LICENSE
README.md
pyproject.toml
setup.py
dnallm/__init__.py
dnallm/version.py
dnallm.egg-info/PKG-INFO
dnallm.egg-info/SOURCES.txt
dnallm.egg-info/dependency_links.txt
dnallm.egg-info/entry_points.txt
dnallm.egg-info/requires.txt
dnallm.egg-info/top_level.txt
dnallm/cli/__init__.py
dnallm/cli/cli.py
dnallm/cli/inference.py
dnallm/cli/model_config_generator.py
dnallm/cli/train.py
dnallm/configuration/__init__.py
dnallm/configuration/configs.py
dnallm/datahandling/__init__.py
dnallm/datahandling/data.py
dnallm/datahandling/dataset_auto.py
dnallm/finetune/__init__.py
dnallm/finetune/trainer.py
dnallm/inference/__init__.py
dnallm/inference/benchmark.py
dnallm/inference/inference.py
dnallm/inference/interpret.py
dnallm/inference/mutagenesis.py
dnallm/inference/plot.py
dnallm/mcp/__init__.py
dnallm/mcp/config_manager.py
dnallm/mcp/config_validators.py
dnallm/mcp/example_sse_usage.py
dnallm/mcp/model_manager.py
dnallm/mcp/run_tests.py
dnallm/mcp/server.py
dnallm/mcp/start_server.py
dnallm/mcp/tests/__init__.py
dnallm/mcp/tests/test_config_manager.py
dnallm/mcp/tests/test_config_validators.py
dnallm/mcp/tests/test_mcp_functionality.py
dnallm/mcp/tests/test_server_integration.py
dnallm/mcp/tests/test_simple.py
dnallm/mcp/tests/test_sse_client.py
dnallm/models/__init__.py
dnallm/models/head.py
dnallm/models/model.py
dnallm/models/modeling_auto.py
dnallm/models/tokenizer.py
dnallm/models/special/__init__.py
dnallm/models/special/basenji2.py
dnallm/models/special/borzoi.py
dnallm/models/special/dnabert2.py
dnallm/models/special/enformer.py
dnallm/models/special/evo.py
dnallm/models/special/gpn.py
dnallm/models/special/lucaone.py
dnallm/models/special/megadna.py
dnallm/models/special/mutbert.py
dnallm/models/special/omnidna.py
dnallm/models/special/space.py
dnallm/models/special/enformer_model/configuration_enformer.py
dnallm/models/special/enformer_model/configuration_space.py
dnallm/models/special/enformer_model/data.py
dnallm/models/special/enformer_model/modeling_enformer.py
dnallm/models/special/enformer_model/modeling_space.py
dnallm/models/special/enformer_model/modules.py
dnallm/tasks/__init__.py
dnallm/tasks/metrics.py
dnallm/tasks/task.py
dnallm/tasks/metrics/accuracy/accuracy.py
dnallm/tasks/metrics/accuracy/app.py
dnallm/tasks/metrics/bertscore/app.py
dnallm/tasks/metrics/bertscore/bertscore.py
dnallm/tasks/metrics/bleu/app.py
dnallm/tasks/metrics/bleu/bleu.py
dnallm/tasks/metrics/bleu/tokenizer_13a.py
dnallm/tasks/metrics/bleurt/app.py
dnallm/tasks/metrics/bleurt/bleurt.py
dnallm/tasks/metrics/brier_score/app.py
dnallm/tasks/metrics/brier_score/brier_score.py
dnallm/tasks/metrics/cer/app.py
dnallm/tasks/metrics/cer/cer.py
dnallm/tasks/metrics/cer/test_cer.py
dnallm/tasks/metrics/character/app.py
dnallm/tasks/metrics/character/character.py
dnallm/tasks/metrics/charcut_mt/app.py
dnallm/tasks/metrics/charcut_mt/charcut_mt.py
dnallm/tasks/metrics/chrf/app.py
dnallm/tasks/metrics/chrf/chrf.py
dnallm/tasks/metrics/code_eval/app.py
dnallm/tasks/metrics/code_eval/code_eval.py
dnallm/tasks/metrics/code_eval/execute.py
dnallm/tasks/metrics/comet/app.py
dnallm/tasks/metrics/comet/comet.py
dnallm/tasks/metrics/competition_math/app.py
dnallm/tasks/metrics/competition_math/competition_math.py
dnallm/tasks/metrics/confusion_matrix/app.py
dnallm/tasks/metrics/confusion_matrix/confusion_matrix.py
dnallm/tasks/metrics/coval/app.py
dnallm/tasks/metrics/coval/coval.py
dnallm/tasks/metrics/cuad/app.py
dnallm/tasks/metrics/cuad/compute_score.py
dnallm/tasks/metrics/cuad/cuad.py
dnallm/tasks/metrics/exact_match/app.py
dnallm/tasks/metrics/exact_match/exact_match.py
dnallm/tasks/metrics/f1/app.py
dnallm/tasks/metrics/f1/f1.py
dnallm/tasks/metrics/frugalscore/app.py
dnallm/tasks/metrics/frugalscore/frugalscore.py
dnallm/tasks/metrics/glue/app.py
dnallm/tasks/metrics/glue/glue.py
dnallm/tasks/metrics/google_bleu/app.py
dnallm/tasks/metrics/google_bleu/google_bleu.py
dnallm/tasks/metrics/google_bleu/tokenizer_13a.py
dnallm/tasks/metrics/indic_glue/app.py
dnallm/tasks/metrics/indic_glue/indic_glue.py
dnallm/tasks/metrics/mae/app.py
dnallm/tasks/metrics/mae/mae.py
dnallm/tasks/metrics/mahalanobis/app.py
dnallm/tasks/metrics/mahalanobis/mahalanobis.py
dnallm/tasks/metrics/mape/app.py
dnallm/tasks/metrics/mape/mape.py
dnallm/tasks/metrics/mase/app.py
dnallm/tasks/metrics/mase/mase.py
dnallm/tasks/metrics/matthews_correlation/app.py
dnallm/tasks/metrics/matthews_correlation/matthews_correlation.py
dnallm/tasks/metrics/mauve/app.py
dnallm/tasks/metrics/mauve/mauve.py
dnallm/tasks/metrics/mean_iou/app.py
dnallm/tasks/metrics/mean_iou/mean_iou.py
dnallm/tasks/metrics/meteor/app.py
dnallm/tasks/metrics/meteor/meteor.py
dnallm/tasks/metrics/mse/app.py
dnallm/tasks/metrics/mse/mse.py
dnallm/tasks/metrics/nist_mt/app.py
dnallm/tasks/metrics/nist_mt/nist_mt.py
dnallm/tasks/metrics/nist_mt/tests.py
dnallm/tasks/metrics/pearsonr/app.py
dnallm/tasks/metrics/pearsonr/pearsonr.py
dnallm/tasks/metrics/perplexity/app.py
dnallm/tasks/metrics/perplexity/perplexity.py
dnallm/tasks/metrics/poseval/app.py
dnallm/tasks/metrics/poseval/poseval.py
dnallm/tasks/metrics/precision/app.py
dnallm/tasks/metrics/precision/precision.py
dnallm/tasks/metrics/r_squared/app.py
dnallm/tasks/metrics/r_squared/r_squared.py
dnallm/tasks/metrics/recall/app.py
dnallm/tasks/metrics/recall/recall.py
dnallm/tasks/metrics/rl_reliability/app.py
dnallm/tasks/metrics/rl_reliability/rl_reliability.py
dnallm/tasks/metrics/roc_auc/app.py
dnallm/tasks/metrics/roc_auc/roc_auc.py
dnallm/tasks/metrics/rouge/app.py
dnallm/tasks/metrics/rouge/rouge.py
dnallm/tasks/metrics/sacrebleu/app.py
dnallm/tasks/metrics/sacrebleu/sacrebleu.py
dnallm/tasks/metrics/sari/app.py
dnallm/tasks/metrics/sari/sari.py
dnallm/tasks/metrics/seqeval/app.py
dnallm/tasks/metrics/seqeval/seqeval.py
dnallm/tasks/metrics/smape/app.py
dnallm/tasks/metrics/smape/smape.py
dnallm/tasks/metrics/spearmanr/app.py
dnallm/tasks/metrics/spearmanr/spearmanr.py
dnallm/tasks/metrics/squad/app.py
dnallm/tasks/metrics/squad/compute_score.py
dnallm/tasks/metrics/squad/squad.py
dnallm/tasks/metrics/squad_v2/app.py
dnallm/tasks/metrics/squad_v2/compute_score.py
dnallm/tasks/metrics/squad_v2/squad_v2.py
dnallm/tasks/metrics/super_glue/app.py
dnallm/tasks/metrics/super_glue/record_evaluation.py
dnallm/tasks/metrics/super_glue/super_glue.py
dnallm/tasks/metrics/ter/app.py
dnallm/tasks/metrics/ter/ter.py
dnallm/tasks/metrics/trec_eval/app.py
dnallm/tasks/metrics/trec_eval/trec_eval.py
dnallm/tasks/metrics/wer/app.py
dnallm/tasks/metrics/wer/wer.py
dnallm/tasks/metrics/wiki_split/app.py
dnallm/tasks/metrics/wiki_split/wiki_split.py
dnallm/tasks/metrics/xnli/app.py
dnallm/tasks/metrics/xnli/xnli.py
dnallm/tasks/metrics/xtreme_s/app.py
dnallm/tasks/metrics/xtreme_s/xtreme_s.py
dnallm/utils/__init__.py
dnallm/utils/logger.py
dnallm/utils/sequence.py
dnallm/utils/support.py