arXiv subjects

Aditya Pillai

Publications and source records attributed to Aditya Pillai.

5 recordsLinked to original sources

arXiv2025

CHAMMI-75: Pre-training multi-channel models with heterogeneous microscopy images

Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy imaging type. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels). Here, we present CHAMMI-75, an open access dataset of heterogeneous, multi-channel microscopy images from 75 diverse biological studies. We curated this resource from publicly available sources to investigate cellular morphology models that are channel-adaptive and can process any microscopy image type. Our experiments show that training with CHAMMI-75 can improve performance in multi-channel bioimaging tasks primarily because of its high diversity in microscopy modalities. This work paves the way to create the next generation of cellular morphology models for biological studies.

cs.CV↗

arXiv2024

Computing Experiment-Constrained D-Optimal Designs

In optimal experimental design, the objective is to select a limited set of experiments that maximizes information about unknown model parameters based on factor levels. This work addresses the generalized D-optimal design problem, allowing for nonlinear relationships in factor levels. We develop scalable algorithms suitable for cases where the number of candidate experiments grows exponentially with the factor dimension, focusing on both first- and second-order models under design constraints. Particularly, our approach integrates convex relaxation with pricing-based local search techniques, which can provide upper bounds and performance guarantees. Unlike traditional local search methods, such as the ``Fedorov exchange" and its variants, our method effectively accommodates arbitrary side constraints in the design space. Furthermore, it yields both a feasible solution and an upper bound on the optimal value derived from the convex relaxation. Numerical results highlight the efficiency and scalability of our algorithms, demonstrating superior performance compared to the state-of-the-art commercial software, JMP

cs.DS↗

arXiv2024

Factcheck-Bench: Fine-Grained Evaluation Benchmark for Automatic Fact-checkers

The increased use of large language models (LLMs) across a variety of real-world applications calls for mechanisms to verify the factual accuracy of their outputs. In this work, we present a holistic end-to-end solution for annotating the factuality of LLM-generated responses, which encompasses a multi-stage annotation scheme designed to yield detailed labels concerning the verifiability and factual inconsistencies found in LLM outputs. We further construct an open-domain document-level factuality benchmark in three-level granularity: claim, sentence and document, aiming to facilitate the evaluation of automatic fact-checking systems. Preliminary experiments show that FacTool, FactScore and Perplexity.ai are struggling to identify false claims, with the best F1=0.63 by this annotation solution based on GPT-4. Annotation tool, benchmark and code are available at https://github.com/yuxiaw/Factcheck-GPT.

cs.CL↗

arXiv2023

Linear Programming based Reductions for Multiple Visit TSP and Vehicle Routing Problems

Multiple TSP ($\mathrm{mTSP}$) is a important variant of $\mathrm{TSP}$ where a set of $k$ salesperson together visit a set of $n$ cities. The $\mathrm{mTSP}$ problem has applications to many real life applications such as vehicle routing. Rothkopf introduced another variant of $\mathrm{TSP}$ called many-visits TSP ($\mathrm{MV\mbox{-}TSP}$) where a request $r(v)\in \mathbb{Z}_+$ is given for each city $v$ and a single salesperson needs to visit each city $r(v)$ times and return back to his starting point. A combination of $\mathrm{mTSP}$ and $\mathrm{MV\mbox{-}TSP}$ called many-visits multiple TSP $(\mathrm{MV\mbox{-}mTSP})$ was studied by Bérczi, Mnich, and Vincze where the authors give approximation algorithms for various variants of $\mathrm{MV\mbox{-}mTSP}$. In this work, we show a simple linear programming (LP) based reduction that converts a $\mathrm{mTSP}$ LP-based algorithm to a LP-based algorithm for $\mathrm{MV\mbox{-}mTSP}$ with the same approximation factor. We apply this reduction to improve or match the current best approximation factors of several variants of the $\mathrm{MV\mbox{-}mTSP}$. Our reduction shows that the addition of visit requests $r(v)$ to $\mathrm{mTSP}$ does $\textit{not}$ make the problem harder to approximate even when $r(v)$ is exponential in number of vertices. To apply our reduction, we either use existing LP-based algorithms for $\mathrm{mTSP}$ variants or show that several existing combinatorial algorithms for $\mathrm{mTSP}$ variants can be interpreted as LP-based algorithms. This allows us to apply our reduction to these combinatorial algorithms as well achieving the improved guarantees.

cs.DS↗

arXiv2023

An Improved Approximation Algorithm for the Max-$3$-Section Problem

We consider the Max-$3$-Section problem, where we are given an undirected graph $ G=(V,E)$ equipped with non-negative edge weights $w :E\rightarrow \mathbb{R}_+$ and the goal is to find a partition of $V$ into three equisized parts while maximizing the total weight of edges crossing between different parts. Max-$3$-Section is closely related to other well-studied graph partitioning problems, e.g., Max-$k$-Cut, Max-$3$-Cut, and Max-Bisection. We present a polynomial time algorithm achieving an approximation of $ 0.795$, that improves upon the previous best known approximation of $ 0.673$. The requirement of multiple parts that have equal sizes renders Max-$3$-Section much harder to cope with compared to, e.g., Max-Bisection. We show a new algorithm that combines the existing approach of Lassere hierarchy along with a random cut strategy that suffices to give our result.

cs.DS↗