Phylogenetic Trees

What did an ancestral bird species sound like? Existing ancestral state reconstruction methods can infer low-dimensional traits such as morphological characters at internal nodes of a phylogenetic tree, but no one has tried to produce rich perceptual signals such as audio. Some of the challenges include inferred representations that are either too low-dimensional to decode or lie in non-generative feature spaces, so no method to date can produce ancestral audio. We introduce the first framework that generates plausible ancestral vocalizations. Our pipeline encodes bird recordings into a VAE latent space, learns a low-dimensional trait projection aligned with phylogenetic distances, performs ancestral inference in this trait space, and recovers decodable latents through an anchored inverse lift before emitting novel waveforms for each ancestral node. Because the entire pipeline stays within a decodable latent space, every internal node receives a genuinely new audio output representing plausible intermediate ancestral sounds unavailable to retrieval-based alternatives. Experiments on two phylogenetically distant bird clades, 21-species Tyrannidae and 19-species Paridae, show that our method is the only approach that simultaneously achieves genuine generation, phylogenetic consistency, and naturalistic audio quality across both datasets.

Do learned audio embeddings encode structure that nobody told them to encode? We probe four large pretrained audio models (AST, CLAP, BEATs-bio and BirdNET) with a downstream task none of them saw during training: recovering phylogenetic distance from species vocalizations. If the geometry of the embedding space tracks the tree of life, the representation is picking up something deeper than the labels the model was optimized for. We run Mantel tests across two independent radiations. In 32 marine mammal species (1,754 recordings from the Watkins Marine Mammal Sound Database) the foundation models recover strong phylogenetic signal within the 26 cetaceans (CLAP r=0.82, BEATs-bio r=0.82, AST r=0.74; all p<0.001), among the highest acoustic-phylogenetic correlations reported for any taxon. Hand-crafted MFCC features (105d) find nothing (r=0.040, p=0.338). The gap survives after PCA-projecting every embedding down to 105 dimensions, so it is not an artefact of representation size. It also survives a partial Mantel test controlling for dominant frequency (partial Mantel r=0.404, keeping 97% of the variance explained), so it is not just pitch in disguise. We repeat the analysis on 20 bird species using the Jetz et al. (2012) phylogeny, and this time add BirdNET, a classifier trained end-to-end on around 6,000 bird species. The general-purpose foundation models recover the signal again (AST r=0.55, CLAP r=0.52). The unexpected result is that neither BirdNET nor the bioacoustic BEATs-bio beat them (r around 0.32 to 0.36). Matching the training domain to the target taxon does not, by itself, help. Pretrained audio embeddings carry evolutionary information across two independent radiations, and domain-specific pretraining is not required for it to emerge.

Comparing phylogenetic tree topologies is essential for understanding epidemic dynamics, yet biologically meaningful distances such as the Subtree Prune and Regraft (SPR) distance are NP-hard to compute and intractable on large datasets. We investigate whether a Graph Neural Network (GNN) can approximate SPR distances in near-constant time per comparison after training. Our contributions are fourfold. First, we build and publicly release a dataset of 864 phylogenetic trees inferred with UPGMA and Neighbor-Joining over four bacterial species, spanning up to 9{,}500 isolates, together with 388 labelled tree pairs. Second, we establish a reproducible pre-processing pipeline including midpoint re-rooting, which reduces tree depth and supplies the rooting required for exact distance computation and for the model's root-based features. Third, we validate the supervision target: on small trees, where exact SPR is tractable, the unrooted phangorn::SPR.dist heuristic correlates almost perfectly with the exact rooted distance computed by rspr (Pearson $0.98$--$0.99$), making it an excellent monotonic surrogate. Lastly, we train a Siamese Graph Isomorphism Network (GIN) regressor. In-distribution, i.e., held-out trees from the same species and size range as training, it explains roughly 87--90% of the variance ($R^2 \approx 0.87$ on a held-out split; $0.90 \pm 0.19$ under stratified cross-validation), with about four times lower error than a mean-predictor baseline, and shows partial transfer to unseen species ($R^2 \approx 0.37$). Its main limitation is extrapolation to trees larger than those seen in training, where accuracy collapses. The released dataset and the validated heuristic versus exact relationship provide a reproducible basis for scaling learned SPR approximation.

Dependency parsing consists of finding a tree representation for a sequence. Unsupervised dependency parsing aims to develop parsing methods without a gold standard during model training. In human languages, an unsupervised parser can be evaluated because some gold standard is usually available or can be created. For other species, a gold standard is unknown. Thus one may conclude that it is impossible to determine the accuracy of an unsupervised parser and, consequently, dependency parsing is unfeasible in other species. However, here we apply recent advances in network science to demonstrate that the proportion of correct edges retrieved by a parser must be high for the sequences of vocalizations or gestures that non-human primates produce due to the fast decay of the sequence length distribution. In contrast, human language sequences lack that property. Therefore, evaluation without a gold standard is feasible in non-human primates but a hard problem in humans.

Reconstructing who infected whom often relies on case timing and published transmission links. However, two important questions remain: can a temporal pattern learned from other diseases transfer to a new outbreak, and how reliable are the transmission links used as ground truth? We learned a temporal prior from eleven disease groups using logistic regression. The model was locked before any target-outbreak data were accessed and was then tested without refitting on 29 Andes virus (ANDV) parent-ranking tasks. The locked prior achieved a mean reciprocal rank (MRR) of 0.571, compared with 0.274 for the strongest fair source-trained temporal baseline (permutation p<0.001). Its Top-1 accuracy was 37.9%, compared with 13.8%. The MRR advantage remained significant unless 7-8 favorable task outcomes were reversed. We separately examined the reliability of published transmission links. Among 75 epidemiologically linked inter-host pairs from the 2022 New York City mpox outbreak, 54.67% were genomically unresolved or unsupported as direct transmission links (exact 95% CI: 42.75-66.21%). We also tested whether retaining uncertain transmission edges changed source prioritization. In ANDV and Guangdong Delta outbreak graphs, the top-5 priority sets changed, with Jaccard similarity ranging from 0.429 to 0.667. These results show that temporal information learned across diseases can provide a useful ranking signal without target-specific refitting. They also show that uncertainty in published transmission links can affect which source cases are prioritized for investigation.

Morphological traits provide important evidence for phylogenetic reconstruction and evolutionary relationship analysis. Recent image-based approaches have introduced deep learning, particularly convolutional models, to derive morphological features from specimen images, but these methods generally rely on single-modality visual representations and do not explicitly incorporate morphological semantics. This study proposes a morphology-aware multimodal alignment framework for insect phylogenetic reconstruction. The framework combines specimen images with curated morphological descriptions by adapting a vision transformer through parameter-efficient fine-tuning and supervised contrastive learning, followed by image-text alignment in a shared latent space. The learned image embeddings are then used as continuous traits for Bayesian phylogenetic reconstruction. On the public Rove-Tree-11 dataset, comparative and ablation experiments across multiple visual backbones and feature adaptation strategies demonstrate that multimodal alignment improves topological agreement with the reference phylogeny. The results indicate that the proposed framework can derive morphology-aware visual traits for computational phylogenetic reconstruction.

Compositional data -- vectors encoding relative proportions -- arise across scientific domains, including ecology, geochemistry, and genomics. The features in these data often come with known hierarchical structure (e.g., taxonomies, phylogenies, ontologies), yet existing methods either ignore this structure, discard the intrinsic Aitchison geometry, are designed for binary trees, or yield incomplete coordinate systems. We describe PolyILR, a canonical orthonormal decomposition of the Aitchison tangent space aligned with any tree topology. Our construction defines a weighted local geometry at each internal node capturing full branching structure, then lifts these to a global orthonormal basis where every coordinate corresponds to a specific tree location. On microbiome and single-cell benchmarks, PolyILR yields stable, interpretable features and enables inference at multiscale tree resolution. We also establish a novel theoretical connection to softmax classifiers, suggesting possible applications to probabilistic modeling.

Streaming 3D Gaussian Splatting requires highly scalable, progressive representations. Existing progressive methods rely on \textit{discrete layering}, accumulating separate splat sets for each level of detail. This structural independence between layers inherently leads to error accumulation, severe splat redundancy, and uncontrolled quality transitions. We propose EvoGS, the first \textit{continuous-layering} representation. Organized as an Evolution Tree, EvoGS generates finer details via an explicit, wavelet-inspired parent-child refinement. This empowers child nodes to structurally correct ancestral errors, yield inherently sparse and highly compressible inter-layer signals. Extensive experiments show EvoGS eliminates splat redundancy from over 65% to under 25%. Compared to state-of-the-art baselines, it reduces transmission payload and GPU VRAM footprint by up to 2.4$\times$ and 5.5$\times$, respectively, and achieves smooth quality transitions optimal for real-time adaptive streaming. Project page: https://yuang-ian.github.io/evogs/

Malware detection remains largely reactive: machine learning models trained on known samples degrade as threats evolve. Understanding evolutionary relationships among malware families can inform proactive defense, but traditional reverse engineering can take months to years to uncover such lineage relationships. We propose MalTree, a framework that applies bioinformatics inspired phylogenetic techniques (UPGMA and Neighbor-Joining) at scale to model malware evolution automatically using structural, behavioral, and image-based features. We introduce temporal validation using VirusTotal timestamps to assess whether inferred trees reflect actual evolutionary order. MalTree achieves 87% temporal consistency, indicating that inferred evolutionary relationships closely align with real-world emergence timelines. Our analysis shows that some families mutate over 10 times faster than others, suggesting that detection strategies should be tailored to family-specific evolutionary tempos. Case studies, including the Mirai botnet, confirm that inferred relationships from our phylogenetic tree align with documented threat intelligence. Our framework provides a foundation for shifting malware analysis from sample-by-sample classification toward lineage-aware evolutionary modeling.

Phylogenetic trees are hybrid objects: branch lengths vary continuously, while topologies change discretely through edge contractions and expansions. Billera-Holmes-Vogtmann (BHV) tree space provides a canonical geometry for this structure, representing each resolved topology as a Euclidean orthant and topological changes as motion across shared lower-dimensional boundaries. We introduce PhylaFlow, a hybrid flow-matching model that learns posterior-basin transport in BHV tree space. PhylaFlow is trained on BHV geodesic paths from random starting trees to short-run posterior samples, coupling continuous branch-length motion within orthants with learned boundary events and discrete topology transitions. We evaluate the learned geometry operationally: if the flow reaches posterior-relevant regions, finite-budget Bayesian refinement initialized from, or guided by, its terminal trees should recover posterior-supported topologies more efficiently. Across DS1-DS8 phylogenetic posterior benchmarks, PhylaFlow substantially reduces initial Tree-KL relative to classical initializers. After finite-budget MrBayes refinement, direct PhylaFlow improves early and intermediate topology-recovery trajectories on most datasets, while split-guided PhylaFlow-MCMC obtains the strongest hard-case results. The best PhylaFlow variant outperforms short-warmup on seven of eight datasets and PhyloGFN on five of eight under the same refinement budget. In a joint sequence-conditioned experiment, sequence embeddings steer posterior split recovery, although exact posterior topology recovery remains preliminary. These results show that hybrid flow matching can learn actionable transport in BHV tree space and provide a geometry-aware proposal mechanism for Bayesian phylogenetic inference.

In this work, we introduce a Tropical Axial Attention neural reasoning architecture that replaces vanilla softmax dot-product attention with max-plus operators, inducing a piecewise-linear structure aligned with dynamic programming formulations. From multi-species sequence alignments, our model learns all possible pairwise distances and is trained using a combination of $\ell_1$ and tropical symmetric distance metric losses with an ultrametric violation penalty. We leverage the well known isomorphic relationship between the space of all phylogenetic trees with $n$ species and tropical Grassmannian to show that tropical attention provides a natural geometric framework for phylogenetic inference. On empirical $DS1-DS11$ alignments, where true trees are unknown, the tropical model produces distance matrices that are substantially closer to their BME-induced tree metrics than the baseline models. These results suggest that tropical attention is a useful geometric inductive bias for neural phylogenetic inference, especially under distribution shift and when tree-metric consistency is important.

Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely independently and handle insertions and deletions only weakly or not at all. We introduce a tree-conditioned edit-flow model for variable-length ASR. Given two descendant sequences and their branch distances to a shared ancestor, the model reconstructs the ancestor through paired bidirectional edit trajectories constrained to agree on a common ancestral state. On a benchmark of experimentally evolved sequences with only context-independent substitutions, the model does not match the accuracy of the best classical method, yet still achieves reasonable performance despite being trained on natural sequences that include insertions, deletions, and substitutions. On a benchmark of natural homologous sequences with abundant insertions and deletions, the model most accurately localizes inferred evolutionary change.

Evolutionary methods have long been useful for analysis and explanation in genetics, biology, ecology, and related fields. In this work, we extend these methods to neural networks, specifically large language models (LLMs), to better analyze and explain relationships among models. We show how relating weights to genotypes and output text to phenotypes can improve our understanding of model lineage, important datasets, the roles of different model layers, and visualization of model relationships. We demonstrate this in a controlled experiment, where our estimated evolutionary trees reliably recover the topology of the ground-truth training tree. We further identify the most important weight layers according to weight differences and show through phenotypic experiments that one training dataset appears to contribute more useful information than the others. Finally, we generate an unsupervised evolutionary tree of black-box foundation models. Throughout, we provide visualizations that support a clearer understanding of evolutionary relationships among LLMs.

Designing heuristics for combinatorial optimization problems (COPs) is a fundamental yet challenging task that traditionally requires extensive domain expertise. Recently, Large Language Model (LLM)-based Automated Heuristic Design (AHD) has shown promise in autonomously generating heuristic components with minimal human intervention. However, most existing LLM-based AHD methods enforce fixed algorithmic templates to ensure executability, which confines the search to component-level tuning and limits system-level algorithmic expressiveness. To enable open-ended solver synthesis beyond rigid templates, we propose Automated Algorithm Design via Evolutionary Program Trees (A2DEPT), which treats LLMs as system-level algorithm architects. A2DEPT explores the vast program space via a tree-structured evolutionary search with hybrid selection and hierarchical operators, enabling iterative refinement of complete algorithms. To make open-ended generation practical, we enforce executability with a lightweight program-maintenance loop that performs feedback-driven repair. In experiments, A2DEPT consistently outperforms representative LLM-based baselines on both standard and highly constrained benchmarks. On the standard benchmarks, it reduces the mean normalized optimality gap by 9.8% relative to the strongest competing AHD baseline.

Creativity has become a core competence in the era of LLMs and human-AI collaboration, underpinning innovation in real-world problem solving. Crucially, the systematic improvement of creativity necessitates scientifically valid assessment instruments. Psychometric research recognizes context-based assessment as an effective way to measure creative thinking. However, high-quality expert-designed contexts remain scarce. Existing LLM-based generators often struggle with insufficient assessment cues, weak narrative coherence, limited stylistic diversity, and poor support for creative thinking. To address these challenges, we propose AlphaContext, an evolutionary tree-based psychometric context generator for creativity assessment. First, the HyperTree Outline Planner formalizes expert-designed outlining as a rule-guided hypertree and performs top-down hierarchical planning. The MCTS-based Context Generator fills the outline via MCTS to balance global structure and local quality. Then, the Evolutionary Context Optimizer evolves contexts with MAP-Elites by repeatedly updating niche elites to jointly improve diversity and quality. Finally, the Assessment-Guided Evolution Refiner simulates virtual participants with diverse styles and recycles weak contexts for further evolution. Experiments show that AlphaContext yields an average improvement of 8% over competitive methods across 6 quality metrics.

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

In recent years, the rapid development of language models has transformed the field of Natural Language Processing through a wide range of applications. However, the development of language models has not progressed uniformly across all languages. In the case of the Portuguese language, there has recently been a growing effort by academia and companies to develop language models and create data resources for Portuguese. These efforts have resulted in the rise of an increasingly diverse ecosystem of language models for Portuguese. However, information on these models remains dispersed in scientific publications, technical reports, model repositories, and project documentation. This survey presents a systematic mapping study of language models developed for Portuguese, providing a comprehensive overview of the current state of the field. We map a total of 46 models, characterizing them by various aspects, including base model, architecture, computational resources, training datasets, licensing, code availability, data, and model weights. Furthermore, we analyzed the evolution and relationships among these models through a phylogenetic perspective, identified current research gaps and opportunities, and discussed future directions for the development of language models for Portuguese.