded individual degree" condition in [DSY09] at the cost of strengthening the hardness assumption to hold for polynomials of low degree. As direct applications of our techniques, we also show that the complexity class VNP is closed under taking factors, thereby confirming a conjecture of Bürgisser and get an alternate proof of the fact (first shown by Dutta et al.) that if a polynomial $Q$ of degree at most $d$ divides a polynomial $P$ computable by a formula of size $s$, then $Q$ has a formula of size at most poly$(s, d^{\log d}, deg(P))$.

cs.CC↗
arXiv2017

Incidences between points on a variety and planes in R^3

In this paper we establish an improved bound for the number of incidences between a set $P$ of $m$ points and a set $H$ of $n$ planes in $\mathbb R^3$, provided that the points lie on a two-dimensional nonlinear irreducible algebraic variety $V$ of constant degree. Specifically, the bound is $$ O\left( m^{2/3}n^{2/3} + m^{6/11}n^{9/11}\log^β(m^3/n) + m + n + \sum_\ell |P_\ell|\cdot |H_\ell| \right) , $$ where the constant of proportionality and the constant exponent $β$ depend on the degree of $V$, and where the sum ranges over all lines $\ell$ that are fully contained in $V$ and contain at least one point of $P$, so that, for each such $\ell$, $P_\ell = P\cap\ell$ and $H_\ell$ is the set of the planes of H that contain $\ell$. In addition, $\sum_\ell |P_\ell| = O(m)$ and $\sum_\ell |H_\ell| = O(n)$. This improves, for this special case, the earlier more general bound of Apfelbaum and Sharir (see also Brass and Knauer as well as Elekes and Tóth). This is a generalization of the incidence bound for points and circles in the plane (cf. Aronov et al., Aronov and Sharir, Marcus and Tardos), and is based on a recent result of Sharir and Zahl on the number of cuts that turn a collection of algebraic curves into pseudo-segments. The case where $V$ is a quadric is simpler to analyze, does not require the result of Sharir and Zahl, and yields the same bound as above, with $β=2/11$. We present an interesting application of our results to a problem, studied by Rudnev, on obtaining a lower bound on the number of distinct cross-ratios determined by $n$ real points, where our bound leads to a slight improvement in Rudnev's bound.

math.CO↗
arXiv2017

Incidences with curves and surfaces in three dimensions, with applications to distinct and repeated distances

We study a wide spectrum of incidence problems involving points and curves or points and surfaces in $\mathbb R^3$. The current (and in fact the only viable) approach to such problems, pioneered by Guth and Katz [2010,2015], requires a variety of tools from algebraic geometry, most notably (i) the polynomial partitioning technique, and (ii) the study of algebraic surfaces that are ruled by lines or, in more recent studies [Guth-Zahl 2016], by algebraic curves of some constant degree. By exploiting and refining these tools, we obtain new and improved bounds for numerous incidence problems in $\mathbb R^3$. In broad terms, we consider two kinds of problems, those involving points and constant-degree algebraic \emph{curves}, and those involving points and constant-degree algebraic \emph{surfaces}. In some variants we assume that the points lie on some fixed constant-degree algebraic variety, and in others we consider arbitrary sets of points in 3-space. our results provide a "grand generalization" of most of the previous studies of (special instances of) previous works for both curves and surfaces. As an application of our point-curve incidence bound, we consider the problem of bounding the number of similar triangles spanned by a set of $n$ points in $\mathbb R^3$, and obtain the bound $O(n^{15/7}),$ thus improving the bound of Agarwal et al [2007]. As applications of our point-surface incidence bounds, we consider the problems of distinct and repeated distances determined by a set of $n$ points in $\mathbb R^3$, two of the most celebrated open problems in combinatorial geometry. We obtain new and improved bounds for two special cases, one in which the points lie on some algebraic variety of constant degree, and one involving incidences between pairs in $P_1\times P_2$, where $P_1$ is contained in a variety and $P_2$ is arbitrary.

math.CO↗
arXiv2016

Highly incidental patterns on a quadratic hypersurface in $\mathbb{R}^4$

In [Sharir and Solomon 2015], Sharir and Solomon showed that the number of incidences between $m$ distinct points and $n$ distinct lines in $\mathbb R^4$ is $$O^*\left(m^{2/5}n^{4/5}+ m^{1/2}n^{1/2}q^{1/4} + m^{2/3}n^{1/3}s^{1/3} + m + n\right),$$ provided that no 2-flat contains more than $s$ lines, and no hyperplane or quadric contains more than $q$ lines, where the $O^*$ hides a multiplicative factor of $2^{c\sqrt {\log m}}$ for some absolute constant $c$. In this paper we prove that, for integers $m,n,$ satisfying $n^{9/8}<m<n^{3/2}$, there exist $m$ points and $n$ lines on the quadratic hypersurface in $\mathbb{R}^4$ $$ \{(x_1,x_2,x_3,x_4)\in \mathbb R^4 \mid x_1 = x_2^2 + x_3^2 - x_4^2\}, $$ such that (i) at most $s=O(1)$ lines lie on any 2-flat, (ii) at most $q=O(n/m^{1/3})$ lines lie on any hyperplane, and (iii) the number of incidences between the points and the lines is $Θ(m^{2/3}n^{1/2})$, which is asymptotically larger than the upper bound by Sharir and Solomon. This shows that the assumption that no quadric contains more than $q$ lines (in the above mentioned theorem of Sharir and Solomon) is necessary in this regime of $m$ and $n$. By a suitable projection from this quadratic hypersurface onto $\mathbb{R}^3$, we obtain $m$ points and $n$ lines in $\mathbb{R}^3$, with at most $s=O(1)$ lines on a common plane, such that the number of incidences between the $m$ points and the $n$ lines is $Θ(m^{2/3}n^{1/2})$. It remains an interesting question to determine if this bound is also tight in general.

math.CO↗
arXiv2016

Subquadratic Algorithms for Algebraic Generalizations of 3SUM

The 3SUM problem asks if an input $n$-set of real numbers contains a triple whose sum is zero. We consider the 3POL problem, a natural generalization of 3SUM where we replace the sum function by a constant-degree polynomial in three variables. The motivations are threefold. Raz, Sharir, and de Zeeuw gave a $O(n^{11/6})$ upper bound on the number of solutions of trivariate polynomial equations when the solutions are taken from the cartesian product of three $n$-sets of real numbers. We give algorithms for the corresponding problem of counting such solutions. Grønlund and Pettie recently designed subquadratic algorithms for 3SUM. We generalize their results to 3POL. Finally, we shed light on the General Position Testing (GPT) problem: "Given $n$ points in the plane, do three of them lie on a line?", a key problem in computational geometry. We prove that there exist bounded-degree algebraic decision trees of depth $O(n^{\frac{12}{7}+\varepsilon})$ that solve 3POL, and that 3POL can be solved in $O(n^2 {(\log \log n)}^\frac{3}{2} / {(\log n)}^\frac{1}{2})$ time in the real-RAM model. Among the possible applications of those results, we show how to solve GPT in subquadratic time when the input points lie on $o({(\log n)}^\frac{1}{6}/{(\log \log n)}^\frac{1}{2})$ constant-degree polynomial curves. This constitutes a first step towards closing the major open question of whether GPT can be solved in subquadratic time. To obtain these results, we generalize important tools --- such as batch range searching and dominance reporting --- to a polynomial setting. We expect these new tools to be useful in other applications.

cs.DS↗
arXiv2016

Incidences between points and lines on two- and three-dimensional varieties

Let $P$ be a set of $m$ points and $L$ a set of $n$ lines in $\mathbb R^4$, such that the points of $P$ lie on an algebraic three-dimensional surface of degree $D$ that does not contain hyperplane or quadric components, and no 2-flat contains more than $s$ lines of $L$. We show that the number of incidences between $P$ and $L$ is $$ I(P,L) = O\left(m^{1/2}n^{1/2}D + m^{2/3}n^{1/3}s^{1/3} + nD + m\right) , $$ for some absolute constant of proportionality. This significantly improves the bound of the authors, for arbitrary sets of points and lines in $\mathbb R^4$, when $D$ is not too large. The same bound holds when the three-dimensional surface is embedded in any higher dimensional space. For the proof of this bound, we revisit certain parts of [Sharir-Solomon16], combined with the following new incidence bound. Let $P$ be a set of $m$ points and $L$ a set of $n$ lines in $\mathbb R^d$, for $d\ge 3$, which lie in a common two-dimensional algebraic surface of degree $D$ (assumed to be $\ll n^{1/2}$) that does not contain any 2-flat, so that no 2-flat contains more than $s$ lines of $L$ (here we require that the lines of $L$ also be contained in the surface). Then the number of incidences between $P$ and $L$ is $$ I(P,L) = O\left(m^{1/2}n^{1/2}D^{1/2} + m^{2/3}D^{2/3}s^{1/3} + m + n\right). $$ When $d=3$, this improves the bound of Guth and Katz for this special case, when $D \ll n^{1/2}$. Moreover, the bound does not involve the term $O(nD)$, that arises in most standard approaches, and its removal is a significant aspect of our result. Finally, we also obtain (slightly weaker) variants of both results over the complex field. For two-dimensional varieties, the bound is as in the real case, with an added term of $O(D^3)$. For three-dimensional varieties, the bound is as in the real case, with an added term of $O(D^6)$.

math.CO↗