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Missing data in multiple variables is a common issue. We investigate the applicability of the framework of graphical models for handling missing data to a complex longitudinal pharmacological study of children with HIV treated with an efavirenz-based regimen as part of the CHAPAS-3 trial. Specifically, we examine whether the causal effects of interest, defined through static interventions on multiple continuous variables, can be recovered (estimated consistently) from the available data only. So far, no general algorithms are available to decide on recoverability, and decisions have to be made on a case-by-case basis. We emphasize sensitivity of recoverability to even the smallest changes in the graph structure, and present recoverability results for three plausible missingness directed acyclic graphs (m-DAGs) in the CHAPAS-3 study, informed by clinical knowledge. Furthermore, we propose the concept of "closed missingness mechanisms" and show that under these mechanisms an available case analysis is admissible for consistent estimation for any type of statistical and causal query, even if the underlying missingness mechanism is of missing not at random (MNAR) type. Both simulations and theoretical considerations demonstrate how, in the assumed MNAR setting of our study, a complete or available case analysis can be superior to multiple imputation, and estimation results vary depending on the assumed missingness DAG. Our analyses are possibly the first to show the applicability of missingness DAGs (m-DAGs) to complex longitudinal real-world data, while highlighting the sensitivity with respect to the assumed causal model.

Forensic experts use specialized training and knowledge to enable other members of the judicial system to make better informed and more just decisions. Factfinders, in particular, are tasked with judging how much weight to give to experts' reports and opinions. Many references describe assessing evidential weight from the perspective of a forensic expert. Some recognize that stakeholders are each responsible for evaluating their own weight of evidence. Morris (1971, 1974, 1977) provided a general framework for recipients to update their own uncertainties after learning an expert's opinion. Although this framework is normative under Bayesian axioms and several forensic scholars advocate the use of Bayesian reasoning, few resources describe its application in forensic science. This paper addresses this gap by examining how recipients can combine principles of science and Bayesian reasoning to evaluate their own likelihood ratios for expert opinions. This exercise helps clarify how an expert's role depends on whether one envisions recipients to be logical and scientific or deferential. Illustrative examples with an expert's opinion expressed as a categorical conclusion, likelihood ratio, or range of likelihood ratios, or with likelihood ratios from multiple experts, each reveal the importance and influence of validation data for logical recipients' interpretations.

Statistical mechanics has made significant contributions to the study of biological neural systems by modeling them as recurrent networks of interconnected units with adjustable interactions. Several algorithms have been proposed to optimize the neural connections to enable network tasks such as information storage (i.e. associative memory) and learning probability distributions from data (i.e. generative modeling). Among these methods, the Unlearning algorithm, aligned with emerging theories of synaptic plasticity, was introduced by John Hopfield and collaborators. The primary objective of this thesis is to understand the effectiveness of Unlearning in both associative memory models and generative models. Initially, we demonstrate that the Unlearning algorithm can be simplified to a linear perceptron model which learns from noisy examples featuring specific internal correlations. The selection of structured training data enables an associative memory model to retrieve concepts as attractors of a neural dynamics with considerable basins of attraction. Subsequently, a novel regularization technique for Boltzmann Machines is presented, proving to outperform previously developed methods in learning hidden probability distributions from data-sets. The Unlearning rule is derived from this new regularized algorithm and is showed to be comparable, in terms of inferential performance, to traditional Boltzmann-Machine learning.

A growing literature in computational neuroscience leverages gradient descent and learning algorithms that approximate it to study synaptic plasticity in the brain. However, the vast majority of this work ignores a critical underlying assumption: the choice of distance for synaptic changes - i.e. the geometry of synaptic plasticity. Gradient descent assumes that the distance is Euclidean, but many other distances are possible, and there is no reason that biology necessarily uses Euclidean geometry. Here, using the theoretical tools provided by mirror descent, we show that the distribution of synaptic weights will depend on the geometry of synaptic plasticity. We use these results to show that experimentally-observed log-normal weight distributions found in several brain areas are not consistent with standard gradient descent (i.e. a Euclidean geometry), but rather with non-Euclidean distances. Finally, we show that it should be possible to experimentally test for different synaptic geometries by comparing synaptic weight distributions before and after learning. Overall, our work shows that the current paradigm in theoretical work on synaptic plasticity that assumes Euclidean synaptic geometry may be misguided and that it should be possible to experimentally determine the true geometry of synaptic plasticity in the brain.

Algorithm evaluation and comparison are fundamental questions in machine learning and statistics -- how well does an algorithm perform at a given modeling task, and which algorithm performs best? Many methods have been developed to assess algorithm performance, often based around cross-validation type strategies, retraining the algorithm of interest on different subsets of the data and assessing its performance on the held-out data points. Despite the broad use of such procedures, the theoretical properties of these methods are not yet fully understood. In this work, we explore some fundamental limits for answering these questions with limited amounts of data. In particular, we make a distinction between two questions: how good is an algorithm $A$ at the problem of learning from a training set of size $n$, versus, how good is a particular fitted model produced by running $A$ on a particular training data set of size $n$? Our main results prove that, for any test that treats the algorithm $A$ as a ``black box'' (i.e., we can only study the behavior of $A$ empirically), there is a fundamental limit on our ability to carry out inference on the performance of $A$, unless the number of available data points $N$ is many times larger than the sample size $n$ of interest. (On the other hand, evaluating the performance of a particular fitted model is easy as long as a holdout data set is available -- that is, as long as $N-n$ is not too small.) We also ask whether an assumption of algorithmic stability might be sufficient to circumvent this hardness result. Surprisingly, we find that this is not the case: the same hardness result still holds for the problem of evaluating the performance of $A$, aside from a high-stability regime where fitted models are essentially nonrandom. Finally, we also establish similar hardness results for the problem of comparing multiple algorithms.

The solution of a sparse system of linear equations is ubiquitous in scientific applications. Iterative methods, such as the Preconditioned Conjugate Gradient method (PCG), are normally chosen over direct methods due to memory and computational complexity constraints. However, the efficiency of these methods depends on the preconditioner utilized. The development of the preconditioner normally requires some insight into the sparse linear system and the desired trade-off of generating the preconditioner and the reduction in the number of iterations. Incomplete factorization methods tend to be black box methods to generate these preconditioners but may fail for a number of reasons. These reasons include numerical issues that require searching for adequate scaling, shifting, and fill-in while utilizing a difficult to parallelize algorithm. With a move towards heterogeneous computing, many sparse applications find GPUs that are optimized for dense tensor applications like training neural networks being underutilized. In this work, we demonstrate that a simple artificial neural network trained either at compile time or in parallel to the running application on a GPU can provide an incomplete sparse Cholesky factorization that can be used as a preconditioner. This generated preconditioner is as good or better in terms of reduction of iterations than the one found using multiple preconditioning techniques such as scaling and shifting. Moreover, the generated method also works and never fails to produce a preconditioner that does not reduce the iteration count.

The problem PosSLP is the problem of determining whether a given straight-line program (SLP) computes a positive integer. PosSLP was introduced by Allender et al. to study the complexity of numerical analysis (Allender et al., 2009). PosSLP can also be reformulated as the problem of deciding whether the integer computed by a given SLP can be expressed as the sum of squares of four integers, based on the well-known result by Lagrange in 1770, which demonstrated that every natural number can be represented as the sum of four non-negative integer squares. In this paper, we explore several natural extensions of this problem by investigating whether the positive integer computed by a given SLP can be written as the sum of squares of two or three integers. We delve into the complexity of these variations and demonstrate relations between the complexity of the original PosSLP problem and the complexity of these related problems. Additionally, we introduce a new intriguing problem called Div2SLP and illustrate how Div2SLP is connected to DegSLP and the problem of whether an SLP computes an integer expressible as the sum of three squares. By comprehending the connections between these problems, our results offer a deeper understanding of decision problems associated with SLPs and open avenues for further exciting research

There is substantial interest in the use of machine learning (ML)-based techniques throughout the electronic computer-aided design (CAD) flow, particularly methods based on deep learning. However, while deep learning methods have achieved state-of-the-art performance in several applications, recent work has demonstrated that neural networks are generally vulnerable to small, carefully chosen perturbations of their input (e.g. a single pixel change in an image). In this work, we investigate robustness in the context of ML-based EDA tools -- particularly for congestion prediction. As far as we are aware, we are the first to explore this concept in the context of ML-based EDA. We first describe a novel notion of imperceptibility designed specifically for VLSI layout problems defined on netlists and cell placements. Our definition of imperceptibility is characterized by a guarantee that a perturbation to a layout will not alter its global routing. We then demonstrate that state-of-the-art CNN and GNN-based congestion models exhibit brittleness to imperceptible perturbations. Namely, we show that when a small number of cells (e.g. 1%-5% of cells) have their positions shifted such that a measure of global congestion is guaranteed to remain unaffected (e.g. 1% of the design adversarially shifted by 0.001% of the layout space results in a predicted decrease in congestion of up to 90%, while no change in congestion is implied by the perturbation). In other words, the quality of a predictor can be made arbitrarily poor (i.e. can be made to predict that a design is "congestion-free") for an arbitrary input layout. Next, we describe a simple technique to train predictors that improves robustness to these perturbations. Our work indicates that CAD engineers should be cautious when integrating neural network-based mechanisms in EDA flows to ensure robust and high-quality results.

The problem of substructure characteristic modes is reformulated using a scattering matrix-based formulation, generalizing subregion characteristic mode decomposition to arbitrary computational tools. It is shown that the scattering formulation is identical to the classical formulation based on the background Green's function for lossless systems. The scattering formulation, however, opens a variety of new subregion scenarios unavailable within previous formulations, including cases with lumped or wave ports or subregions in circuits. Thanks to its scattering nature, the formulation is solver-agnostic with the possibility to utilize an arbitrary full-wave method.

We introduce a multi-task setup of identifying and classifying entities, relations, and coreference clusters in scientific articles. We create SciERC, a dataset that includes annotations for all three tasks and develop a unified framework called Scientific Information Extractor (SciIE) for with shared span representations. The multi-task setup reduces cascading errors between tasks and leverages cross-sentence relations through coreference links. Experiments show that our multi-task model outperforms previous models in scientific information extraction without using any domain-specific features. We further show that the framework supports construction of a scientific knowledge graph, which we use to analyze information in scientific literature.