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Manuela Geiß

Manuela Geiß contributes to research discovery and scholarly infrastructure.

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Published work

8 published item(s)

preprint2026arXiv

Kernel Affine Hull Machines for Compute-Efficient Query-Side Semantic Encoding

Transformer-based semantic retrieval is highly effective, yet in many deployments the dominant cost lies in online query encoding rather than corpus indexing. We study the fixed-teacher query-adaptation problem and ask whether repeated neural inference can be replaced by a lightweight, analytically explicit estimator without degrading decision-relevant retrieval quality. We propose Kernel Affine Hull Machines (KAHMs), which map inexpensive lexical features into a frozen semantic embedding space by estimating prototype-mixture weights in a rigorously specified RKHS and refining prototypes via normalized least-mean-squares, yielding a transparent decomposition of encoding error into posterior-approximation, generalization, and teacher-noise components. On a controlled Austrian-law benchmark (5,000 queries; 84 laws; 10,762 units), KAHM attains the strongest teacher-space reconstruction among matched learned adapters (MSE 0.000091, R^2 0.9071, cosine 0.9536) and consistently leads rank-sensitive metrics, including mean reciprocal rank at 20 (MRR@20, the average inverse rank of the first relevant result within the top 20), Hit rate at 20 (Hit@20, the fraction of queries with at least one relevant result in the top 20), and Top-1 accuracy (the fraction of queries whose correct item is ranked first), with scores of 0.504, 0.694, and 0.411, respectively. It also reduces per-query latency by a factor of 8.5 relative to direct transformer encoding. These results demonstrate that, in fixed-teacher regimes, lightweight geometric estimators can substitute for online neural encoding, preserving retrieval performance while substantially improving efficiency and interpretability.

preprint2022arXiv

Automatic Bounding Box Annotation with Small Training Data Sets for Industrial Manufacturing

In the past few years, object detection has attracted a lot of attention in the context of human-robot collaboration and Industry 5.0 due to enormous quality improvements in deep learning technologies. In many applications, object detection models have to be able to quickly adapt to a changing environment, i.e., to learn new objects. A crucial but challenging prerequisite for this is the automatic generation of new training data which currently still limits the broad application of object detection methods in industrial manufacturing. In this work, we discuss how to adapt state-of-the-art object detection methods for the task of automatic bounding box annotation for the use case where the background is homogeneous and the object's label is provided by a human. We compare an adapted version of Faster R-CNN and the Scaled Yolov4-p5 architecture and show that both can be trained to distinguish unknown objects from a complex but homogeneous background using only a small amount of training data.

preprint2022arXiv

Fast and Automatic Object Registration for Human-Robot Collaboration in Industrial Manufacturing

We present an end-to-end framework for fast retraining of object detection models in human-robot-collaboration. Our Faster R-CNN based setup covers the whole workflow of automatic image generation and labeling, model retraining on-site as well as inference on a FPGA edge device. The intervention of a human operator reduces to providing the new object together with its label and starting the training process. Moreover, we present a new loss, the intraspread-objectosphere loss, to tackle the problem of open world recognition. Though it fails to completely solve the problem, it significantly reduces the number of false positive detections of unknown objects.

preprint2021arXiv

Best Match Graphs with Binary Trees

Best match graphs (BMG) are a key intermediate in graph-based orthology detection and contain a large amount of information on the gene tree. We provide a near-cubic algorithm to determine whether a BMG is binary-explainable, i.e., whether it can be explained by a fully resolved gene tree and, if so, to construct such a tree. Moreover, we show that all such binary trees are refinements of the unique binary-resolvable tree (BRT), which in general is a substantial refinement of the also unique least resolved tree of a BMG. Finally, we show that the problem of editing an arbitrary vertex-colored graph to a binary-explainable BMG is NP-complete and provide an integer linear program formulation for this task.

preprint2021arXiv

Least resolved trees for two-colored best match graphs

2-colored best match graphs (2-BMGs) form a subclass of sink-free bi-transitive graphs that appears in phylogenetic combinatorics. There, 2-BMGs describe evolutionarily most closely related genes between a pair of species. They are explained by a unique least resolved tree (LRT). Introducing the concept of support vertices we derive an $O(|V|+|E|\log^2|V|)$-time algorithm to recognize 2-BMGs and to construct its LRT. The approach can be extended to also recognize binary-explainable 2-BMGs with the same complexity. An empirical comparison emphasizes the efficiency of the new algorithm.

preprint2020arXiv

Best Match Graphs

THIS IS A CORRECTED VERSION INCLUDING AN APPENDED CORRIGENDUM. Best match graphs arise naturally as the first processing intermediate in algorithms for orthology detection. Let $T$ be a phylogenetic (gene) tree $T$ and $σ$ an assignment of leaves of $T$ to species. The best match graph $(G,σ)$ is a digraph that contains an arc from $x$ to $y$ if the genes $x$ and $y$ reside in different species and $y$ is one of possibly many (evolutionary) closest relatives of $x$ compared to all other genes contained in the species $σ(y)$. Here, we characterize best match graphs and show that it can be decided in cubic time and quadratic space whether $(G,σ)$ derived from a tree in this manner. If the answer is affirmative, there is a unique least resolved tree that explains $(G,σ)$, which can also be constructed in cubic time.

preprint2020arXiv

From Best Hits to Best Matches

Many of the commonly used methods for orthology detection start from mutually most similar pairs of genes (reciprocal best hits) as an approximation for evolutionary most closely related pairs of genes (reciprocal best matches). This approximation of best matches by best hits becomes exact for ultrametric dissimilarities, i.e., under the Molecular Clock Hypothesis. It fails, however, whenever there are large lineage specific rate variations among paralogous genes. In practice, this introduces a high level of noise into the input data for best-hit-based orthology detection methods. If additive distances between genes are known, then evolutionary most closely related pairs can be identified by considering certain quartets of genes provided that in each quartet the outgroup relative to the remaining three genes is known. \emph{A priori} knowledge of underlying species phylogeny greatly facilitates the identification of the required outgroup. Although the workflow remains a heuristic since the correct outgroup cannot be determined reliably in all cases, simulations with lineage specific biases and rate asymmetries show that nearly perfect results can be achieved. In a realistic setting, where distances data have to be estimated from sequence data and hence are noisy, it is still possible to obtain highly accurate sets of best matches. Improvements of tree-free orthology assessment methods can be expected from a combination of the accurate inference of best matches reported here and recent mathematical advances in the understanding of (reciprocal) best match graphs and orthology relations.

preprint2020arXiv

Hierarchical and Modularly-Minimal Vertex Colorings

Cographs are exactly the hereditarily well-colored graphs, i.e., the graphs for which a greedy vertex coloring of every induced subgraph uses only the minimally necessary number of colors $χ(G)$. We show that greedy colorings are a special case of the more general hierarchical vertex colorings, which recently were introduced in phylogenetic combinatorics. Replacing cotrees by modular decomposition trees generalizes the concept of hierarchical colorings to arbitrary graphs. We show that every graph has a modularly-minimal coloring $σ$ satisfying $|σ(M)|=χ(M)$ for every strong module $M$ of $G$. This, in particular, shows that modularly-minimal colorings provide a useful device to design efficient coloring algorithms for certain hereditary graph classes. For cographs, the hierarchical colorings coincide with the modularly-minimal coloring. As a by-product, we obtain a simple linear-time algorithm to compute a modularly-minimal coloring of $P_4$-sparse graphs.